A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
The most common of the microsatellite tandem repeats (MICROSATELLITE REPEATS) dispersed in the euchromatic arms of chromosomes. They consist of two nucleotides repeated in tandem; guanine and thymine, (GT)n, is the most frequently seen.
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
Microsatellite repeats consisting of three nucleotides dispersed in the euchromatic arms of chromosomes.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The occurrence of highly polymorphic mono- and dinucleotide MICROSATELLITE REPEATS in somatic cells. It is a form of genome instability associated with defects in DNA MISMATCH REPAIR.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Any method used for determining the location of and relative distances between genes on a chromosome.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Genotypic differences observed among individuals in a population.
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
The loss of one allele at a specific locus, caused by a deletion mutation; or loss of a chromosome from a chromosome pair, resulting in abnormal HEMIZYGOSITY. It is detected when heterozygous markers for a locus appear monomorphic because one of the ALLELES was deleted.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
Deoxyribonucleic acid that makes up the genetic material of plants.
Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
An increased number of contiguous trinucleotide repeats in the DNA sequence from one generation to the next. The presence of these regions is associated with diseases such as FRAGILE X SYNDROME and MYOTONIC DYSTROPHY. Some CHROMOSOME FRAGILE SITES are composed of sequences where trinucleotide repeat expansion occurs.
An individual having different alleles at one or more loci regarding a specific character.
MutS homolog 2 protein is found throughout eukaryotes and is a homolog of the MUTS DNA MISMATCH-BINDING PROTEIN. It plays an essential role in meiotic RECOMBINATION and DNA REPAIR of mismatched NUCLEOTIDES.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
An animal or plant species in danger of extinction. Causes can include human activity, changing climate, or change in predator/prey ratios.
DNA present in neoplastic tissue.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).
Protein motif that contains a 33-amino acid long sequence that often occurs in tandem arrays. This repeating sequence of 33-amino acids was discovered in ANKYRIN where it is involved in interaction with the anion exchanger (ANION EXCHANGE PROTEIN 1, ERYTHROCYTE). Ankyrin repeats cooperatively fold into domains that mediate molecular recognition via protein-protein interactions.
Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
A DNA repair pathway involved in correction of errors introduced during DNA replication when an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. Excinucleases recognize the BASE PAIR MISMATCH and cause a segment of polynucleotide chain to be excised from the daughter strand, thereby removing the mismatched base. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)
A sequential pattern of amino acids occurring more than once in the same protein sequence.
The change in gene frequency in a population due to migration of gametes or individuals (ANIMAL MIGRATION) across population barriers. In contrast, in GENETIC DRIFT the cause of gene frequency changes are not a result of population or gamete movement.
A group of autosomal-dominant inherited diseases in which COLON CANCER arises in discrete adenomas. Unlike FAMILIAL POLYPOSIS COLI with hundreds of polyps, hereditary nonpolyposis colorectal neoplasms occur much later, in the fourth and fifth decades. HNPCC has been associated with germline mutations in mismatch repair (MMR) genes. It has been subdivided into Lynch syndrome I or site-specific colonic cancer, and LYNCH SYNDROME II which includes extracolonic cancer.
The relationships of groups of organisms as reflected by their genetic makeup.
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
A region of DNA that is highly polymorphic and is prone to strand breaks, rearrangements or other MUTATIONS because of the nature of its sequence. These regions often harbor palindromic, or repetitive sequences (REPETITIVE SEQUENCES, NUCLEIC ACID). Variability in stability of the DNA sequence is seen at CHROMOSOME FRAGILE SITES.
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
The total relative probability, expressed on a logarithmic scale, that a linkage relationship exists among selected loci. Lod is an acronym for "logarithmic odds."
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next.
An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.
A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymes
Biochemical identification of mutational changes in a nucleotide sequence.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Establishing the father relationship of a man and a child.
Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.

Superimposed histologic and genetic mapping of chromosome 9 in progression of human urinary bladder neoplasia: implications for a genetic model of multistep urothelial carcinogenesis and early detection of urinary bladder cancer. (1/8354)

The evolution of alterations on chromosome 9, including the putative tumor suppressor genes mapped to the 9p21-22 region (the MTS genes), was studied in relation to the progression of human urinary bladder neoplasia by using whole organ superimposed histologic and genetic mapping in cystectomy specimens and was verified in urinary bladder tumors of various pathogenetic subsets with longterm follow-up. The applicability of chromosome 9 allelic losses as non-invasive markers of urothelial neoplasia was tested on voided urine and/or bladder washings of patients with urinary bladder cancer. Although sequential multiple hits in the MTS locus were documented in the development of intraurothelial precursor lesions, the MTS genes do not seem to represent a major target for p21-23 deletions in bladder cancer. Two additional tumor suppressor genes involved in bladder neoplasia located distally and proximally to the MTS locus within p22-23 and p11-13 regions respectively were identified. Several distinct putative tumor suppressor gene loci within the q12-13, q21-22, and q34 regions were identified on the q arm. In particular, the pericentromeric q12-13 area may contain the critical tumor suppressor gene or genes for the development of early urothelial neoplasia. Allelic losses of chromosome 9 were associated with expansion of the abnormal urothelial clone which frequently involved large areas of urinary bladder mucosa. These losses could be found in a high proportion of urothelial tumors and in voided urine or bladder washing samples of nearly all patients with urinary bladder carcinoma.  (+info)

Level of retinoblastoma protein expression correlates with p16 (MTS-1/INK4A/CDKN2) status in bladder cancer. (2/8354)

Recent studies have shown that patients whose bladder cancer exhibit overexpression of RB protein as measured by immunohistochemical analysis do equally poorly as those with loss of RB function. We hypothesized that loss of p16 protein function could be related to RB overexpression, since p16 can induce transcriptional downregulation of RB and its loss may lead to aberrant RB regulation. Conversely, loss of RB function has been associated with high p16 protein expression in several other tumor types. In the present study RB negative bladder tumors also exhibited strong nuclear p16 staining while each tumor with strong, homogeneous RB nuclear staining were p16 negative, supporting our hypothesis. To expand on these immunohistochemical studies additional cases were selected in which the status of the p16 encoding gene had been determined at the molecular level. Absent p16 and high RB protein expression was found in the tumors having loss of heterozygosity within 9p21 and a structural change (mutation or deletion) of the remaining p16 encoding gene allele, confirming the staining results. These results strongly support the hypothesis that the RB nuclear overexpression recently associated with poor prognosis in bladder cancer is also associated with loss of p16 function and implies that loss of p16 function could be equally deleterious as RB loss in bladder and likely other cancers.  (+info)

Multiple target sites of allelic imbalance on chromosome 17 in Barrett's oesophageal cancer. (3/8354)

Twelve Barrett's adenocarcinomas have been analysed for the occurrence of allelic imbalance (LOH) on chromosome 17 using 41 microsatellite markers. This study provides evidence for 13 minimal regions of LOH, six on 17p and seven on 17q. Four of these centre in the vicinity of the known tumour suppressor genes (TSGs) TP53 (17p13.1), NFI (17q11.2), BRCA1 (17q21.1), and a putative TSG (17p13.3). The tumours all displayed relatively small regions of LOH (1-10 cM), and in several tumours extensive regions of LOH were detected. One tumour displayed only two very small regions of LOH; 17p11.2 and 17p13.1. The frequency of allelic imbalance has been calculated based on the LOH encompassing only one minimal region, and based on all the LOH observations. By both evaluations the highest LOH frequencies were found for regions II (p53), III (17p13.1 centromeric to p53), IV (17p12), V (17p11.2) and VII (NF1, 17q11.2). Our data supports the existence of multiple TSGs on chromosome 17 and challenges the view that p53 is the sole target of LOH on 17p in Barrett's adenocarcinoma.  (+info)

p73 at chromosome 1p36.3 is lost in advanced stage neuroblastoma but its mutation is infrequent. (4/8354)

p73, a novel p53 family member, is a recently identified candidate neuroblastoma (NBL) suppressor gene mapped at chromosome 1p36.33 and was found to inhibit growth and induce apoptosis in cell lines. To test the hypothesis that p73 is a NBL suppressor gene, we analysed the p73 gene in primary human NBLs. Loss of heterozygosity (LOH) for p73 was observed in 19% (28/151) of informative cases which included 92 mass-screening (MS) tumors. The high frequency of p73 LOH was significantly associated with sporadic NBLs (9% vs 34%, P<0.001), N-myc amplification (10% vs 71%, P<0.001), and advanced stage (14% vs 28%, P<0.05). Both p73alpha and p73beta transcripts were detectable in only 46 of 134 (34%) NBLs at low levels by RT-PCR methods, while they were easily detectable in most breast cancers and colorectal cancers under the same conditions. They found no correlation between p73 LOH and its expression levels (P>0.1). We found two mutations out of 140 NBLs, one somatic and one germline, which result in amino acid substitutions in the C-terminal region of p73 which may affect transactivation functions, though, in the same tumor samples, no mutation of the p53 gene was observed as reported previously. These results suggest that allelic loss of the p73 gene may be a later event in NBL tumorigenesis. However, p73 is infrequently mutated in primary NBLs and may hardly function as a tumor suppressor in a classic Knudson's manner.  (+info)

Genomic organization of the KCNQ1 K+ channel gene and identification of C-terminal mutations in the long-QT syndrome. (5/8354)

The voltage-gated K+ channel KVLQT1 is essential for the repolarization phase of the cardiac action potential and for K+ homeostasis in the inner ear. Mutations in the human KCNQ1 gene encoding the alpha subunit of the KVLQT1 channel cause the long-QT syndrome (LQTS). The autosomal dominant form of this cardiac disease, the Romano-Ward syndrome, is characterized by a prolongation of the QT interval, ventricular arrhythmias, and sudden death. The autosomal recessive form, the Jervell and Lange-Nielsen syndrome, also includes bilateral deafness. In the present study, we report the entire genomic structure of KCNQ1, which consists of 19 exons spanning 400 kb on chromosome 11p15.5. We describe the sequences of exon-intron boundaries and oligonucleotide primers that allow polymerase chain reaction (PCR) amplification of exons from genomic DNA. Two new (CA)n repeat microsatellites were found in introns 10 and 14. The present study provides helpful tools for the linkage analysis and mutation screening of the complete KCNQ1 gene. By use of these tools, five novel mutations were identified in LQTS patients by PCR-single-strand conformational polymorphism (SSCP) analysis in the C-terminal part of KCNQ1: two missense mutations, a 20-bp and 1-bp deletions, and a 1-bp insertion. Such mutations in the C-terminal domain of the gene may be more frequent than previously expected, because this region has not been analyzed so far. This could explain the low percentage of mutations found in large LQTS cohorts.  (+info)

Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas. (6/8354)

Expression of CDX2, a caudal-related homeobox gene, was found to be decreased in colorectal carcinomas. Heterozygous null mutant mice as to Cdx2 develop multiple intestinal adenomatous polyps. To clarify the role of CDX2 in colorectal carcinogenesis, we determined its genomic structure, and searched for mutations of CDX2 in 49 sporadic colorectal carcinomas and ten hereditary non-polyposis colorectal cancers (HNPCC) without microsatellite instability. None of them exhibited a mutation. We further examined 19 HNPCC carcinomas with microsatellite instability for mutations in a (G)7 repeat site within CDX2. One of them (5.3%) exhibited one G insertion. Loss of heterozygosity was observed in 2 of the 20 (10%) informative sporadic carcinomas, and in one of the three (33.3%) informative HNPCC cancers. These data indicate that CDX2 may play only a minor role in colorectal carcinogenesis.  (+info)

Microsatellite instability, Epstein-Barr virus, mutation of type II transforming growth factor beta receptor and BAX in gastric carcinomas in Hong Kong Chinese. (7/8354)

Microsatellite instability (MI), the phenotypic manifestation of mismatch repair failure, is found in a proportion of gastric carcinomas. Little is known of the links between MI and Epstein-Barr virus (EBV) status and clinicopathological elements. Examination of genes mutated through the MI mechanism could also be expected to reveal important information on the carcinogenic pathway. Seventy-nine gastric carcinomas (61 EBV negative, 18 EBV positive) from local Hong Kong Chinese population, an intermediate-incidence area, were examined. Eight microsatellite loci, inclusive of the A10 tract of type II transforming growth factor beta receptor (TbetaR-II), were used to evaluate the MI status. MI in the BAX and insulin-like growth factor II receptor (IGF-IIR) genes were also examined. High-level MI (>40% unstable loci) was detected in ten cases (12.7%) and low-level MI (1-40% unstable loci) in three (3.8%). High-level MI was detected in two EBV-associated cases (11%) and the incidence was similar for the EBV-negative cases (13%). The high-level MIs were significantly associated with intestinal-type tumours (P = 0.03) and a more prominent lymphoid infiltrate (P = 0.04). Similar associations were noted in the EBV-positive carcinomas. The high-level MIs were more commonly located in the antrum, whereas the EBV-associated carcinomas were mostly located in body. Thirteen cardia cases were negative for both high-level MI and EBV. All patients aged below 55 were MI negative (P = 0.049). Of the high-level MIs, 80% had mutation in TbetaR-II, 40% in BAX and 0% in IGF-IIR. Of low-level MIs, 33% also had TbetaR-II mutation. These mutations were absent in the MI-negative cases. Of three lymphoepithelioma-like carcinomas, two cases were EBV positive and MI negative, one case was EBV negative but with high-level MI. In conclusion, high-level MIs were present regardless of the EBV status, and were found in a particular clinicopathological subset of gastric carcinoma patient. Inactivation of important growth regulatory genes observed in these carcinomas confirms the importance of MI in carcinogenesis.  (+info)

Characterization of a CACAG pentanucleotide repeat in Pasteurella haemolytica and its possible role in modulation of a novel type III restriction-modification system. (8/8354)

In a previous study, a recombinant plasmid that contains a CACAG pentanucleotide repeat was isolated from a Pasteurella haemolytica A1 library. Southern hybridization analysis using a (CACAG)5probe indicated the presence of two loci that contain the pentanucleotide repeats on the genome of P.haemolytica A1. Additional hybridization analyses against genomic DNA from related microorganisms indicated that the repeats are only present in P.haemolytica and Pasteurella trehalosi T3. The various serotypes of P.haemolytica werefound to have either one or two of the CACAG repeat-containing loci. Examination of the locus designated Rpt2 by PCR and sequence analysis indicated that the number of CACAG repeats could change upon serial subculture which most likely occurs as a result of DNA slipped-strand mispairing. A plasmid carrying the Rpt2 locus was isolated and characterized. Sequenceanalysis indicated that the CACAG repeats are contained within the 5'-end of a gene that showed homology to mod genes of type III restriction-modification systems. A second open reading frame downstream was identified which showed homology to res genes of type III restriction-modification systems. Both the modification and restriction proteins could be expressed and polypeptides of the expected sizes were detected by SDS-PAGE. Restriction activity could also be detected in crude cytoplasmic extracts of Escherichia coli strains carrying the mod and res genes on recombinant plasmids.  (+info)

Define Microsatellite repeats. Microsatellite repeats synonyms, Microsatellite repeats pronunciation, Microsatellite repeats translation, English dictionary definition of Microsatellite repeats. n. 1. A short sequence of DNA consisting of multiple repetitions of a set of two to nine base pairs, used as a genetic marker when individuals differ in the...
Hybridisation-capture was used to create 12 unique alpaca DNA libraries each enriched for a different tetranucleotide microsatellite motif. Two hundred and forty nine microsatellites were found, of which 26 were polymorphic (motifs GGAT, GTTT and GCAC). Nine markers were fully characterised on 45 samples. Allele numbers ranged from 6 (Locus P135) to 12 (loci P149 and PCTD17). There was no evidence of linkage disequilibrium at any locus (p = 0.064 - 1). Deviation from Hardy-Weinberg equilibrium was observed in three loci after Bonferroni correction (PCTD17, P135 and P193). Null alleles were detected at loci P147, P193 and P194. Polymorphic information content ranged from 0.48 to 0.82. When combined, the markers had an exclusion probability of 97.7%. Two polymerase chain reaction multiplex sets comprising six and three markers each were optimized. These multiplex sets will be useful for parentage determination, and individually the markers will add to the pool of markers available for mapping of ...
The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. The reported markers provide a novel
An experimental procedure using biotin-labelled probes and streptavidin-bound magnetic beads (FIASCO) was used to produce a microsatellite-enriched library for the collembolan Orchesella villosa. PCR primers were successfully constructed for seven loci containing, respectively, five pure, one interrupted, and one compound dinucleotide microsatellite repeats. As a preliminary test of their variability, we investigated 15 individuals from 5 locations inside a dismissed mining area in southern Tuscany. All microsatellite loci showed high levels of polymorphism. The mean number of different alleles at each locus across populations was 10.1 and observed heterozygosity per locus was 0.13-0.86. Only 2 out of the 7 loci appeared to be in Hardy-Weinberg equilibrium. The potential application of these loci to test the effects of environmental contamination on the genetic structure of exposed populations is discussed.. ...
Figure 1: (a) Microsatellite instability was originally assessed using gel electrophoresis and autoradiographic detection. In the left panel, additional bands (black arrows) in the tumor lane illustrate multiple contracted microsatellite alleles relative to the genomic control lane. In the right panel, an information (heterozygous) microsatellite is shown in the genomic control sample, and a significant loss of signal intensity for the smaller allele is observed in the tumor sample, characteristic of allelic imbalance/loss of heterozygosity (LOH). (b) Microsatellite loci are now commonly assessed using fluorescent PCR amplifications, capillary electrophoresis, and automated sequencing techniques. Laser scanners detect fluorescent PCR products and generate a chromatogram displaying microsatellite allele frequencies. Note in the tumor panel, one of the alleles has undergone contraction, depicting MSI in this tumor specimen. (c) Subcloning and direct sequencing of microsatellite amplifications can ...
The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM) analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence of Mycospherlla graminicola and Fusarium graminearum. A total of 20 new microsatellite primers as easy-to-score markers were developed. Microsatellite primer PCR (MP-PCR) yielded highly reproducible and complex genomic fingerprints, with several bands ranging in size from 200 to 3000 bp. Of the 20 primers tested, only (TAGG)4, (TCC)5 and (CA)7T produced a high number of polymorphic bands from either F. graminearum or F. culmorum. (ATG)5 led to successful amplifications in M. graminicola isolates collected from Germany. Percentage of polymorphic bands among Fusarium species ranged from 9 to 100%. Cluster analysis of banding patterns of the isolates corresponded well to the established species delineations based
Despite the central significance of microsatellite mutations to issues of genomic instability, forensic testing, and population genetic analyses, the rate of origin and spectrum of effects of such mutations are still poorly understood, with many estimates being derived from reporter constructs in yeast cultures (e.g., Henderson and Petes 1992; Strand et al. 1995; Wierdl et al. 1996; Sia et al. 1997). Our long-term series of mutation-accumulation lines of C. elegans and D. pulex provide a useful platform for a more direct evaluation of the properties of microsatellite mutations in two key model organisms.. As in previous studies (Wierdl et al. 1997; Brinkmann et al. 1998; Kayser et al. 2000; Beck et al. 2003; Whittaker et al. 2003; Legendre et al. 2007), we find a strong correlation between allele size (repeat number) and mutation rate in C. elegans (Figure 1). In addition, although the variation of repeat numbers among loci sampled in D. pulex does not permit a formal evaluation of length ...
Objectives: Tumors with high-frequency microsatellite instability (MSI-H) have unique biological behavior and the predictive role of microsatellite instability (MSI) status on survival of colorectal cancer is still debated. The prognostic significance of MSI status in sporadic stage II and III rectal cancer patients needs to be more precisely defined. So we investigated the relationship between MSI status and clinicopathological features and prognosis in these patients. Methods: DNAs from fresh-frozen paired samples of tumors and corresponding normal tissue from 128 stage II and III rectal cancer patients were analyzed for MSI by PCR amplification using markers recommended by a National Cancer Institute workshop on MSI. To assess prognostic significance, Cox proportional hazards modeling was used. Results: Twelve (9.3%) tumors in our study were MSI-H, 28 (21.9%) were low-frequency MSI (MSI-L) and 88 (68.8%) were microsatellite stable (MSS). Most of the MSI-H tumors compared with MSI-L and MSS ...
Inactivation from the DNA mismatch restoration pathway manifests while microsatellite instability, a build up of mutations that drives carcinogenesis. analyzed using immunocytochemical evaluation. SNP karyotyping was utilized to review chromosomal instability. RNA silencing, Traditional western blotting and gene manifestation analysis was utilized to review the functional effects of mutations. Acute myeloid leukemia cell lines (4 of 12, 33%) and main examples (2 of 18, 11%) exhibited microsatellite instability with 925681-41-0 IC50 mono-allelic mutations in and high-risk myelodysplastic symptoms exhibited microsatellite instability. Considerably, all 11 individuals with microsatellite instability experienced cytogenetic abnormalities with 4 of these (36%) having a mono-allelic microsatellite mutation in worth cut offs had been dependant on Bonferronis multiple check correction using the threshold arranged at 0.05. Further information on Design and Strategies can be purchased in the and and in ...
Somatic and germ-line mutations: An understanding of microsatellite mutation patterns is central to their use for the accurate reconstruction of population processes. We have developed and validated an experimental approach to estimate the distribution of mutation sizes for each individual microsatellite locus. These distributions were estimated from somatic mutations observed in the tumor tissue of sporadic patients with colorectal cancer.. It is not known whether such mutations arise from the same events that produce variation in the normal population. Microsatellite instability in some cancer patients may reflect defects in mismatch repair; but, in other patients, it may be a consequence of the higher number of cell divisions that occurs in the tumor compared to the normal tissue. Nevertheless, in the absence of specific mechanistic or genetic information on the source of these mutations, it is still possible to test whether they reflect the mutation process in the general population by using ...
To date, two forms of microsatellite instability (MSI) have been described in human cancer. MSI typical of hereditary nonpolyposis colon cancer (HNPCC), is due to deficient DNA mismatch repair (MMR) and is defined with mono- and dinucleotide repeat microsatellites. A second variety of instability is best seen at selective tetranucleotide repeats (EMAST; elevated microsatellite alterations at select tetranucleotides). While MSI occurs infrequently in bladder cancers, EMAST is common. Sporadic tumours with the largest proportion showing MSI are those found most frequently in HNPCC kindreds. While bladder cancer is not frequently seen in HNPCC, upper urinary tract tumours (UTTs) are. Having previously found a low frequency of MSI in bladder cancer, we sought to determine the relative levels of MSI and EMAST in transitional cell carcinoma (TCC) of the upper and lower urinary tracts. Microsatellite analysis was performed at 10 mono- and dinucleotide and eight tetranucleotide loci, in 89 bladder and 71 UTT
TY - JOUR. T1 - Microsatellite instability and allelic imbalance in primary and secondary colorectal cancer. AU - Schneider, Anne. AU - Rohr, Serge. AU - Kelly, Michael D.. AU - Mitry, Ragai. AU - Pignatelli, Massimo. AU - Dore, Caroline J.. AU - Gaub, Marie Pierre. AU - Jaeck, Daniel. AU - Meyer, Christian. AU - Oudet, Pierre. AU - Habib, Nagy A.. PY - 2000. Y1 - 2000. N2 - Background: Several studies of colorectal cancer have shown an association between the number and type of genomic defects and the stage of disease. A subset of colorectal tumours are due to inactivation of DNA mismatch repair genes and these tumours exhibit microsatellite instability. The aim of the present study was to compare and contrast the genomic defects present in both the primary and metastatic stages of the disease using microsatellite probes. Methods: Modifications of the allelic profiles of 25 microsatellite regions were studied in a total of 85 colorectal tumours using fluorescent polymerase chain reaction (PCR) ...
Microsatellite analysis includes PCR amplification of the microsatellite loci using fluorescently labeled primers; labeled PCR products are then analyzed by capillary electrophoresis (CE) or electrophoresis to separate the alleles by size. We have more than 800 markers to choose from and will be happy to discuss them in more detail with you. We will need 10ul/marker of 30-50ng/ul DNA in Strip tubes.. We ask that all new clients either call or email Ross Wilson to discuss your projects details.. Phone: 214-648- ...
Microsatellite enrichment is a method in molecular biology used for enriching the amount of microsatellite sequences in a DNA sample. This can be achieved by designing oligonucleotide probes that hybridize with the repeats in the microsatellites and then pull out the probe/microsatellite complexes from the solution. This has been shown to be a cost-effective method to sample the genetic diversity in non-model organisms. Kaukinen KH, Supernault KJ, Miller KM (2004). Enrichment of tetranucleotide microsatellite loci from invertebrate species. Journal of Shellfish Research. 23 (2): 621. Jennings, TN; Knaus, BJ; Mullins, TD; Haig, SM; Cronn, RC (2011-06-16). Multiplexed microsatellite recovery using massively parallel sequencing. Molecular ecology resources. 11 (6): 1060-7. doi:10.1111/j.1755-0998.2011.03033.x. PMID 21676207 ...
In 10-20% of patients with colorectal cancer (CRC), carcinogenesis is due to genomic defects in the mismatch repair machinery. Defective DNA repair as a result of germ-line mutations has been linked to sporadic colorectal carcinoma, and also to those carcinomas arising in hereditary non-polyposis colorectal carcinoma (HNPCC) syndrome. In both settings, the mutations and promoter hypomethylation occur mainly in the genes hMLH1 and hMSH2 of the mismatch repair system, and result in loss of their expression.1 Further, defects in the mismatch repair process with subsequent base pair mismatches lead to microsatellite instability (MSI).1 2 Since the failure of the repair system as a cause of genomic instability is associated with a better prognosis1 3 many different microsatellite loci have been used to identify MSI in tumours for diagnostic and prognostic purposes.2 In an attempt to provide uniformity in clinical diagnoses, an international meeting at the National Cancer Institute (NCI) recommended ...
Mismatch repair protein deficiency (MMR-D) and high microsatellite instability (MSI-H) are features of Lynch syndrome-associated colorectal carcinomas and have implications in clinical management. We evaluate the ability of a targeted next-generation sequencing panel to detect MMR-D and MSI-H based on mutational phenotype. Using a criterion of ,40 total mutations per megabase or ,5 single-base insertion or deletion mutations in repeats per megabase, sequencing achieves 92% sensitivity and 100% specificity for MMR-D by immunohistochemistry in a training cohort of 149 colorectal carcinomas and 91% sensitivity and 98% specificity for MMR-D in a validation cohort of 94 additional colorectal carcinomas. False-negative samples are attributable to tumor heterogeneity, and next-generation sequencing results are concordant with analysis of microsatellite loci by PCR. In a subset of 95 carcinomas with microsatellite analysis, sequencing achieves 100% sensitivity and 99% specificity for MSI-H in the ...
The present study deals with the assessment of genetic diversity using microsatellite marker in the fish Labeo gonius from Nanak Sagar and Dhaura reservoirs of Uttarakhand having different morpho-edhaphic features and self- recruiting populations of this fish. These reservoirs are distantly located and distinctly separated without any connection having negligible possibility of gene exchange with each other. Total 12 cross amplified microsatellite primers after using software Primer-BLAST and Primer-3 were screened in all 100 DNA samples of fish collected from both the reservoirs. 12 cross amplified microsatellite primers were screened and successfully amplified. After PCR amplification of microsatellite loci and performing native PAGE using amplified DNA samples as above, POP GENE Version 1.32 was used to calculate Neis observed heterozygosity, expected heterozygosity, Neis genetic diversity, Fixation index (Fis) and Shannons information index (SI) and genetic variability indices viz. Gene flow(Nm),
Read Isolation and characterization of twelve polymorphic microsatellite loci in the buff-throated partridge (Tetraophasis szechenyii), Russian Journal of Genetics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
TY - JOUR. T1 - Kanniadu goats of Tamilnadu, India. T2 - genetic characterisation through microsatellite markers. AU - Thilagam, K. AU - Jayaraj, Rama. AU - Sivaselvam, S N. AU - Karthickeyan, S M. AU - Thangaraju, P. PY - 2006. Y1 - 2006. N2 - Characterisation of Kanniadu goats was done using microsatellite markers. The genomic DNA from 50 unrelated Kanniadu goats were PCR-amplified with a panel of 20 microsatellite markers and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining.The number of alleles ranged from 5 to 14 with allele sizes ranging from 90 to 222bp. The allele frequencies ranged from 0.0106 to 0.4480. Polymorphism information content ranged from 0.5710 to 0.8570. Except four loci, thepopulation was not in Hardy-Weinberg equilibrium. The observed heterozygosity ranged from 0.7142 to 0.9778 while the expected heterozygosity ranged from 0. 6390 to 0.8702, indicating the heterogenous nature of the population distributed in the breeding ...
Genetic diversity and relationships among 38 Iranian durum wheat accessions were analysed using conserved DNA-derived polymorphism (CDDP) and start codon targeted (SCoT) markers. A total of 10 CDDP and 10 SCoT primers were used to estimate genetic polymorphism among 38 durum wheat accessions. Comparatively, both CDDP and SCoT markers proved to be more effective and in terms of percentage of polymorphisms and polymorphic information content value were relatively similar. The average polymorphic information content value of CDDP was 0.39 which was relatively higher than those of SCoT where the respective values of polymorphic information content was 0.35. Using the neighbor joining clustering method, CDDP and SCoT markers were used to generate dendrograms, which revealed that the durum accessions were clustered into three and two major groups, respectively. According to the present results, CDDP markers proved more informative in studying genetic diversity among durum accessions. In both marker ...
Xiao Bingbing, Han Lingxia, Niu Chengming, Si Changde and Han Jianlin. 2010. Population genetic variation in BWEL-SPF chickens inferred from microsatellite DNA markers. China Animal Husbandry and Veterinary Medicine 37(9):106-111 ...
BEHEREGARAY, L. B., SCHWARTZ, T. S., MÖLLER, L. M., CALL, D., CHAO, N. L. and CACCONE, A. (2004), A set of microsatellite DNA markers for the one-lined pencilfish Nannostomus unifasciatus, an Amazonian flooded forest fish. Molecular Ecology Notes, 4: 333-335. doi: 10.1111/j.1471-8286.2004.00687.x ...
Genetic variation in three Iranian pelt sheep breeds namely: Gray Shiraz, Zandi and Karakul were investigated using fifteen microsatellite loci. Genomic DNA was extracted from 360 blood samples by extraction kits and salting-out procedure with some modifications. The total number of alleles ranged from 6 to12 in loci. The fifteen tested loci were all polymorphic in the three breeds. The average direct count of heterozygosity overall loci in each tested breed was more than the expected heterozygosity. Tests of genotype frequencies for deviation from the Hardy-Weinberg equilibrium (HWE) were performed at each locus of overall breeds and revealed significant departure from HWE (P , 0.001) due to heterozygote excess. Polymorphism information content value in Gray Shiraz, Zandi and Karakul were 0.815, 0.808 and 0.808, respectively. Rate of inbreeding within the three breeds was not noticeable (global Fis = - 0.19). Low genetic differentiation was detected by estimation of Fst index between all pairs ...
Defective DNA mismatch repair in human tumors leads to genome-wide instability of microsatellite repeats and a molecular phenotype referred to as microsatellite instability (MSI). MSI has been reported in a variety of cancers and is a consistent feature of tumors from patients with hereditary non-po …
Hybridization and/or incomplete sorting of ancestral polymorphism are commonly implicated to explain discordant phylogenetic analyses of closely related species complexes. One genus in which these phenomena have been suggested to have played major roles based on phylogenetic data is Conradina, a genus of mints (Lamiaceae) endemic to the southeastern USA containing several endangered species. The goals of this study were to use microsatellite data to better understand patterns of genetic structure in Conradina, to test hypotheses of recent or ancient hybridization and incomplete lineage sorting, and to clarify species boundaries. Individuals from 55 populations representing all Conradina species were genotyped using 10 microsatellite loci. Analyses of the patterns of genetic structure in Conradina revealed a clear differentiation of populations following recognized species boundaries, indicating that species have diverged from one another genetically and interspecific hybridization has not ...
Patterns of biodiversity and evolutionary processes controlling them are still poorly studied in desert biomes. Fine-scale markers could help answer some of the pressing research questions for desert biomes and Sahara in particular. Such markers are available for some large mammals and crocodiles, but not for small vertebrates. Here we present a battery of microsatellite loci developed for Agama boulengeri, a promising model to study evolutionary and demographic processes in the Sahara-Sahel. Loci were selected by sequencing enriched DNA libraries with 454 pyrosequencing. A total of 23 polymorphic loci were successfully amplified in four multiplex reactions. Cross-amplification of the microsatellite loci in A. agama and A. boueti was partially successful. These markers are a promising tool for assessing genetic diversity, gene-flow dynamics and demographic patterns in this group. Given the genus Agama is distributed throughout Africa, results presented here might also facilitate studies in other ...
Aberrant Wnt signaling activation occurs commonly in colorectal carcinogenesis, leading to upregulation of many target genes. APC (adenomatous polyposis coli) is an important component of the β-catenin destruction complex, which regulates Wnt signaling, and is often mutated in colorectal cancer (CRC). In addition to mutational events, epigenetic changes arise frequently in CRC, specifically, promoter hypermethylation which silences tumor suppressor genes. APC and the Wnt signaling target gene ITF2 (immunoglobulin transcription factor 2) incur hypermethylation in various cancers, however, methylation-dependent regulation of these genes in CRC has not been studied in large, well-characterized patient cohorts. The microsatellite instability (MSI) subtype of CRC, featuring DNA mismatch repair deficiency and often promoter hypermethylation of MutL homolog 1 (MLH1), has a favorable outcome and is characterized by different chemotherapeutic responses than microsatellite stable (MSS) tumors. Other epigenetic
Microsatellite instability has been observed in both sporadic and hereditary forms of colorectal cancer. In the hereditary form, this instability is generally due to germline mutations in mismatch repair (MMR) genes. However, only one in ten patients with sporadic tumours exhibiting microsatellite i …
Microsatellite loci mutate at an extremely high rate and are generally thought to evolve through a stepwise mutation model. Several differentiation statistics taking into account the particular mutation scheme of the microsatellite have been proposed. The most commonly used is R(ST) which is independent of the mutation rate under a generalized stepwise mutation model. F(ST) and R(ST) are commonly reported in the literature, but often differ widely. Here we compare their statistical performances using individual-based simulations of a finite island model. The simulations were run under different levels of gene flow, mutation rates, population number and sizes. In addition to the per locus statistical properties, we compare two ways of combining R(ST) over loci. Our simulations show that even under a strict stepwise mutation model, no statistic is best overall. All estimators suffer to different extents from large bias and variance. While R(ST) better reflects population differentiation
Alterations at microsatellite DNA markers in cells exfoliated in urine have been correlated to the presence of bladder cancer. To check the feasibility of such noninvasive analysis to routinely diagnose bladder cancers, we have developed a highly sensitive method using fluorescent PCR to search for DNA microsatellite alterations in urine sediment compared with a blood paired sample. One hundred eighty-three patients were included in our study. This population comprised 103 bladder cancers (64 pTa stages), the complement representing controls and other benign or malignant diseases. Results of the analysis at 17 loci in a blinded study were compared with cystoscopy and/or pathology. The high reproducibility of this technique and the analysis of 26 control patients allowed us to determine for each microsatellite a cutoff characterizing a significant allelic imbalance. For bladder cancer detection, the overall sensitivity of the test was 84%. Using this procedure, we identified alterations in 81%, ...
In order to identify polymorphic microsatellite markers and evaluae genetic variation within Baluchi sheep population, nineteen microsatellite loci were studied. Whole Blood samples were collected from 156 sheep at north eastern animal breeding station of Iran (Abbasabad-Mashhad). DNA was extracted by salting-out procedure with some modifications. Polymerase chain reactions were ...
Dec 21, 2009. From 7-18 December 2009, the project RER/5/015 Supporting Early Warning and Surveillance of Avian Influenza Infection in Wild and Domestic Birds and Assessing Genetic Markers for Bird Resistance, held a Regional Training Course on Genomic DNA Preparation, Microsatellite Analyses and Sequencing, at the IAEA and FAO Agriculture and Biotechnology Laboratory in Seibersdorf, Austria.. This IAEA Technical Cooperation Programme in Europe initiated a new regional programme to establish early bird-flu diagnosis and assessment of genetic markers for Avian Influenza reistsance with nuclear molecular methods in the region to prevent spread of Avian Influenza for better animal health and economic benefits.. The purpose of the training course was to enhance knowledge on highly pathogenic avian influenza (advanced molecular genetic tools by use of nuclear and nuclear related and molecular technologies), in genomic DNA preparation, microsatellite analyses and sequencing, with the ultimate goal to ...
Microsatellite instability (MSI) is a major predictive and diagnostic marker in several cancers including colorectal carcinomas. Diagnostic testing for microsatellites is generally performed using capillary sequencers, which requires expensive high-end equipment including expensive chemistry using fluorescent dyes labelling the PCR products of interest. In this study we have modified such a diagnostic protocol and established the microsatellite testing on the QiaXcel Advanced platform. MSI testing was based on a previously established protocol describing a multiplex PCR followed by fluorescent detection of PCR products in a capillary sequencing device. Ten microsatellites were included in the new protocol: BAT25, BAT26, BAT40, D2s123, D10s197, D13s153, D17s250, D18s58, D5s346, and MycI. In this protocol the PCR was demultiplexed and established on the QiaXcel Advanced system (Qiagen, Hilden, Germany). Making use of a series of FFPE control samples with known MSI status including those with and without
To facilitate large-scale genetic mapping of the human genome, we have developed chromosome-specific sets of microsatellite marker loci suitable for use with a fluorescence-based automated DNA fragment analyser. We present 254 dinucleotide repeat marker loci (80% from the Genethon genetic linkage map) arranged into 39 sets, covering all 22 autosomes and the X chromosome. The average distance between adjacent markers is 13 centiMorgans, and less than 4% of the genome lies more than 20 cM from the nearest marker. Each set of microsatellites consists of up to nine marker loci, with allele size ranges that do not overlap. We selected marker loci on the basis of their reliability in the polymerase chain reaction, polymorphism content, map position and the accuracy with which alleles can be scored automatically by the Genotyper(TM) program ...
Laboratory and field protocols, and scripts used in the LEGAL laboratory.. For scripts check out our GitHub repository.. For PDF versions of protocols also check out our GitHub repository.. ...
Comparing different methods of estimating the genetic diversity could define their usefulness in plant breeding programs. In this study, a total of 18 morphological traits and 20 simple sequence repeat (SSR) loci were used to study the morphological and genetic diversity among 20 maize hybrids selected from different countries, and to classify the hybrids into groups based on molecular profiles and morphological traits. To collect morphological data, a field experiment was carried out using an RBCD design with three replications in Moghan, Ardabil, Iran. The highest estimates for genetic coefficients of variation were observed in anthesis-silking interval, followed by grain yields, leaf chlorophyll rates, kernel row numbers, and ear heights. The total number of PCR-amplified products was 84 bands, all of which were polymorphic. Among the studied primers,NC009,BNLG1108,BNLG1194,PHI026 and PHI057 showed the maximum polymorphism information content(PIC) and the greatest diversity. To determine the genetic
AIMS: To detect microsatellite abnormalities in the primary tumours and plasma of patients with breast carcinoma. METHODS: Plasma was obtained from 17 breast carcinoma patients before surgery. Corresponding tumour and benign lymph node (control) samples for each of the carcinoma patients were obtained from paraffin blocks. DNA was extracted from the plasma samples and the paraffin embedded tissue using previously described methods. RESULTS: The 17 primary tumours showed two examples of loss of heterozygosity and three examples of microsatellite instability; the 17 plasma samples showed three and one, respectively. Many of the longer microsatellites (over 200 base pairs) were difficult to amplify from plasma. The investigations suggested that this was because of the highly fragmented nature of plasma DNA. Only one example of loss of heterozygosity and one example of microsatellite instability showed a concordant pattern in both primary tumour and plasma. These were both in the same patient. ...
In total, 41 different microsatellite variants have been typed in one or more of four different sets of recombinant inbred (RI) mouse strains. Microsatellite variants were selected that were located in chromosomal regions previously lacking markers. These markers extend the regions swept in these RI strains.
Parentage Testing Procedures - DNA - $35. A DNA profile-which provides allele sizes for all microsatellite markers-is obtained, and parentage analysis is performed. A variety of sample types can be utilized for routine testing, including blood, hair, semen, buccal swabs and FTA cards. Non-routine sample types include bone, teeth, saliva, dried blood, urine and feces. DNA is extracted from the samples, and microsatellite marker analysis begins with the PCR procedure. In this process a computer program compares the DNA profile of the offspring to those of the presumed parents. A parentage analyst reviews the results and sends the final report. If a listed parent or parents are excluded, additional analysis is performed including retesting of samples and the possible use of additional DNA markers to confirm the exclusion.. *If there is any question about a kid(s) sire, i.e. more than one buck in a doe pen, All kids will be required to have a DNA test completed as well as at least one of the bucks ...
Hi bionetters I am doing research on the occurrence and polymorphism of microsatellites in co nifers. I havent found a lot of polymorphisms in GT/CA repeats or CT/GA. Howev er, I have an AT/AT microsatellite that shows a high rate of variability. There are a few problems with it though. 1) I originally isolated it as a CA-repeat that was followed by a stretch of TA s. I amplified it from the genomic DNA and found that all the products I obtain ed are shorter than the original. Then I cloned the PCR amplified fragments and sequenced them. To my surprise, the CA/GT microsatellite was not present. What was left was a stretch of TAs. Am I amplifying a microsatellite family and is the CA/GT + TA member that I cloned only a minority???? I am not so sure since I havent obtained more than 2 alleles from a single tree up to now. 2) When I PCR the plasmids containing the different AT stretches, I obtain two or more distinct bands as a result. Instability of the TA repeat in the plasmid /bacterial host ...
TY - JOUR. T1 - Band-specific localization of the microsatellite at D13S71 by microdissection and enzymatic amplification. AU - Spielvogel, H.. AU - Hennies, H. C.. AU - Claussen, U.. AU - Washington, S. S.. AU - Chakravarti, A.. AU - Reis, A.. PY - 1992/6/1. Y1 - 1992/6/1. N2 - Microsatellite DNA consists of tandemly repeated simple DNA sequence motifs, the number of these repeats being polymorphic. These recently described polymorphisms are ubiquitously distributed throughout the human genome and are highly informative, making them ideal markers for linkage analysis. Physical localization of these microsatellites is an important prerequisite for aligning physical and genetic maps. We have physically mapped the microsatellite at D13S71, which has previously been assigned to chromosome 13. Band-specific mapping of D13S71 to the distal part of band 13q32, near 13q33, was achieved by microdissection of GTG-banded chromosomes and subsequent enzymatic amplification with a heminested PCR approach. ...
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Genomic copy number changes are frequently found in cancers and they have been demonstrated to contribute to carcinogenesis; and it is widely accepted that tumors with microsatellite instability (MSI) are genetically stable and mostly diploid. In the present study we compared the copy number alterations and the gene-expression profiles of microsatellite stable (MSS) and MSI colorectal tumors. A total number of 31 fresh-frozen primary tumors (16 MSS and 15 MSI) were used. Twenty-eight samples (15 MSS and 13 MSI) were analyzed with metaphase comparative genomic hybridization (CGH), nine of which plus one additional sample (4 MSS and 6 MSI) were further analyzed by cDNA-based array-CGH. Gene expression analysis was performed with six samples [3 MSS and 3 MSI, four of these used in metaphase CGH (mCGH) analysis] to identify differentially expressed genes possibly located in the lost or amplified regions found by CGH, stressing the biological significance of copy number changes. Metaphase and ...
Immunotherapy has achieved long-term durable responses for multiple types of previously difficult-to-treat solid cancers, such as lung cancer and melanoma.40 MSI-H tumors cancer have been approved for the application of ICI such as pembrolizumab.3 Nivolumab (anti-PD1) plus ipilimumab (anti-CTLA-4) has demonstrated high response rates, improving progression-free survival and overall survival at 12 months, and is a promising treatment option for patients with dMMR MSI-H metastatic colorectal cancer.41 In contrast, MSS colon cancer seems to obtain limited benefits from immunotherapy. Chalabi et al42 tested ipilimumab plus nivolumab in early stage dMMR and pMMR colon cancers. Major pathological responses were observed in 7/7 (100%) dMMR tumors, with 4/7 (57%) complete responses, and no major pathological responses were found in pMMR tumors. Interestingly, significant increases in T-cell infiltration, particularly in CD8+ T cells, were seen post-treatment in both pMMR and dMMR tumors, indicating the ...
OBJECTIVE: To compare the potential of two diagnostic methods for detecting recurrence of urothelial cell carcinoma (UCC) of the bladder, by (i) detecting alterations in microsatellite DNA markers and loss of heterozygosity (LOH), and (ii) detecting aberrant gene hypermethylation, as UCC has a high recurrence rate in the urinary tract and the disease can invade muscle if new tumours are overlooked. PATIENTS AND METHODS: Over 1 year, urine samples were retrieved from 40 patients already diagnosed with bladder UCC (30 pTa, two pTis, eight pT1). Samples were collected 6 months after bladder tumour resection, during the follow-up schedule. We used samples to analyse nine microsatellite markers and the methylation status of 11 gene promoters. Receiver operating characteristic curves were generated and Bayesian statistics used to create an interaction network between recurrence and the biomarkers. RESULTS: During the study, 15 of the 40 patients (38%) had a tumour recurrence and 14 were identified by
Crohn disease (CD) is a chronic relapsing inflammatory condition of the gastrointestinal tract. Recently, polymorphisms in NOD2 (CARD15), a gene mapping to the chromosome 16 IBD1 susceptibility locus, have been associated with susceptibility to CD. One group identified the gene by using classic positional cloning methods. Here, we report linkage and fine mapping analyses using 27 microsatellite markers encompassing the IBD1 susceptibility locus in 131 CD affected sibling pairs, and a simplex family cohort. No evidence for linkage was observed, and microsatellite markers close to NOD2 did not show association. However, significant association was confirmed in 294 CD trios for the NOD2 variants Arg702Trp and Leu1007fsinsC. Our fine mapping study of the IBD1 locus did not enable us to identify NOD2 as a CD gene, despite the presence of association with disease-causing alleles. This study illustrates the difficulties facing microsatellite linkage and linkage disequilibrium mapping methods for identifying
Profound MSI is a hallmark of hereditary nonpolyposis colon carcinoma (HNPCC) and is also found in a proportion of sporadic HNPCC-spectrum tumors, such as endometrial carcinoma.21 The underlying cause of MSI is a defect in mismatch repair, which results in tumorigenesis through an accumulation of somatic mutations in genes important for regulating cell cycle, growth, or apoptosis. A lower level of MSI occurs in tumors that are outside the HNPCC spectrum. Previous studies of endothelial cells microdissected from plexiform lesions of PAH lungs have shown monoclonal expansion in 17 of 22 lesions (77%) from 4 patients and microsatellite mutation rates ranging from 21% for BAX to 50% for BAT26.13,15 This suggested that endothelial cell expansion in plexiform lesions is akin to neoplasia and might result from an accumulation of somatic mutations, either through MSI or other mutational mechanisms. We have now conducted similar analyses in a series of FPAH cases in whom BMPR2 has been fully ...
Microsatellite combines several features of an ultimate molecular marker and they are used increasingly in various plant genetic studies and applications. Characterization of mungbean genotypes on the basis of DNA fingerprinting has become an efficient tool to link genotypic variation. This work is reporting the utilization of a small set of five previously developed mungbean microsatellite (SSR) markers for the identification and discrimination of six HYVs and 36 landraces. All five microsatellite markers were found to be polymorphic. Variation was found in number of alleles, allele frequency, observed and expected heterozygosity. Using five primers across 42 genotypes a total of 20 alleles with an average number of 4 alleles per locus were found of which GBssr-MB91 showed highest number of alleles (6) (size ranging from 135 to 152 bp) followed by 4 alleles (from 160 to 176 bp and 175 to 195 bp) and 3 alleles (from 264 to 282 bp and 283 to 304 bp) were detected at the loci LR7322B, LR7323A, LR7323B and
A total of 83 prostate adenocarcinomas was evaluated for allelic loss on chromosome 10 by analysis of loss of polymorphic microsatellite repeats. Initially, 64 stage B carcinomas were analyzed at 12 loci on chromosome 10. Nine cases showed loss of chromosome 10 sequences, with a fractional allelic loss of 20%. These nine cases were then analyzed at an additional 19 loci to define better the regions of loss. Four areas of loss were identified, including 10p (2 of 64 cases), 10q23.1 (7 of 64 cases), 10q23.3 (4 of 64 cases), and 10q26 (2 of 64 cases). Three loci in these regions, D10S111, D10S185, and D10S192, were then analyzed in 19 advanced (stage C and D) carcinomas. Seven (37%) of 19 advanced carcinomas showed allelic loss at one or more of these loci. A statistically significant increase in the fractional allelic loss at both D10S111 (10p) and D10S185 (10q23.1) was observed. Thus, a complex pattern of loss is seen on chromosome 10 in prostate carcinoma, with regions of loss on 10p and 10q, ...
Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. We designed |13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at
TY - JOUR. T1 - Novel Polymorphic Microsatellite Markers for Panulirus ornatus and their Cross-species Primer Amplification in Panulirus homarus. AU - Delghandi, Madjid. AU - Afzal, Hasifa. AU - Al Hinai, Manal Saif Nasser. AU - Al-Breiki, Rafaida Dhuhai Gharib. AU - Jerry, Dean R.. AU - Dao, Hoc Tan. PY - 2016/10/1. Y1 - 2016/10/1. N2 - Polymorphic microsatellite loci were isolated for Panulirus ornatus using 454 GS-FLX Titanium pyrosequencing. Fifteen markers containing perfect di-, tri-, tetra-, and penta-nucleotide motifs were consistently co-amplified in five multiplexes in a panel of 91 randomly selected samples. Observed number of alleles varied from 2 to 14 per locus. Observed and expected heterozygosity ranged from 0.090 to 0.79 and 0.08 to 0.87, respectively. Ten loci deviated from Hardy-Weinberg equilibrium after sequential Bonferroni correction. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between 11 loci. ...
TY - JOUR. T1 - Microsatellite DNA markers for the study of horseshoe crab (Limulus polyphemus) population structure. AU - King, Tim L.. AU - Eackles, Michael S.. PY - 2004/9. Y1 - 2004/9. N2 - Twenty-two microsatellite DNA loci were identified and characterized for horseshoe crabs (Limulus polyphemus) collected from two Atlantic coast and one Gulf of Mexico site. These markers revealed a high degree of genetic diversity (8-35 alleles per locus), heterozygosity (25.0% to 100.0%), and allelic heterogeneity (69.8% of comparisons). Considerable regional differentiation was observed as genetic distances (chord) ranged between 0.25 and 0.45, and all FST values (0.014-0.092) were significant. These preliminary findings are consistent with patterns of regional differentiation observed using allozyme variation and contradictory to findings of limited gene flow reported for sequence variation at the mitochondrial DNA COI region.. AB - Twenty-two microsatellite DNA loci were identified and characterized ...
Relatively few studies have investigated the genetic population structure of sea anemones. This is particularly true for sea anemones that host some of the most iconic fishes on coral reefs, the anemonefishes. One of the main reasons for this knowledge gap is the lack of appropriate genetic markers. We developed and characterized a total of 47 novel polymorphic microsatellite markers for four host sea anemone species from the Indo-Pacific: Entacmaea quadricolor (n = 16 microsatellite markers), Heteractis magnifica (n = 8), Stichodactyla mertensii (n = 13), and Stichodactyla gigantea (n = 10). Here, we report genetic diversity statistics from two different sampling locations for each anemone species. Overall, we found that most markers were highly polymorphic. On average, we found a mean of seven alleles per locus. Observed and expected heterozygosities displayed high variation among loci, ranging from 0.033 to 0.980 and from 0.038 to 0.927, respectively. Only four loci showed deviations of ...
TY - JOUR. T1 - Genetic structure of Tellicherry goats (capra hircus) based on microsatellite markers. AU - Jayaraj, Rama. AU - Sivaselvam, S N. AU - Subramanian, A. AU - Kumarasamy, P. AU - Karthickeyan, S M. AU - Thangaraju, P. PY - 2006. Y1 - 2006. N2 - Tellicherry goats were characterized by FAO recommended microsatellite markers. All 21 loci were highly polymorphic with PIC values ranging from 0.5785 to 0.8349. Significant differences (P,0.01) were noticed between observed and expected proportions of genotypes at 14 loci in the Tellicherry population studied. The highest expected heterozygosity value was 0.8504 and lowest was 0.6445 in this breed. AB - Tellicherry goats were characterized by FAO recommended microsatellite markers. All 21 loci were highly polymorphic with PIC values ranging from 0.5785 to 0.8349. Significant differences (P,0.01) were noticed between observed and expected proportions of genotypes at 14 loci in the Tellicherry population studied. The highest expected ...
Microsatellite markers from a transcriptome sequence library were initially isolated, and their genetic variation was characterized in a wild population of the mud crab (Scylla paramamosain). We then tested the association between these microsatellite markers and the growth performance of S. paramamosain. A total of 129 polymorphic microsatellite markers were identified, with an observed heterozygosity ranging from 0.19 to 1.00 per locus, an expected heterozygosity ranging from 0.23 to 0.96 per locus, and a polymorphism information content (PIC) ranging from 0.21 to 0.95 per locus. Of these microsatellite markers, 30 showed polymorphism in 96 full-sib individuals of a first generation family. Statistical analysis indicated that three microsatellite markers were significantly associated with 12 growth traits of S. paramamosain. Of these three markers, locus Scpa36 was significantly associated with eight growth traits, namely, carapace length, abdomen width (AW), body height (BH), fixed finger length of
The Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. edulis, the most important commercial Passiflora species, are still incipient. In spite of many recognized applications of microsatellite markers in genetics and breeding, their availability for passion fruit research remains restricted. Microsatellite markers in P. edulis are usually limited in number, show reduced polymorphism, and are mostly based on compound or imperfect repeats. Furthermore, they are confined to only a few Passiflora species. We describe the use of NGS technology to partially assemble the P. edulis genome in order to develop hundreds of new microsatellite markers. A total of 14.11 Gbp of Illumina paired-end sequence reads were analyzed to detect simple sequence repeat sites in the sour passion fruit genome. A sample of 1300 contigs containing perfect repeat microsatellite
The oval squid Sepioteuthis lessoniana is one of the most economically important squid species in Japan; however, its population structure is poorly understood due to the lack of hypervariable markers. Such information is critical for managing sustainable fisheries, as well as for ensuring the existence of wild S. lessoniana stocks. Eleven candidate microsatellite loci were isolated from a small insert genomic DNA library. Polymorphisms in these 11 loci were screened in 24 wild individuals. The number of alleles per locus was found to range from 5 to 19 alleles, and the observed heterozygosity ranged from 0.292 to 0.958. No evidence for linkage disequilibrium was detected among all the loci. The genotypic proportions conformed to Hardy-Weinberg equilibrium, except at one locus. In conclusion, these polymorphic microsatellite loci may be used to develop a genetic framework to manage S. lessoniana in the future.
Evans, K. M. , Bates, S. S. , Medlin, L. and Hayes, P. K. (2004): . Microsatellite marker development and genetic variation in the toxic marine diatom Pseudo-nitzschia multiseries (Bacillariophyceae). , Journal of Phychology ...
The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic
The Use of DNA Microsatellite Markers for Genetic Diversity Identification of Soybean (Glycine max (L) Meriil.) as a Supplementary Method in Reference Collections Management
A total of 10,089 simple sequence repeat (SSR) loci were identified from 81,072 Illumina-based transcriptomic unigenes of white calla lily (Zantedeschia aethiopica), an evergreen ornamental plant of Zantedeschia section Zantedeschia, cultivated worldwide. Of these SSRs, dinucleotide repeats were the most common type (63.43%), followed by trinucleotide repeats (35.02%). Microsatellite motifs AG/CT and AGG/CCT separately predominated in dimeric and trimeric repeat motifs. PCR primer pairs were successfully designed for 5104 SSR loci with appropriate flanking sequences. To validate the usefulness of SSRs in white calla lily, 153 perfect markers (repeat length ≥20 bp) were selected, of which 120 yielded stable and repeatable products, while the remaining failed to generate any clear DNA products. Twenty-seven SSR markers were then randomly selected to assess genetic diversity in 16 white calla lily accessions and cross-species transferability in 16 colored calla lily cultivars of Zantedeschia ...
Mercurialis annua is a wind-pollinated annual plant that has long been used as a model for the study of ploidy and sexual-systems evolution. However, no molecular markers are yet available for genetic studies of its diploid populations. Here, we develop and characterize a set of eight polymorphic microsatellite markers for diploid dioecious M. annua. Following an SSR-enrichment protocol, 13 microsatellite markers were proposed, eight of which yielded successful amplification and polymorphism. We screened the eight microsatellite loci in 100 individuals. The number of alleles per marker ranged from 6 to 12, and observed heterozygosity ranged from 0.57 to 0.76. To estimate potential allele scoring errors, these individuals offspring were genotyped for the same loci, and error rates were estimated from parentage analyses. Error rates ranged from 0 to 6.8%. Cross-amplification tests were performed for congeneric M. huetti and M. canariensis, with successful amplification for
MTILENI, B.J. et al. A comparison of genetic diversity between South African conserved and field chicken populations using microsatellite markers. S. Afr. j. anim. sci. [online]. 2010, vol.40, n.5, pp.462-466. ISSN 2221-4062.. The objective of the study was to determine genetic diversity within South African indigenous chicken populations and the effectiveness of the current conservation flocks in capturing the available diversity in the founder populations. Two chicken populations, Venda (VD_C) and Ovambo (OV_C) conservation flocks (n = 56) from the Animal Production Institute in Irene and two founder population from which these conservation flocks were sampled; Venda (VD_F) and Ovambo (OV_F) field populations (n = 72) were genotyped for 29 autosomal microsatellite markers. All microsatellites typed were found to be polymorphic. A total of 213 alleles were observed for all four populations. The mean number of alleles per population ranged from 3.52 ± 1.09 (VD_C) to 6.62 ± 3.38 (OV_F). Mean ...
In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers ...
A Phase III Study of Pembrolizumab (MK-3475) vs. Chemotherapy in Microsatellite Instability-High (MSI-H) or Mismatch Repair Deficient (dMMR) Stage IV Colorectal Carcinoma (KEYNOTE-177)
The whole broodstock of two Hungarian common carp farms-80 and 196 individuals-was analyzed by using random amplified polymorphic DNA (RAPD) assay and microsatellite analysis. Ten polymorphic RAPD markers and four microsatellites were selected to genotype both of the stocks. As expected, microsatellite analysis revealed more detailed information on genetic diversities than RAPD assay. Results obtained with both types of DNA markers showed lack of major differences between the genetic structure of the two stocks: heterozygosity values and allele frequencies were very similar. Dendrograms created from both sets of data did not show grouping of individuals according to stocks. Genotypes from the two stocks were also compared to those from a limited number of samples collected from other hatcheries and two rivers. Allele frequencies in the groups were similar, with the exception of wild carps. An interesting observation was that three private microsatellite alleles were found in the eight wild carp ...
Title: Microsatellite Instability (MSI) as Genomic Marker in Endometrial Cancer: Toward Scientific Evidences. VOLUME: 10 ISSUE: 14. Author(s):A. Tinelli, V. Mezzolla, G. Leo, M. Pisano, F. Storelli, G. Alemanno, A. Malvasi, S. Tommasi, G. Ronzino and V. Lorusso. Affiliation:Department of Gynecology and Obstetric, Division of Experimental Endoscopic Surgery, Imaging, Minimally Invasive Therapy&Technology, Vito Fazzi Hospital, P.zza Muratore, 73100 Lecce, Italy.. Keywords:Endometrial cancer, microsatellite instability, MSI, HNPCC, endometrial hyperplasia, Lynch sindrome, genomics, proteomics, laparoscopy, endoscopy, Genomic Marker, tumors, menopause, hyperestrogenism, Lynch Syndrome, Hereditary NonPolyposis Colorectal Cancer, DNA replication, neoplastic transformations, gynecological cancers, malignant uterine cancers, uterine tumors, MisMatch Repair genes, MMR genes, replication errors in repeats, adenomas, Familiar Adenomatous Polyposis, breast cancer, National Cancer Institute, ...
Seagrasses are one of the most productive and economically important habitats in the coastal zone, but they are disappearing at an alarming rate, with more than half the worlds seagrass area lost since the 1990s. They now face serious threat from climate change, and there is much current speculation over whether they will survive the coming decades. The future of seagrasses depends on their ability to recover and adapt to environmental change-i.e. their resilience. Key to this, is understanding the role that genetic diversity plays in the resilience of this highly clonal group of species. To investigate population structure, genetic diversity, mating system (sexual versus asexual reproduction) and patterns of connectivity, we isolated and characterised 23 microsatellite loci using next generation sequencing for the Australian seagrass species, Zostera muelleri (syn. Z. capricorni), which is regarded as a globally significant congeneric species. Loci were tested for levels of variation based ...
Thirteen new microsatellite loci were isolated and tested on two land snail species, Trochulus villosus and T. sericeus (Pulmonata: Hygromiidae), resulting in a set of eight polymorphic markers for each species. The expected heterozygosity was high for all loci and species (between 0.616 and 0.944). Such levels of variability will allow detailed insights into the population genetic structure of some Trochulus species.
Cowpea [Vigna unguiculata (L.) Walp] is an important grain legume crop grown for its protein rich grains. It is an inexpensive source of protein in the diets of people in sub-Saharan Africa. The International Institute of Tropical Agriculture (IITA) has been working on the improvement of cowpea for more than 30 yr. Over 60 countries receive cowpea cultivars improved by IITA for testing and adoption where needed. Many of these cultivars have identical parentage but look very different morphologically when grown in the field. Forty-six microsatellite DNA markers were used to evaluate genetic similarities among 90 cowpea breeding lines developed at IITA. Twenty-seven primer pairs could amplify polymorphic single-locus microsatellites from all of these materials. Two to seven alleles per primer were detected with a polymorphic information content varying from 0.02 to 0.73. By means of only five polymorphic microsatellite primers, 88 of the 90 cowpea lines could be distinguished. A dendrogram based ...
Anmarkrud, Jarl Andreas; Kleven, Oddmund; Bachmann, Lutz & Lifjeld, Jan Terje (2008). Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10. BMC Evolutionary Biology. ISSN 1471-2148. 8(138) . doi: 10.1186/1471-2148-8-138 Vis sammendrag BACKGROUND Microsatellites are frequently used genetic markers in a wide range of applications, primarily due to their high length polymorphism levels that can easily be genotyped by fragment length analysis. However, the mode of microsatellite evolution is yet not fully understood, and the role of interrupting motifs for the stability of microsatellites remains to be explored in more detail. Here we present a sequence analysis of mutation events and a description of the structure of repeated regions in the hypervariable, pentanucleotide microsatellite locus HrU10 in barn swallows (Hirundo rustica) and tree swallows (Tachycineta bicolor). RESULTS In a large-scale parentage analysis in barn ...
Jabon merah (Anthocephalus macrophyllus Roxb) is an endemic tree to Sulawesi having high economic value. It has rarely been investigated, either in genetic population or genetic consevation aspects. The information regarding genetic diversity is very important in order to gain more understanding for breeding and conservation strategies. Genetic diversity is used as material selection of expected genotype. The study was aimed to determine genetic diversity of Jabon merah from Sulawesi provenances that will be used in further development of this species. Leaf samples were collected from 108 families of Jabon merah belong to Sulawesi provenances. Four out of ten microsatellite markers that had high polymorphism were used for amplifying the 108 DNA samples. Results showed alleles number and mean of allele were 3 to 4 alleles and 3,5, respectively. Moreover, PIC mean of the evaluated loci was 3,7. The analysis of genetic relationship showed that the 108 families had moderate level of genetic ...
Anopheles culicifacies sensu lato is an important vector of malaria in Southeast Asia contributing to almost 70% of malaria cases in India. It exists as morphologically similar sibling species A, B, C, D and E with varied geographical distribution patterns. Vector control measures have been difficult for this important vector as the sibling species have developed varying levels of resistance to the currently used insecticides. In view of the importance of this vector, we developed and validated a set of microsatellite markers and the same were used to analyze the population genetic structure of five different geographical populations of An. culicifacies A. Anopheles culicifacies A samples were collected from different localities across India, and genotyping was performed using eight microsatellite markers on ABI Prism 310 Genetic Analyzer. Several statistical analyses were performed to ascertain the genetic diversity that exists within and between the populations. The markers were found to be moderately
TY - JOUR. T1 - Mismatch repair deficiency in hematological malignancies with microsatellite instability. AU - Gu, Liya. AU - Cline-Brown, Brandee. AU - Zhang, Fujian. AU - Qiu, Lu. AU - Li, Guo Min. N1 - Funding Information: We thank Steve Presnell and Cecilia Ramilo for helpful comments on the manuscript. This work was supported in part by grants CA85377 (from the National Cancer. PY - 2002. Y1 - 2002. N2 - Mutations in human mismatch repair (MMR) genes are the genetic basis for certain types of solid tumors displaying microsatellite instability (MSI). MSI has also been observed in hematological malignancies, but whether these hematological malignancies are associated with MMR deficiency is still unclear. Using both biochemical and genetic approaches, this study analysed MMR proficiency in 11 cell lines derived from patients with hematological malignancies and demonstrated that six out of seven hematological cancer cell lines with MSI were defective in strand-specific MMR. In vitro ...
In an analysis of the PETACC-8 trial reported by Taieb et al in JAMA Oncology, BRAF V600 and KRAS mutations were associated with shorter disease-free and overall survival in patients with microsatellite-stable colon cancer-but not in those with tumors with microsatellite instability-in the setting of adjuvant therapy. The PETACC-8 trial showed that the addition of cetuximab to FOLFOX4 (leucovorin, fluorouracil, and oxaliplatin) did not improve disease-free survival in patients with KRAS exon 2 wild-type disease.. Study Details. The analysis included patients with available tumor blocks from among the total of 2,599 patients in the trial. Microsatellite instability was found in 9.9% (177 of 1,791; microsatellite-stable tumors in 1,614 [90.1%]), KRAS mutation was found in 33.1% (588 of 1,776), and BRAF V600E mutation was found in 9.0% (148 of 1,643) of cases.. Outcome by Mismatch Repair and Mutation Status. In multivariate analysis, no significant prognostic effect for disease-free survival or ...
Background: Germline mutations in DNA mismatch repair (MMR) genes cause Lynch syndrome colon and extra-colonic cancers. Less understood is the risk of colon cancer associated with common polymorphisms in MMR genes and the potential interacting role of lifestyle factors known to damage DNA. Methods: We examined whether MLH1 (-93G,A and Ile219Val) and MSH6 (Gly39Glu) polymorphisms were associated with risk of colon cancer in data from 1,609 colon cancer cases and 1,972 controls. Genotype data were further stratified by microsatellite instability status, smoking, alcohol, Western-diet, alcohol, and obesity, to investigate potential heterogeneity.. Results: The MSH6 39Glu allele was associated with increased risk of colon cancer among men (Gly/Glu or Glu/Glu vs Gly/Gly odds ratio (OR): 1.27; 95% confidence interval (CI): 1.04-1.54). Neither MLH1 polymorphism was associated with colon cancer risk overall. When stratified by microsatellite stability status, however, the MLH1 -93 A allele was ...
Alemu, T. 2004. Genetic characterization of indigenous goat populations of Ethiopia using Microsatellite DNA markers. PhD thesis. Haryana, India: National Dairy Research Institute, Deemed University ...
Read Molecular structure of the allelic variants of (AAT)n microsatellite locus Du47D in the parthenogenetic species Darevskia unisexualis and bisexual parental species D. valentini and D. raddei, Russian Journal of Genetics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
In this study, we developed 134 novel polymorphic polynucleotide-repeat microsatellite markers for silver carp (Hypophthalmichthys molitrix) and characterized 40 loci for polymorphism and genetic diversity in a test population. The number of alleles per locus ranged from 3 to 19 (mean 9.4), and the average observed and expected heterozygosities were 0.74-0.76, respectively. Thirty-five loci were highly informative (PIC > 0.5) in silver carp population. After Bonferroni adjustments, no pairs of loci showed evidence of significant linkage disequilibrium, and none of the loci significantly deviated from the Hardy-Weinberg equilibrium. All 134 silver carp microsatellite loci could be successfully amplified in bighead carp (Hypophthalmichthys nobilis) with 65 loci being polymorphic, indicating a high transferability of these microsatellites across species. This set of novel highly polymorphic polynucleotide-repeat microsatellites would be powerful tools for population and conservation genetics ...
Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units) are present within exonic sequences of ,350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement with previous computational analyses of germ-line biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA ...
TY - JOUR. T1 - Allelic imbalance and microsatellite instability in resected Dukes D colorectal cancer. AU - Kochhar, Ruby. AU - Halling, Kevin C.. AU - McDonnell, Shannon. AU - Schaid, Daniel J.. AU - French, Amy J.. AU - OConnell, Michael J.. AU - Nagorney, David M.. AU - Thibodeau, Stephen N.. PY - 1997/4/1. Y1 - 1997/4/1. N2 - Hepatic resection is the treatment of choice for selected patients with liver metastases from colorectal cancer (CRC). Although the 5-year survival rate among patients after liver resection is 25-45%, 55-75% of patients die from progressive disease. The purpose of this study was to characterize molecular genetic alterations, including microsatellite instability and allelic imbalance, in patients with potentially curative resected liver metastases from CRC and to correlate these molecular features with clinical and pathologic characteristics. We examined DNA from formalin-fixed, paraffin-embedded archival tumor specimens from 141 surgically resected hepatic metastases ...
Fruit breeding programs usually use controlled hand pollination among cultivars and advanced selections for obtaining segregating populations to select new cultivars. In sweet cherries, however, sometimes in controlled pollination few hybrids are obtained. Caging whole trees with bees and flowers of the pollinating cultivar is sometimes used to obtain larger hybrid populations. To generate large segregating populations for the Chilean Sweet Cherry Breeding Program (run by the Consortium of BioFrutales S.A. and Instituto de Investigaciones Agropecuarias), the initial strategy was to harvest seeds from open pollinated self-incompatible cultivars maintained at the germplasm collection orchard of Univiveros, one of the leading fruit tree nurseries in Chile. While the female parent is known, the male parent is unknown. The pollen source will depend on the cultivars present in the area, the flowering time and the compatibility of the cultivars involved. In order to identify pollinators of the ...
In the present study, seven populations of J. regia were characterized using 11 highly polymorphic microsatellite markers. The average number of alleles per locus was 5.73, much higher than 1.3 and 3.9 detected in J. regia with RAPDs (Nicese et al., 1998) and ISSRs (Potter et al., 2002), respectively. For all loci, the observed numbers of alleles was lower than that reported in J. nigra (Victory et al., 2006), the species from which the markers were originally developed (Woeste et al., 2002). This may be because of the large number of samples and populations analyzed in previous J. nigra studies or because SSRs may show a decrease in allele number when applied in related species (Ana et al., 2000). For most of the loci, the length ranges of the amplification products obtained here were wider than those detected in J. nigra (Victory et al., 2006), a bias reported in other species as well (Donini et al., 1998).. Although a great number of population genetic studies have been conducted on Juglans ...
The SSR enriched library was constructed from the genotype TMV2 following by modified method of Fischer and Bachmann [23]. This library was enriched for CA and CT SSR repeat motifs. From this library, 3,072 clones were picked from 32 96-well plates. Hybridization of these clones with digoxigenin-labeled SSR probes (CA and CT) provided 720 (23.4%) putatively positive clones. Sequencing of these clones indicated the insert size in the range of 50 bp to 792 bp with an average size of 309 bp. Majority of clones (43.9%) contained the insert of moderate size (200 bp-400 bp) while 34.6% clones contained small inserts (50 bp-200 bp) and 21.5% clones contained inserts of , 500 bp.. Analysis of sequence data mentioned above with Tandem Repeat Finder (TRF) had 490 (68%) clones which contained one or more SSRs. The efficiency of the enrichment procedure for the constructed library was higher as compared to other SSR isolation studies of groundnut. Like the present study, 61% of clones were found to contain ...
PV mediated by simple sequences or microsatellites is a common feature of many bacteria, but, in Hi, a conspicuous feature is the predominance of tetranucleotide repeat tracts. In this report, we show that mutation of Hi polI, but not of seven other Hi genes, whose products are involved in MMR or other pathways of DNA repair or recombination, increases PV rates mediated by a tetranucleotide repeat tract. Conversely, loss of MMR activity, but not of polI activity, increased PV rates mediated by a dinucleotide repeat tract. This is the first report of a trans‐acting factor that alters PV rates in Hi, and also demonstrates that this bacterial species has apparently uncoupled the hypermutability of tetranucleotides that mediate PV from some important MMR functions. In the context of the biology of commensal and virulence behaviour of pathogenic bacteria, these findings are of particular interest because it has been proposed that mutations in MMR genes are an important source of adaptive evolution ...
TY - JOUR. T1 - Accuracy and sensitivity of DNA pooling with microsatellite repeats using capillary electrophoresis. AU - Breen, G AU - Sham, P AU - Li, T AU - Shaw, D AU - Collier, D A AU - St Clair, D PY - 1999. Y1 - 1999. N2 - DNA pooling is a genetic screening method that combines DNA from many individuals in a single polymerase chain reaction (PCR) reaction to generate a representation of allele frequencies. The substantial saving in effort with DNA pooling over individual genotyping facilitates linkage disequilibrium scanning of the human genome using many thousands of genetic markers, and is applicable to mapping of complex diseases such as schizophrenia. However, the literature to date has not addressed several crucial technical aspects of DNA pooling. These include: DNA quantification; the choice of electrophoresis methods; sensitivity (the minimum reliably detectable difference between poets); and methods of dealing with plus-A stutter. We have examined these points and make ...
Background: Colorectal malignancies with high microsatellite instability (MSI-H), either hereditary (Lynch syndrome) or sporadic, demonstrate better prognosis and altered response to 5FU chemotherapy. It is now recommended to perform MSI testing for all new cases of colorectal cancer regardless of being categorized as hereditary or sporadic. For MSI detection, immunohistochemistry or PCR-based protocols using a cohort of various sets of STR markers are recommended. Here we aimed to evaluate a simplified protocol using just a single STR marker, MT1XT20 mononucleotide repeat, for detection of MSI in Lynch syndrome patients. A Promega five-marker MSI testing panel and immunohistochemistry (IHC) were used as the gold standard in conjunction with MT1XT20. Materials and Methods: Colorectal patients with a positive history of familial cancers were selected by evaluating medical records. Based on Amsterdam II criteria for Lynch syndrome 20 families were short listed. DNA was extracted from formalin ...
TY - JOUR. T1 - Microsatellite analysis of childhood brain tumors. AU - Blaeker, Hendrik. AU - Rasheed, B. K.Ahmed. AU - McLendon, Roger E.. AU - Friedman, Henry S.. AU - Batra, Surinder K.. AU - Fuchs, Herbert E.. AU - Bigner, Sandra H.. PY - 1996/1. Y1 - 1996/1. N2 - Loss of heterozygosity at specific chromosomal locations has been taken as evidence of a tumor suppressor gene located in that area. We performed a genomic allelotyping study on 46 childhood brain tumors of different histopathological types in order to identify and confirm common areas of deletion in different tumor types. Two hundred microsatellite DNA probes equally distributed over the 22 autosomes were applied, covering the genome in steps of approximately 25 cM. Our results confirm frequent loss of heterozygosity of chromosome arms 9q, 10q, 11p, 11q, 16q, and 22q in high- grade gliomas, medulloblastomas, and ependymomas. In addition, we found a new region of loss on chromosome segment 2p21-23 affected predominantly in high- ...
The Guineagrass (Panicum maximum Jacq.) is one of the most important tropical forage grasses, but genetic knowledge and tools regarding this species are still limited. Therefore, 20 novel polymorphic microsatellite markers were developed, validated, and employed in estimating genetic relationships among 25 P. maximum genotypes selected from a Brazilian germplasm collection. In addition, they were tested for cross-species amplification in four other forage grass species. The number of alleles observed for each locus ranged from 4 to 12 (average 6.7). The values of polymorphism information content (PIC) varied from 0.41 to 0.83 (average 0.61) and the discriminating power (D) ranged from 0.53 to 0.98 (average 0.72). Cross-amplification demonstrated the potential transferability of these microsatellites to four tropical forage grass species. Cluster analysis based on the unweighted pair group method revealed three distinct groups: two clusters consisted of P. maximum genotypes and a third cluster, ...
Citation: Arias De Ares, R.S., Stetina, S.R., Tonos, J.L., Scheffler, J.A., Scheffler, B.E. 2010. Microsatellites Reveal Genetic Diversity in Reniform Nematode Populations. National Cotton Council Beltwide Cotton Conference, New Orleans, Louisiana, January 4-7, 2010 Interpretive Summary: Technical Abstract: Reniform nematode (Rotylenchulus reniformis) is the predominant parasitic nematode of cotton in the Mid South area of the United States. To document genetic variability within this species, we developed microsatellite-enriched libraries and designed 192 simple sequence repeats (SSR) markers for reniform nematode. The markers were tested on six reniform nematode cultures that originated in Texas, Louisiana, Mississippi and Georgia. Based on performance we selected 156 SSR markers for reniform nematode, 88 of which were polymorphic across the six reniform nematode populations. The most frequent motif was the dinucleotide AG. The polymorphic information content of the markers ranged from 0.00 to ...
Freeman, JS and Potts, BM and Shepherd, M and Vaillancourt, RE (2006) Parental and consensus linkage maps of Eucalyptus globulus using AFLP and microsatellite markers. Silvae Genetica, 55 (4-5). pp. 202-217. ISSN 0037-5349 ...
Diversity in crops provides opportunity for plant breeders to develop new and improved cultivars with desirable characteristics, genetic improvement for existing varieties thus meet subsistence food requirement. DNA marker is reliable in genetic diversity study due to variations at sequence level, not influenced by environment and its expression in all tissues. Marker used in our study is Inter Simple Sequence Repeats (ISSR) for 30 different accessions of white yam including dwarf, semi dwarf and tall. Cluster analysis was done based on Euclidean distance of 30 accessions for ISSR, Dendrogram showed the partition of most of the dwarf and tall genotypes in to two different clusters and semi dwarf comes under the dwarf cluster. The ISSR primers produced an average of six polymorphic alleles with a mean Hobs and PIC values of 0.738 and 0.707 respectively. The higher PIC and Hobs values obtained in the present study for ISSR markers indicate high variability of population studied. Hence, ISSR markers can be
use str analysis in a sentence, and str analysis meaning 1. The power of STR analysis comes from looking at multiple STR loci simultaneously. 2. The true power of STR analysis is in its statistical power of discrimination. click for more sentences of str analysis...
"Impeding Transcription of Expanded Microsatellite Repeats by Deactivated Cas9". Molecular Cell. 68 (3): 479-490.e5. doi:10.1016 ... CRISPR loci are composed of short, palindromic repeats that occur at regular intervals composed of alternate CRISPR repeats and ... Essentially, when multiple repeat codons are produced, it elicits a response, or recruits an abundance of dCas9 to combat the ... When the dCas9 attaches to a form of RNA called guide-RNA, it prevents the proliferation of repeating codons and DNA sequences ...
short tandem repeat (STR) See microsatellite. shotgun sequencing silencer A region of DNA that can be bound by a repressor. ... copy-number variation (CNV) A phenomenon in which sections of a genome are repeated and the number of repeats varies between ... Contents: Top 0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z tandem repeat A pattern within a nucleic acid sequence in ... TATA box A highly conserved non-coding DNA sequence containing a consensus of repeating T and A base pairs that is commonly ...
Arcot, Santosh S.; Wang, Zhenyuan; Weber, James L.; Deininger, Prescott L.; Batzer, Mark A. (September 1995). "Alu Repeats: A ... Source for the Genesis of Primate Microsatellites". Genomics. 29 (1): 136-144. doi:10.1006/geno.1995.1224. ISSN 0888-7543. PMID ... Jurka, J; Smith, T (1988). "A fundamental division in the Alu family of repeated sequences". Proceedings of the National ... Deininger, Prescott L; Batzer, Mark A (1999). "Alu Repeats and Human Disease". Molecular Genetics and Metabolism. 67 (3): 183- ...
Microsatellites in nuclear repeats require longer reads. The following sequencing platforms have been used in genome skimming: ... These repeats can be clustered de novo and their abundance is estimated. The distribution and occurrence of these repeat types ... and nuclear repeats such as microsatellites and transposable elements. It employs high-throughput, next generation sequencing ... Nuclear repeats in the genome are an underused source of phylogenetic data. When the nuclear genome is sequenced at 5% of the ...
Zak, Anatoly (28 November 2017). "Baumanets student micro-satellite repeats the sad fate of its predecessor". RussianSpaceWeb. ...
Between the strand-biased microsatellite repeats and C:G mononucleotide repeats, all sequence variations retained one or two ... The most prevalent repeated sequences in the embedded microsatellite regions were CT:AG, CCT:AGG, CCCT:AGGG, and CGCAC:GTGCG ... Microsatellite expansion (trinucleotide repeat expansion) is often found in transcription units. Often the base pair repetition ... This sequence feature appeared between microsatellite repeats and C:G mononucleotides in all four of the strand-biased domains ...
SNPSTR is a database of Snpstrs (a microsatellite with one or more tightly linked SNPs). Snpstr Short tandem repeat ... a database of compound microsatellite-SNP markers". Nucleic Acids Res. England. 35 (Database issue): D71-5. doi:10.1093/nar/ ... Microsatellite Single-nucleotide polymorphism Agrafioti, I; Stumpf M P H (Jan 2007). "SNPSTR: ...
"Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements". PLOS ONE. 8 (2): ... erratum) Emmanuel Buschiazzo; Neil J Gemmell (1 October 2006). "The rise, fall and renaissance of microsatellites in eukaryotic ... Sterling M Sawaya; Andrew T Bagshaw; Emmanuel Buschiazzo; Neil J Gemmell (1 January 2012). "Promoter microsatellites as ... cost-effective development of species-specific microsatellite markers by genomic sequencing". BioTechniques. 46 (3): 185-192. ...
A third-related finding is that frequent selection for different responses also enriches for microsatellite repeat tracts, ... His lab's work also elucidated how a mutational mechanism (microsatellite repeat slippage) plays a significant evolutionary ... Brittain, A; Stroebele, E; Erives, A (2015). "Microsatellite repeat instability fuels evolution of embryonic enhancers in ... As indels are largely produced by unstable microsatellite repeats, which are fast-evolving and difficult to genotype accurately ...
Microsatellite regions are usually characterized by short, repeated sequences of nucleotides. Primers that are specific to a ... A microsatellite null allele is an allele at a microsatellite locus that does not amplify to detectable levels in a polymerase ... Paetkau, D.; Strobeck, C. (1995-08-01). "The molecular basis and evolutionary history of a microsatellite null allele in bears ... 416 (6882). Dakin, E E; Avise, J C (2004-08-04). "Microsatellite null alleles in parentage analysis". Heredity. 93 (5): 504-509 ...
Microsatellites are repeats of 1-6 base pairs of DNA sequence. Microsatellites are commonly used as a molecular markers ... "Difference Between Minisatellite and Microsatellite". Hou, S.-M. (2002-04-01). "The XPD variant alleles are associated with ...
The microsatellite (AGAT)8 is strongly repeated near the Y chromosome centromere. The Y chromosome also contains the (AC)15 ... "Karyotypic analysis and FISH mapping of microsatellite motifs reveal highly differentiated XX/XY sex chromosomes in the pink- ...
... microsatellite repeats. They have attempted and succeeded in using this technique to isolate an amount of six microsatellite ... "Vectorette PCR isolation of microsatellite repeat sequences using anchored dinucleotide repeat primers". Nucleic Acids Research ... Further research has experimented with the creation of a method that progresses the isolation of microsatellite repeats. By ... Vectorette PCR was used to uncover SSRs which flank the trinucleotide repeat that was targeted for testing. This is also known ...
However, there is no evidence of preferential transmission of AVPR1A microsatellite repeats to hypersexual or uninhibited ... The AVPR1A repeat polymorphism RS3 is a complex (CT)4-TT-(CT)8-(GT)24 repeat that is 3625 bp upstream of the transcription ... The AVPR1A repeat polymorphism RS1 is a (GATA)14 tetranucleotide repeat that is 553 bp upstream from the transcription start ... Chimpanzees populations have individuals with single (only (GT)25 microsatellite) and duplicated (the (GT)25 microsatellite as ...
Some families of Helitrons also carry tandem repeats, like microsatellites and minisatellites which are generally highly ... De novo repeat identification approaches which can be used to build consensus libraries of all repeated sequences, but De novo ... A repeat-based search requires extensive manual curation to identify Helitron families, an overwhelming task in large genomes ... These approaches are limited by the quality of the genome assembly and the homogeneity of the repeats. Another approach is ...
... genes with somatic frameshift mutations within coding mononucleotide repeats in colorectal tumors with high microsatellite ...
These diseases are all caused by the expansion of microsatellite tandem repeats consisting of a stretch of three nucleotides. ... Prominent trinucleotide repeat disorders include Fragile X syndrome and Huntington's disease. In the case of Fragile X syndrome ... Individuals with a number of repeats that falls in the premutation range have a good chance of having affected children. Those ... With each successive generation, there is a chance that the number of repeats will expand. As this occurs, progeny can progress ...
"Mutation Rate in Human Microsatellites: Influence of the Structure and Length of the Tandem Repeat". Am J Hum Genet. 62 (6): ... DNA length mutations of repetitive DNA (such as telomeres and microsatellites), caused by cellular copying errors ...
2001.Characterization of duck microsatellite repeat sequences. JARQ 35(4): 217-219. (in Indonesian) Sari L, Purwadaria T. 2004 ...
Zenklusen JC, Bièche I, Lidereau R, Conti CJ (December 1994). "(C-A)n microsatellite repeat D7S522 is the most commonly deleted ...
Patel MS, Mankoo BS, Brickell PM (Apr 1992). "A polymorphic microsatellite repeat is located close to the promoter region of ...
... and microsatellites are often referred to as short tandem repeats (STRs) or simple sequence repeats (SSRs). Minisatellites ... Microsatellite Tandem repeat Telomere Minisatellite at the US National Library of Medicine Medical Subject Headings (MeSH) Tawn ... Repeat turnover therefore appears to be controlled by recombinational activity in DNA that flanks the repeat array and results ... with many repeated copies lying next to each other. Minisatellites and their shorter cousins, the microsatellites, together are ...
Short tandem repeats (about 5 base pairs) are called microsatellites, while longer ones are called minisatellites. The recent ... A variable number tandem repeat (VNTR) is the variation of length of a tandem repeat. A tandem repeat is the adjacent ... Tandem repeats exist on many chromosomes, and their length varies between individuals. Each variant acts as an inherited allele ...
Short repeats of nucleotides. Microsatellite: Very short repeats of nucleotides. Some trinucleotide repeats are found in coding ... Repeated sequences are of two basic types: unique sequences that are repeated in one area; and repeated sequences that are ... This region is a microsatellite, but its function is more specific than a simple tandem repeat. Throughout the eukaryotic ... They can be classified based on the length of the repeat as: SINE: Short interspersed sequences. The repeats are normally a few ...
Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) are a type of MSI where loci containing AAAG or ... Nakajima E, Orimo H, Ikejima M, Shimada T (1996). "Nine-bp repeat polymorphism in exon 1 of the hMSH3 gene". Jpn. J. Hum. Genet ... This leads to a heightened rate of microsatellite instabilities and increased rates of somatic mutations. This effect is ... 2000). "Association between single nucleotide polymorphisms in the hMSH3 gene and sporadic colon cancer with microsatellite ...
... tandem repeats, microsatellites) are prone to strand slippage during DNA replication and DNA repair. Trinucleotide repeat ... In long repeats, expansions may involve two or more units. For example, insertion of a single repeat unit in GAGAGA expands the ... Tandem repeats (the main influence for slippage replication) can be found in coding and non-coding regions. If these repeats ... In the event that a slippage event occurs there can be a large expansion in the tandem repeats of the HD gene. An individual ...
Smaller k-mers also have the problem of not being able to resolve areas in the DNA where small microsatellites or repeats occur ... This is because most of the k-mers will sit in the repeated region and may just be discarded as repeats of the same k-mer ... Larger k-mer sizes help alleviate the problem of small repeat regions. This is due to the fact that the k-mer will contain a ... This is because smaller k-mers will tend to sit entirely within the repeat region and is therefore hard to determine the amount ...
... he developed Simple Sequence Repeats (Microsatellites) for Echinochloa species as a Visiting Scientist at the Long Ashton ...
1995). "Mapping of the pulmonary surfactant SP5 (SFTP2) locus to 8p21 and characterization of a microsatellite repeat marker ...
Single or repeated krlee or similar component of calls used in other circumstances, but this can be very variable. Alarm calls ... Hailer, F., Gautschi, B., & Helander, B. (2005). Development and multiplex PCR amplification of novel microsatellite markers in ... Studies of microsatellite and mitochondrial DNA in white-tailed eagles from north-central Europe have shown that the recovering ... This may be repeated or gain intensity until they are talon-grappling or "mutual cartwheeling", consisting of the pair locking ...
... tandem repeat),可再依單元序列的長短分為衛星序列(satellite)、小衛星序列(minisatellite)和微衛星序列(microsatellite);分佈較為分散的是
... making repeated treatments unnecessary.[49] This approach to locust control was used in Tanzania in 2009 to treat around 10,000 ... A worldwide survey in a pest plagued by microsatellite null alleles". Molecular Ecology. 17 (16): 3640-3653. doi:10.1111/j.1365 ...
Pang H, Soejima M, Koda Y, Kimura H (2005). "A novel tetrameric short tandem repeat located in the 3' flanking region of the ... within the microsatellite genetic map of chromosome 19". Cytogenet. Cell Genet. 71 (2): 158-62. doi:10.1159/000134098. PMID ...
A Xenon Resistojet Propulsion System for Microsatellites (Surrey Space Centre, University of Surrey, Guildford, Surrey) ... Aerobraking allows a spacecraft to reduce the high point of an elliptical orbit by repeated brushes with the atmosphere at the ...
Dodd's experiment has been easy for others to repeat. It has also been done with other fruit flies and foods.[53] ... Microsatellite variation and evolution of human lactase persistence. Human Genetics 117(4): 329-339. ...
A repeat indicator that was designed to be used for repeating messages over obstacles by relay devices. ... ORBCOMM and Luxspace launched the Vesselsat AIS microsatellites, one in an equatorial orbit and the other in a polar orbit ( ...
Over 41,000 goats were removed during the initial hunting effort (1971-82).[145] This process was repeated until only the " ... Ciofi, Claudio; Milinkovitch, Michel C.; Gibbs, James P.; Caccone, Adalgisa; Powell, Jeffrey R. (2002). "Microsatellite ... and the repeated action over many generations has formed half-sphere depressions in the rock.[39] ...
For other abnormalities, the colonoscopy can be repeated after 1 year. Routine PET or ultrasound scanning, chest X-rays, ... a survey of current practices and re-evaluation of the role of microsatellite instability testing". Modern Pathology. 31 (11): ... If a villous polyp, a polyp ,1 centimeter or high grade dysplasia is found, it can be repeated after 3 years, then every 5 ... Mismatch repair (MMR) deficient tumours are characterized by a relatively high amount of poly-nucleotide tandem repeats.[45] ...
Trinucleotide repeats are classified as insertion mutations[2][3] and sometimes as a separate class of mutations.[4] ... This can often happen in microsatellite regions due to the DNA polymerase slipping. Insertions can be anywhere in size from one ...
This led to repeated misrepresentations or misconceptions in journalistic accounts on the topic. Popular science presentations ... a study of Y chromosome microsatellites.", Mol Biol Evol, 16 (12): 1791-98, doi:10.1093/oxfordjournals.molbev.a026091, PMID ... But the concept of Eve caught on with the public and was repeated in a Newsweek cover story (11 January 1988 issue featured a ...
"A single domestication for maize shown by multilocus microsatellite genotyping". 2002. Proceedings of the National Academy of ... ingl The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system, CRISPR) on bakteriaalsest ...
... mutation rates vary with base position relative to the microsatellite, repeat type, and base identity.[17] ... Microsatellite enrichment). The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/ ... microsatellite mutations lead to the gain or loss of an entire repeat unit, and sometimes two or more repeats simultaneously. ... Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as ...
It was proposed as a distinct subspecies on the basis of mtDNA and micro-satellite sequences that differs from the Indochinese ... It was found to have similar repeat composition to other cat genomes and an appreciably conserved synteny.[23] ...
Tandem repeats. *Satellite DNA. *Variable number tandem repeat/Minisatellite. *Short tandem repeat/Microsatellite ( ... De novo repeat identification[edit]. De novo repeat identification is an initial scan of sequence data that seeks to find the ... This method works best for tandem repeats, but can be used for dispersed repeats as well. However, it is a slow process, making ... Some k-mer approach programs use the k-mer as a base, and extend both ends of each repeated k-mer until there is no more ...
Li, YC; Korol, AB, Fahima, T, Beiles, A, Nevo, E (2002 Dec). "Microsatellites: genomic distribution, putative functions and ... "Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes". Microbiology and Molecular Biology Reviews 72 (4): ... Schlötterer, C (2000 Dec). "Microsatellite analysis indicates genetic differentiation of the neo-sex chromosomes in Drosophila ... "Characterization and Repeat Analysis of the Compact Genome of the Freshwater Pufferfish Tetraodon nigroviridis". Genome ...
... at isang pagkakaibang microsatellite sa mga populasyon sa Europe, Japan, Australia, middle East at Atlantic islands.[242] ... pilohenetiko ay lumalapat din sa sobrang lawak na uri ng mga walang silbing elementong sekwensiya kabilang ang repeats, ...
... microsatellite and mitochondrial DNA) study to date (2016) which found high divergence between Rocky Mountain and Sierra Nevada ... horns can frequently exhibit damage from repeated clashes.[24] Females exhibit a stable, nonlinear hierarchy that correlates ...
Methods frequently include using microsatellites to determine gene flow and hybridization between populations. The development ... Metapopulation structure and the repeated extinctions and recolonizations can significantly affect a population's genetic ...
... inferred with mtDNA and microsatellite loci". Molecular Phylogenetics and Evolution. 53 (2): 556-564. doi:10.1016/j.ympev. ... Competitions were held where bets were placed on which caged chaffinch would repeat its song the greatest number of times. The ...
Within these new patches (sub-clones), the process may have been repeated multiple times, indicated by the still smaller ... 2004). "Frequent inactivation of PTEN by promoter hypermethylation in microsatellite instability-high sporadic colorectal ... Microsatellite shifts[30] and instability,[37] loss of heterozygosity (LOH),[35] Copy number variation (detected both by ... taking repeated tumor biopsies from patients as they develop resistance to these drugs would help to understand the tumor ...
Within these new patches (sub-clones), the process may be repeated multiple times, indicated by the still smaller patches ... "Increased microsatellite instability and epigenetic inactivation of the hMLH1 gene in head and neck squamous cell carcinoma". ... Of polyps less than 10mm in size, found during colonoscopy and followed with repeat colonoscopies for 3 years, 25% were ...
This process is repeated many times, and is usually repeated a higher number of times when used with ancient DNA. Some issues ... Microsatellite DNA, single nucleotide polymorphisms (SNPs), and insertion/deletion polymorphisms (INDELS) have shown that Nilo- ... "low diversity of lineage-associated Y-chromosomal short tandem repeat (Y-STR) haplotypes" provide evidence for a "recent ...
DNA-based- Including microsatellites (also known as short tandem repeats, STRs, or simple sequence repeats, SSRs), restriction ... such as a short tandem repeat) may present as the most realistic option. ... "A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance". Int ...
... genes with somatic frameshift mutations within coding mononucleotide repeats in colorectal tumors with high microsatellite ...
... and the results for microsatellite short tandem repeat sequences (Y-STRs). The UEP results represent the inheritance of events ...
This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and ... The high variance of R1a1 in India (table 12), the spatial frequency distribution of R1a1 microsatellite variance clines (fig. ... which increases the likelihood of diversification and microsatellite variation.[37][38] According to Sengupta et al. (2006), "[ ... "The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time" ...
STR is short tandem repeats which are short DNA regions in the genome and are 2-6 base pairs in length. STR is common in ... Statistical analyses are used in assignment tests based on an individual's microsatellites or Amplified Fragment Length ... Friction ridge paths and the details in small areas of friction ridges are unique and never repeated. ... "nature never repeats," originating from the father of social statistics, Lambert Adolphe Jacques Quetelet. The belief was ...
analyzed King cherry and Yoshino cherry with inter-simple sequence repeat (ISSR) markers and sequence analysis of two ... yedoensis by Microsatellite Markers". Breeding Science. 57: 1-6. doi:10.1270/jsbbs.57.1. natural hybridization either in the ... "Characterization of wild Prunus yedoensis analyzed by inter-simple sequence repeat and chloroplast DNA". Scientia Horticulturae ...
Microsatellite repeats synonyms, Microsatellite repeats pronunciation, Microsatellite repeats translation, English dictionary ... definition of Microsatellite repeats. n. 1. A short sequence of DNA consisting of multiple repetitions of a set of two to nine ... redirected from Microsatellite repeats). Also found in: Medical.. Related to Microsatellite repeats: Simple Sequence Repeat mi· ... Microsatellite repeats - definition of Microsatellite repeats by The Free Dictionary https://www.thefreedictionary.com/ ...
In humans, COL1A2 contains two microsatellite loci: one located at the 5-flanking region is composed of poly CA and poly CG; ... Among the 15 haplotypes, 12 have a mutation at position 2284C,G and 7 at position 2292C,G. Insertions of repeated dinucleotide ... Methods: In this study, repeated dinucleotide GTn of intron 1 COL1A2 was highlighted in 55 patients with uterine fibroids (UF ... Results: Based on reference microsatellite pattern (GT)14CT(GT)3CT(GT)3, 15 haplotypes were found. ...
Associations of Microsatellite Repeats with chemical compounds. *We present microsatellite DNA evidence for the hypothesis that ... Gene context of Microsatellite Repeats. *In yeast, mutations in several genes, including RTH and MSH3, cause microsatellite ... High impact information on Microsatellite Repeats. *A microsatellite, DG10S478, within intron 3 of the transcription factor 7- ... diagnostic and therapeutic context of Microsatellite Repeats. *Haplotyping for these highly polymorphic microsatellites in ...
Evaluation of tumor microsatellite instability using five quasimonomorphic mononucleotide repeats and pentaplex PCR. Download ... T25 repeat in the 3 untranslated region of the CASP2 gene: a sensitive and specific marker for microsatellite instability in ... Detection of microsatellite instability in endometrial cancer: advantages of a panel of five mononucleotide repeats over the ... Evaluation of tumor microsatellite instability using five quasimonomorphic mononucleotide repeats and pentaplex PCR.. ...
What is Microsatellite repeats? Meaning of Microsatellite repeats medical term. What does Microsatellite repeats mean? ... Looking for online definition of Microsatellite repeats in the Medical Dictionary? Microsatellite repeats explanation free. ... microsatellite. (redirected from Microsatellite repeats). Also found in: Dictionary.. Related to Microsatellite repeats: Simple ... and identify microsatellite repeats. Microsatellites were identified as motifs repeated at least five times.. Development and ...
If the repeat is equal to or less than 6 bases, NTRs are named microsatellites, also known as short tandem repeats (STRs). One ... are repeating sequences of multi-base segments of DNA. ... One common example of a microsatellite is a (CA)n repeat, where ... If the repeat is equal to or less than 6 bases, NTRs are named microsatellites, also known as short tandem repeats (STRs). ... Because microsatellites are polymorphic DNA loci present throughout the genome, microsatellite genotyping is a widely accepted ...
Suggested molecular mechanisms for the generation of new tandem repeats of simple sequences indicate that the microsatellite ... Dynamics of Repeat Polymorphisms Under a Forward-Backward Mutation Model: Within- and Between-Population Variability at ... Dynamics of Repeat Polymorphisms Under a Forward-Backward Mutation Model: Within- and Between-Population Variability at ... Dynamics of Repeat Polymorphisms Under a Forward-Backward Mutation Model: Within- and Between-Population Variability at ...
454 pyrosequencing was used to discover repeat motifs, and seven polymorphic microsatellite-primer sets were identified. The ... These microsatellites can be utilized in studies of genetic structure, genetic diversity, and intra- and inter-subspecific ... We developed tetranucleotide-repeat microsatellite markers for the masu salmon (Oncorhynchus masou) complex. ...
Microsatellite instability was infrequent in this series of ovarian tumors, and it was limited to endometrioid and clear cell ... Microsatellite instability analysis was assessed by evaluating three (CA)n dinucleotide repeats (D2S123, D5S346, D17S250) and ... Microsatellite instability, MLH-1 promoter hypermethylation, and frameshift mutations at coding mononucleotide repeat ... Results: Microsatellite instability was identified in only 2 of the 52 (3.8%) tumors of the initial series (1 endometrioid and ...
Leng L., Siu E., Bucala R. (2020) Genotyping Two Promoter Polymorphisms in the MIF Gene: A −794 CATT5-8 Microsatellite Repeat ... Genotyping Two Promoter Polymorphisms in the MIF Gene: A −794 CATT5-8 Microsatellite Repeat and a −173 G/C SNP. ... Zhong X, Leng L, Beitin A et al (2005) Simulaneous detection of microsatellite repeats and SNPs in the macrophage migration ... A variable nucleotide tandem repeat at position −794 comprises five to eight CATT repeats (referred to henceforth by numbers ...
Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability. ... Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability ... Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability ... Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability ...
Microsatellite Instability Causes Repeat Expansion and WRN Dependence Message Subject (Your Name) has forwarded a page to you ... Cells with MSI accumulate unstable, structure-forming (TA)n repeats resolvable by the helicase WRN. ...
To study the occurrence of microsatellites and their inheritance in maize, a search was made of 280 maize GenBank sequences. ... also called simple sequence repeats (SSRs), have yielded an important class of DNA markers most notable for mapping mammalian ... Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer Genome. 1993 ... Microsatellites, also called simple sequence repeats (SSRs), have yielded an important class of DNA markers most notable for ...
... Lowe, Michael R.; Graham, J; Sund ... The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3 untranslated sequence of the CTLA-4 gene to ... The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3 untranslated sequence of the CTLA-4 gene to ... The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3 untranslated sequence of the CTLA-4 gene to ...
Identification and characterisation of thirteen new microsatellites for Atlantic cod (Gadus morhua L.) from a repeat-enriched ... Identification and characterisation of thirteen new microsatellites for Atlantic cod (Gadus morhua L.) from a repeat-enriched ... Identification and characterisation of thirteen new microsatellites for Atlantic cod (Gadus morhua L.) from a repeat-enriched ...
... microsatellite repeats Remove constraint Subject: microsatellite repeats Start Over ... Macrocystis pyrifera; alleles; ecology; genomic libraries; loci; macroalgae; microsatellite repeats; population genetics; ... We report the isolation and characterization of 16 microsatellite loci to study the population genetics of the giant kelp, ... Markers were obtained by screening a genomic library enriched for microsatellite motifs. Of the 37 primer pairs defined, 16 ...
Microsatellites or Short Tandem Repeats (STR). Microsatellites or Short Tandem Repeats (STR). 11 March 2015. da admin Leave a ... Short Tandem Repeats (STRs) are regions of the genome composed of approximately 1-5 bases and repeated up to 17 times. STR ... two or more adjacent repeats) or complex (several different length repeats). They are found on 22 autosomal chromosomes as well ... Though there have been thousands of short tandem repeats found in the human genome, only a small number are utilised in ...
N2 - Colorectal cancers (CRC) with microsatellite instability (MSI) have clinical, pathologic, genetic, and epigenetic features ... title = "An A13 repeat within the 3′-untranslated region of epidermal growth factor receptor (EGFR) is frequently mutated in ... T1 - An A13 repeat within the 3′-untranslated region of epidermal growth factor receptor (EGFR) is frequently mutated in ... An A13 repeat within the 3′-untranslated region of epidermal growth factor receptor (EGFR) is frequently mutated in ...
Microsatellites containing more than 9 GGAA repeats are very significantly enriched in EWS-FLI1 immunoprecipitates. Moreover, ... Importantly, in vivo EWS-FLI1-bound microsatellites are significantly associated with EWS-FLI1-driven gene activation. Put ... in reporter gene experiments, the transcription activation is highly dependent upon the number of repeats that are included in ... together, these results point out the likely contribution of microsatellite elements to long-distance transcription regulation ...
Microsatellite mutation rates vary with base position relative to the microsatellite, repeat type, and base identity.[17] ... Microsatellite enrichment). The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/ ... microsatellite mutations lead to the gain or loss of an entire repeat unit, and sometimes two or more repeats simultaneously. ... Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as ...
Microsatellite repeat discovery. SPUTNIK detected 10,272 repeats of between two and five bases with five or more repeat units ... Microsatellite repeat discovery. Microsatellite markers remain an informative and cost-effective tool for small scale ... To detect repeats which may be screened to find polymorphic microsatellite markers in the great tit, a modified version of ... Microsatellites detected in the great tit transcriptome. an excel table listing repeats detected in the great tit assembly. ...
... microsatellite repeats Remove constraint Subject: microsatellite repeats Start Over ... genetic analysis, etc ; cucumbers; fruit quality; fruits; inbred lines; loci; marker-assisted selection; microsatellite repeats ... genetic analysis, etc ; Lycaon pictus; dogs; genetic variation; heterozygosity; inbreeding; microsatellite repeats; national ... genetic analysis, etc ; endangered species; genetic variation; genotyping; heterozygosity; microsatellite repeats; pioneer ...
Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma.. ... Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma ... Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma ... Tumors not expressing MSH3 show elevated microsatellite alterations at selected tetranucleotide repeats (EMAST). EMAST ...
Frameshift mutations at coding mononucleotide repeat microsatellites in endometrial carcinoma with microsatellite instability. ... Frameshift mutations at coding mononucleotide repeat microsatellites in endometrial carcinoma with microsatellite instability ... Overall, frameshift mutations at i or more of these mononucleotide repeat microsatellites were found in 17 of 24 MI+ tumors ( ... Overall, frameshift mutations at i or more of these mononucleotide repeat microsatellites were found in 17 of 24 MI+ tumors ( ...
... that contains a CA microsatellite repeat that is highly polymorphic, with up to 6 alleles with 12 homozygotic CA repeats ... microsatellite repeat provided by a negative link the hallmark T(H)1 cytokine. , ...
... microsatellite repeats; phase transition; pioneer factor; prion-like domains ...
Frameshift Mutations at Coding Mononucleotide Repeats of the hRAD50 Gene in Gastrointestinal Carcinomas with Microsatellite ... Microsatellite instability (MSI) and frameshift mutations in genes containing nucleotide repeats have been reported in a subset ... Frameshift Mutations at Coding Mononucleotide Repeats of the hRAD50 Gene in Gastrointestinal Carcinomas with Microsatellite ... Frameshift Mutations at Coding Mononucleotide Repeats of the hRAD50 Gene in Gastrointestinal Carcinomas with Microsatellite ...
keywords = "Legumes, Microsatellite, Pea, Phylogeny, Repeat variation, Retrotransposon",. author = "P. Sm{\y}kal and R. ... Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent. / ... T1 - Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent ... Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent. ...
When microsatellites are isolated using standard SSR enrichment protocols and primers designed at complementary repeated ... UTR in over 190 microsatellite markers from 22 lepidopteran species, accounting for 10% of the lepidopteran microsatellites in ... Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran ... Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and ...
... single repeat mutations in microsatellites. Diseases such as myotonic dystrophy and Huntingtons disease are caused by repeat ... REPEAT EXPANSION. Mutation in a repeat tract that increases the number of repeats by a large amount and that may cause a ... MICROSATELLITE (SYNOMYN, SHORT TANDEM REPEAT, STR). DNA segment consisting in the repetition 5-50 times of a motif 1-6 ... DNA polymerases tend to "slip" when copying microsatellite tracts, adding or subtracting repeat units. Given their high ...
  • The microsatellite instability (MSI) phenotype is a characteristic of the hereditary nonpolyposis colorectal cancer syndrome as well as approximately 15% of sporadic colon and gastric tumors. (unboundmedicine.com)
  • Gastrointestinal tumors with DNA mismatch repair (MMR) defects show microsatellite instability (MSI) and harbor frameshift mutations in coding mononucleotide repeats of cancer-related genes. (aacrjournals.org)
  • Microsatellite instability (MI) is frequent in endometrial carcinomas (ECs), but its occurrence in ovarian tumors is uncertain. (nih.gov)
  • Microsatellite instability positive ECs frequently are associated with frameshift mutations in coding mononucleotide tracts in IGFIIR, BAX, hMSH6, and hMSH3. (nih.gov)
  • Microsatellite instability analysis was assessed by evaluating three (CA)n dinucleotide repeats (D2S123, D5S346, D17S250) and two mononucleotide tracts (BAT 25 and BAT 26). (nih.gov)
  • Microsatellite instability was identified in only 2 of the 52 (3.8%) tumors of the initial series (1 endometrioid and 1 clear cell carcinoma). (nih.gov)
  • Microsatellite instability was infrequent in this series of ovarian tumors, and it was limited to endometrioid and clear cell carcinomas. (nih.gov)
  • Colorectal cancers (CRC) with microsatellite instability (MSI) have clinical, pathologic, genetic, and epigenetic features distinct from microsatellite-stable CRC. (elsevier.com)
  • EMAST and microsatellite instability-high (MSI-H) were analyzed using five polymorphic tetranucleotide markers and five mononucleotide markers, respectively. (cdc.gov)
  • Microsatellite instability (MI) is a frequent occurrence in endometrioid carcinoma of the endometrium (EC). (uniroma1.it)
  • Microsatellite instability (MSI) and frameshift mutations in genes containing nucleotide repeats have been reported in a subset of colorectal and gastric carcinomas. (yonsei.ac.kr)
  • Microsatellite instability is found most often in colorectal cancer, other types of gastrointestinal cancer, and endometrial cancer. (cancer.gov)
  • Knowing whether cancer is microsatellite instability high may help plan the best treatment. (cancer.gov)
  • We conducted the present study to evaluate whether systemic chemotherapy could produce microsatellite instability (MSI) in the peripheral blood mononuclear cell fraction of breast cancer patients. (biomedcentral.com)
  • Studies on the association between MTHFR polymorphisms and length changes in short tandem repeat DNA sequences [microsatellite instability (MSI)] are inconsistent. (aacrjournals.org)
  • There are at least three pathways to colon cancer: chromosomal instability, microsatellite instability (MSI), and CpG island methylator phenotype. (aacrjournals.org)
  • Microsatellite repeat instability and neurological disease. (semanticscholar.org)
  • Quantitative Analysis of the Rates for Repeat-Mediated Genome Instability in a Yeast Experimental System. (harvard.edu)
  • We examined the presence of microsatellite instability (MSI) and loss of heterozigosity (LOH) in matched pair samples (tumoral and normal) of 24 patients with less aggressive types (smoldering and chronic) and in aggressive types (acute and lymphoma) of ATL. (nih.gov)
  • Assessment of microsatellite instability-MSI (a) and loss of heterozigosity-LOH (b) in patients with adult T cell leukemia-lymphoma (ATL). (nih.gov)
  • a2) Patient showing allelic shift in tumor sample indicating the presence of microsatellite instability (D10S191 marker-case 8). (nih.gov)
  • a3) Patient showing a novel allele in tumoral sample indicating the presence of microsatellite instability (marker D11S1391 - case 15). (nih.gov)
  • An alternative RNA-mediated toxicity arises from microsatellite repeat instability in the human genome. (hopkinsmedicine.org)
  • The human genome has 50-100,000 microsatellite loci. (thefreedictionary.com)
  • Because microsatellites are polymorphic DNA loci present throughout the genome, microsatellite genotyping is a widely accepted tool for a variety of research applications such as linkage mapping studies, association studies, and identification of organisms. (thermofisher.com)
  • Suggested molecular mechanisms for the generation of new tandem repeats of simple sequences indicate that the microsatellite loci evolve via some form of forward-backward mutation. (genetics.org)
  • Application of this measure to data on 18 microsatellite loci in nine human populations leads to evolutionary trees consistent with the known ethnohistory of the populations. (genetics.org)
  • We report the isolation and characterization of 16 microsatellite loci to study the population genetics of the giant kelp, Macrocystis pyrifera. (usda.gov)
  • A detailed examination of 45 pea (Pisum sativum L.) simple sequence repeat (SSR) loci revealed that 21 of them included homologous sequences corresponding to the long terminal repeat (LTR) of a novel retrotransposon. (edu.kz)
  • Recently we cloned and sequenced the first eight Trypanosoma cruzi polymorphic microsatellite loci and studied 31 clones and strains to obtain valuable information about the population structure of the parasite. (fiocruz.br)
  • Recently, we cloned and sequenced the first eight T. cruzi polymorphic microsatellite loci and studied 31 clones and strains to obtain valuable information about the population structure of the parasite (Oliveira et al. (fiocruz.br)
  • PCR amplification and detection of microsatellite alleles - The microsatellite loci analyzed are shown in Table I . Primers sequences have been published previously (Oliveira et al. (fiocruz.br)
  • Comparison of microsatellite and antigen-coding loci for differentiating recrudescing Plasmodium falciparum infections from reinfections in Kenya. (biomedsearch.com)
  • We have compared the ability of five Plasmodium falciparum microsatellites and three antigen-coding loci to differentiate recrudescence from reinfection. (biomedsearch.com)
  • Overall, microsatellite loci revealed significantly higher expected heterozygosity and multiplicity of infection levels than antigen-coding loci. (biomedsearch.com)
  • The mean expected heterozygosity across all loci in the three populations was significantly higher with microsatellites (0.70, 0.78 and 0.79) than antigen-coding loci (0.53, 0.60 and 0.62) for Mwea, Tiwi and Bondo areas, respectively. (biomedsearch.com)
  • To do this, the draft genome sequence of the biocontrol fungus Trichoderma virens ( T. virens ) was screened for simple sequence repeats (SSRs) and primers were developed for 12 distinct loci. (mdpi.com)
  • A typing method based on the analysis of size polymorphisms in microsatellite loci was investigated. (asm.org)
  • Three loci available from the GenBank database were identified to harbor microsatellites. (asm.org)
  • We analyze published data from 592 AC microsatellite loci from 98 species in five vertebrate classes including fish, reptiles, amphibians, birds, and mammals. (bioone.org)
  • First, we find that larger genomes do not have more microsatellite loci and therefore reject the hypothesis that microsatellites function primarily to package DNA into chromosomes. (bioone.org)
  • Second, we confirm that microsatellite loci are relatively rare in avian genomes, but reject the hypothesis that this is due to physical constraints imposed by flight. (bioone.org)
  • Finally, published microsatellite loci (isolated using conventional hybridization methods) provide a biased estimate of the actual mean repeat length of microsatellites in the genome. (bioone.org)
  • In some bacteria, Agos are associated with CRISPR (clustered regularly interspaced short palindromic repeats) loci and use noncanonical 5′-hydroxylated guide RNAs (gRNAs) for nucleic acid targeting. (pnas.org)
  • A total of 15,125 microsatellite loci had a flanking sequence suitable for setting the primer of a polymerase chain reaction (PCR). (mdpi.com)
  • The Hardy-Weinberg equilibrium test showed significant deviation in four of the 20 microsatellite loci after sequential Bonferroni corrections. (mdpi.com)
  • In this study, we developed 134 novel polymorphic polynucleotide-repeat microsatellite markers for silver carp (Hypophthalmichthys molitrix) and characterized 40 loci for polymorphism and genetic diversity in a test population. (ihb.ac.cn)
  • All 134 silver carp microsatellite loci could be successfully amplified in bighead carp (Hypophthalmichthys nobilis) with 65 loci being polymorphic, indicating a high transferability of these microsatellites across species. (ihb.ac.cn)
  • For several years, gene mappers have used DNA signposts called microsatellite repeats as markers to delineate these sections. (thefreedictionary.com)
  • The microsatellite repeats used as probes for fuorescence in situ hybridizaton experiments have proved to be resolute markers in the analyzed species. (thefreedictionary.com)
  • Development and use of microsatellite markers for germplasm characterization in quinoa (chenopodium quinoa Willd. (thefreedictionary.com)
  • Our five-dye chemistry increases the number of microsatellite markers that can be run in a single capillary, substantially improving the throughput. (thermofisher.com)
  • Microsatellites, also called simple sequence repeats (SSRs), have yielded an important class of DNA markers most notable for mapping mammalian genomes. (nih.gov)
  • Markers were obtained by screening a genomic library enriched for microsatellite motifs. (usda.gov)
  • STR markers will either be simple (identical length repeats), compound (two or more adjacent repeats) or complex (several different length repeats). (scenacriminis.com)
  • [5] The increasing availability of DNA amplification by PCR at the beginning of the 1990s triggered a large number of studies using the amplification of microsatellites as genetic markers for forensic medicine, for paternity testing, and for positional cloning to find the gene underlying a trait or disease. (wikipedia.org)
  • Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. (biomedcentral.com)
  • Furthermore, we identified the C-terminal end of the Reverse Transcriptase/nLTR domain and the associated 3' UTR in over 190 microsatellite markers from 22 lepidopteran species, accounting for 10% of the lepidopteran microsatellites in GenBank. (biomedcentral.com)
  • When microsatellites are isolated using standard SSR enrichment protocols and primers designed at complementary repeated regions, amplification from multiple genomic sites can cause scoring difficulties that compromise their utility as markers. (biomedcentral.com)
  • Microsatellite genetic markers are based on the properties of SSRs (simple sequence repeats) which are numerous and ubiquitous in the DNA of eukaryotes [ 1 , 2 ]. (biomedcentral.com)
  • Another pattern of repetition, however, has proven to be very troublesome in the practical application of microsatellite markers in some organisms, including the insect order Lepidoptera (butterflies and moths). (biomedcentral.com)
  • This expanded set of 54 strains and clones analyzed with the eight microsatellites markers disclosed interesting new features of the population genetic structure of T. cruzi . (fiocruz.br)
  • Microsatellites (SSRs) are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. (biomedcentral.com)
  • The microsatellite markers described here are a useful resource for genetics and genomics in Arachis . (biomedcentral.com)
  • Microsatellites or simple sequence repeats (SSRs) are useful molecular markers, are abundant, highly dispersed through the genomes of eukaryotes, and locus specific. (biomedcentral.com)
  • Much has been learned by studying mitochondrial DNA markers, but autosomal markers such as microsatellites have been applied to only a few nematode species, despite their many advantages for studying gene flow in eukaryotes. (elsevier.com)
  • To obtain a rapid genotyping method of Candida albicans , three polymorphic microsatellite markers were investigated by multiplex PCR. (asm.org)
  • The combined discriminatory power of the three microsatellites markers was 0.97. (asm.org)
  • To obtain greater resolution, we searched for new microsatellite markers located on different chromosomes. (asm.org)
  • Describes cancer cells that have a greater than normal number of genetic markers called microsatellites. (cancer.gov)
  • This track displays regions that are likely to be useful as microsatellite markers. (ucsc.edu)
  • Related men will show the same or very similar patterns in terms of the numbers of repeats seen at a set of markers, while unrelated men will tend not to. (le.ac.uk)
  • Tumors were classified as MSI if two or more microsatellite markers (BAT25, BAT26, D5S346, D2S123, and D17S250) had changes in the number of DNA sequence repeats compared with matched nontumor tissue. (aacrjournals.org)
  • Tumors with one positive marker (MSI-low) or no positive markers (microsatellite stable) were grouped together as non-MSI tumors (microsatellite stable). (aacrjournals.org)
  • Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated from the Chinese mitten crab Eriocheir sinensis , as the crab genome sequence information is unavailable. (mdpi.com)
  • The microsatellite markers are drawn from Marshfield screening sets 10, 13, and 52, and the indels are drawn from Marshfield screening set 100. (stanford.edu)
  • The mechanisms that lead to the development of ATL clinical types have not yet been clarified.Four microsatellite markers D10S190, D10S191, D1391 and DCC were analyzed.MSI was found in four patients, three smoldering and one chronic, and LOH in four patients, three smoldering and one acute. (nih.gov)
  • Four microsatellite markers D10S190, D10S191, D1391 and DCC were analyzed. (nih.gov)
  • One hundred and twenty P. vivax isolates (58 from Piura and 37 from Tumbes in the PNC collected from 2008 to 2010 and 25 from the EAB collected in Pastaza from 2001 to 2004) were assessed by five polymorphic microsatellite markers. (ajtmh.org)
  • Variable nucleotide tandem repeats (VNTRs) are repeating sequences of multi-base segments of DNA. (thermofisher.com)
  • To study the occurrence of microsatellites and their inheritance in maize, a search was made of 280 maize GenBank sequences. (nih.gov)
  • Four of the microsatellites cosegregated with the Adh1, Gpc1, Pdk1, and Tpi genes from which the primer sequences were derived. (nih.gov)
  • Using a ChIP-Seq approach to investigate EWS-FLI1-bound DNA sequences in two Ewing cell lines, we show that this chimeric transcription factor preferentially binds two types of sequences including consensus ETS motifs and microsatellite sequences. (plos.org)
  • Guillon N, Tirode F, Boeva V, Zynovyev A, Barillot E, Delattre O (2009) The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function. (plos.org)
  • Comparison of the LTR sequences from pea and Medicago truncatula elements indicated that microsatellites arise through the expansion of a pre-existing repeat motif. (edu.kz)
  • Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species and can be grouped into microsatellite-associated DNA families. (biomedcentral.com)
  • The fact that they are repeated can be deduced only by comparisons among many flanking sequences, not by any intrinsic pattern of the sequence itself. (biomedcentral.com)
  • Recent studies, however, have shown that as many as 10% to 20% of coding and regulatory sequences in eukaryotes contain an unstable repeat tract. (mdpi.com)
  • The two most common terms used for sequences containing short repeating units are simple sequence repeat (SSR) and microsatellite . (bioinformatics.org)
  • 100 bp repeating unit) are the most common terms for sequences with large repeating units. (bioinformatics.org)
  • From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. (biomedcentral.com)
  • Microsatellites are short, repeated, sequences of DNA. (cancer.gov)
  • These are sequences of at least 15 perfect di-nucleotide and tri-nucleotide repeats and tend to be highly polymorphic in the population. (ucsc.edu)
  • Benson G. Tandem repeats finder: a program to analyze DNA sequences . (ucsc.edu)
  • Microsatellites are short tandem repeat DNA sequences. (aacrjournals.org)
  • Repeated sequences (also known as repetitive elements, repeating units or repeats) are patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. (wikipedia.org)
  • The disposition of repetitive elements consists either in arrays of tandemly repeated sequences, or in repeats dispersed throughout the genome (see below). (wikipedia.org)
  • Tandem repeat sequences, particularly trinucleotide repeats, underlie several human disease conditions. (wikipedia.org)
  • Hexanucleotide GGGGCC repeat sequences in the C9orf72 gene are a common cause of amyotrophic lateral sclerosis and frontotemporal dementia. (wikipedia.org)
  • Huntington's disease results from an unstable expansion of repeated CAG sequences in exon 1 of the huntingtin gene (HTT). (wikipedia.org)
  • Faulty repair of DNA damages in repeat sequences may cause further expansion of these sequences, thus setting up a vicious cycle of pathology. (wikipedia.org)
  • Repeated sequences evolutionary derived from viral infection events. (wikipedia.org)
  • Repeats of short DNA sequences, typically less than 10 bp, flank the centromeres of each chromosome, stretching for hundreds of kilobases along either arm of the chromosome and forming centromeric heterochromatin. (encyclopedia.com)
  • Tandemly repeated short sequences also occur at each chromosome tip (telomeric DNA). (encyclopedia.com)
  • Among these are variable number tandem repeats (VNTRs), sequences of 15-100 nucleotides repeated hundreds or thousands of times at numerous sites within the genome, and represented by minisatellite DNA. (encyclopedia.com)
  • Repeats of shorter sequences (2-10 bp) form so-called microsatellite DNA . (encyclopedia.com)
  • The term is commonly taken to include repetitive DNA , in which base sequences are repeated many times in the genome of a cell (e.g. heterochromatin may contain highly repetitive DNA with the base sequences repeated more than 1000 times). (encyclopedia.com)
  • eotide repeats in humans, we performed a computational analysis by integrating data from a number of relevant databases, including whole-genome sequences (27), Gene Expression Omnibus (GEO) data sets =-=(28)-=- and Agobinding sites (29). (psu.edu)
  • Much of this variation is due to non-coding (i.e. not producing an RNA or protein product), often very simple, repeated sequences. (creation.com)
  • The premise the authors worked upon is through using drift in sequences of microsatellites as a template to estimate the effect of drift in the morphological differences in Neandertal and modern human craniofacial traits. (anthropology.net)
  • Microsatellites are simple repeats of DNA sequences. (anthropology.net)
  • Microsatellites include dinucleotides, trinucleotides and tetranucleotides, repeated in tandem arrays throughout a genome. (thefreedictionary.com)
  • Short Tandem Repeats (STRs) are regions of the genome composed of approximately 1-5 bases and repeated up to 17 times. (scenacriminis.com)
  • Though there have been thousands of short tandem repeats found in the human genome, only a small number are utilised in forensic DNA analysis. (scenacriminis.com)
  • [1] [2] Microsatellites occur at thousands of locations within an organism's genome . (wikipedia.org)
  • Microsatellites are distributed throughout the genome. (wikipedia.org)
  • Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. (elsevier.com)
  • BACKGROUND: Simple sequence repeats (SSRs) are found in most organisms, and occupy about 3% of the human genome. (elsevier.com)
  • This is the first report examining the distribution and density of simple sequence repeats (1-6 base-pairs (bp)) in the entire human genome. (elsevier.com)
  • Dive into the research topics of 'Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. (elsevier.com)
  • The regions closely flanking one or both sides of the SSR may themselves be highly repeated, dispersed throughout the genome rather than occurring tandemly [ 3 , 4 ]. (biomedcentral.com)
  • This database allows retrieval of precomputed tandem repeats from the selected genome. (ehu.es)
  • These showed that T. monococcum chromosomes have fewer, generally weaker, simple sequence repeat (SSR) signals than the A-genome chromosomes of hexaploid wheat. (elsevier.com)
  • Also, long homopolymer tracts are spaced non-randomly in the genome of Dictyostelium discoideum , suggesting a preferential linker DNA location in the repeating nucleosome structure of this AT-rich organism [6] . (bioinformatics.org)
  • Over fifty diseases, most of which primarily affect the nervous system, are caused by expansion of short DNA sequence repeats dispersed throughout the genome. (pfizer.com)
  • For instance in human, mouse and fly, several classes of repetitive elements present a high tendency for co-localization within the nuclear space, suggesting that DNA repeats positions can be used by the cell as a genome folding map. (wikipedia.org)
  • Minisatellite - repeat units from about 10 to 60 base pairs, found in many places in the genome, including the centromeres. (wikipedia.org)
  • repetitive DNA DNA whose base sequence is repeated many times throughout the genome of an organism. (encyclopedia.com)
  • They also convert the PCR fragment lengths in nucleotides to numbers of repeats, by calibration with the human genome reference sequence. (stanford.edu)
  • One common example of a microsatellite is a (CA) n repeat, where n varies between alleles. (thermofisher.com)
  • the 5-repeat allele leads to low expression, and the 6-, 7-, and 8-repeat alleles lead to correspondingly higher expression of MIF. (springer.com)
  • We studied 616 consecutively diagnosed 0-34 year-old Swedish patients and 502 matched controls by PCR-based genotyping to determine the length of the 3'-end (AT)(n)repeat region of the CTLA-4 gene and categorizing alleles as predominantly monomorphic short (S) or highly polymorphic (in length) long (L) alleles. (lu.se)
  • is highly polymorphic, with up to 6 alleles with 12 homozygotic CA repeats provides a negative link between IFN and bone resorption (Naive and effector memory T cells acquire polarized cytokine gene acetylation patterns in part by activating the hallmark T(H)1 cytokine, IFNG . (wordpress.com)
  • We discuss the feasibility of developing microsatellites in parasitic nematodes and the problem of null alleles. (elsevier.com)
  • Moreover, since microsatellites test the presence of different alleles at a given locus, distinguishing heterozygotes in diploid organisms such as C. albicans is possible in contrast to the RFLP and RAPD methods. (asm.org)
  • Fourth, we reject the hypothesis that microsatellite structure (length, number of alleles, allele dispersion, range in allele sizes) differs between poikilotherms and homeotherms. (bioone.org)
  • The difference is found only in fish, which have longer microsatellites and more alleles than the other classes. (bioone.org)
  • Fifth, we find that the range in microsatellite allele size at a locus is largely due to the number of alleles and secondarily to allele dispersion. (bioone.org)
  • Three that have been identified are SOD2 Val-9Ala , GPX1 Pro198Leu , and the GPX1 GCG repeat (three alleles with four, five, or six repeats). (aacrjournals.org)
  • There is a significant trend of increasing risk with increasing number of alleles with four GCG repeats ( P = 0.03). (aacrjournals.org)
  • If the repeat is equal to or less than 6 bases, NTRs are named microsatellites, also known as short tandem repeats (STRs). (thermofisher.com)
  • Microsatellites are often referred to as short tandem repeats ( STRs ) by forensic geneticists and in genetic genealogy , or as simple sequence repeats ( SSRs ) by plant geneticists. (wikipedia.org)
  • Microsatellites are also used in population genetics to measure levels of relatedness between subspecies, groups and individuals. (wikipedia.org)
  • This set of novel highly polymorphic polynucleotide-repeat microsatellites would be powerful tools for population and conservation genetics studies in silver carp and also in its closely-related bighead carp. (ihb.ac.cn)
  • The telomeres at the ends of the chromosomes, thought to be involved in ageing / senescence , consist of repetitive DNA, with the hexanucleotide repeat motif TTAGGG in vertebrates. (wikipedia.org)
  • Triplets and hexamers were more predominant in exonic regions compared to intronic and intergenic regions, except for chromosome Y. Comparison of densities of various SSRs revealed that whereas trimers and pentamers showed a similar pattern (500-1,000 bp/Mb) across the chromosomes, di- tetra- and hexa-nucleotide repeats showed patterns of higher (2,000-3,000 bp/Mb) density. (elsevier.com)
  • In order to provide additional chromosomal landmarks to discriminate the A m and A chromosomes, the microsatellite repeats (GAA) n , (CAG) n , (CAC) n , (AAC) n , (AGG) n and (ACT) n were tested as FISH probes. (elsevier.com)
  • The 2A m and 2A chromosomes were differentiated by the signals given by the (GAA) n , (CAG) n and (AAC) n repeats, while only (GAA) n discriminated the chromosomes 3A m and 3A. (elsevier.com)
  • As potential landmarks for identifying the A m chromosomes, SSR repeats will facilitate the introgression of T. monococcum chromatin into wheat. (elsevier.com)
  • More than two microsatellite repeat motifs were amplified on the sex-specific chromosome, W or Y, in five species (Bassiana duperreyi, Aprasia parapulchella, Notechis scutatus, Chelodina longicollis, and Gallus gallus) of which the sex-specific chromosomes were heteromorphic and heterochromatic. (edu.au)
  • Taken together with previously published studies, our results suggest that the amplification of microsatellite repeats is tightly associated with the differentiation and heterochromatinization of sex-specific chromosomes in sauropsids as well as in other taxa. (edu.au)
  • Different Y chromosomes can carry varying numbers of repeats at a set of specific STRs, called a Y-STR haplotype. (le.ac.uk)
  • Microsatellite repeats consisting of three nucleotides dispersed in the euchromatic arms of chromosomes. (harvard.edu)
  • Polymerase chain reaction (PCR) and DNA sequence analysis indicated that intact repeats of three, four, or five GAAAAT units were responsible for observed allele size differences. (usda.gov)
  • The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3' untranslated sequence of the CTLA-4 gene to diabetes risk. (lu.se)
  • Although no relationship between EGFR overexpression and the length of a CA dinucleotide repeat in intron 1 was observed, a variant A13/A14 repeat sequence within the 3′-untranslated region (3′-UTR) of the EGFR gene was identified, which was mutated by either mononucleotide or dinucleotide adenosine deletions in 64% of MSI cell lines and 69% of MSI colon tumors. (elsevier.com)
  • For example, the sequence TATATATATA is a dinucleotide microsatellite, and GTCGTCGTCGTCGTC is a trinucleotide microsatellite (with A being Adenine , G Guanine , C Cytosine , and T Thymine ). (wikipedia.org)
  • Descriptors are usually used along with the words sequence , repeat , tract or run . (bioinformatics.org)
  • This rearrangement is a series of multiple repeats, forming a minisatellite-like structure that comprises five direct tandem repeats of a 23-bp sequence. (plantcell.org)
  • Transient assays demonstrated that the 23-bp sequence motif is a target of the MYB10 protein itself, and the number of repeat units correlates with an increase in transactivation by MYB10 protein. (plantcell.org)
  • The sequence of TteREP1 is related to the TcREP-class of repeats found in several other trichostrongyloid species including Trichostrongylus colubriformis and Haemonchus contortus. (elsevier.com)
  • One microsatellite marker in the EF3 promoter sequence of C. albicans was previously reported ( 4 ). (asm.org)
  • In all cases, the expanded CAG repeats are translated into an uninterrupted sequence of glutamine residues, forming a polyQ tract, and the accumulation of polyQ proteins damages key cellular functions such as the ubiquitin-proteasome system. (wikipedia.org)
  • Major categories of repeated sequence or repeats: Tandem repeats: are copies which lie adjacent to each other, either directly or inverted. (wikipedia.org)
  • Direct repeats Global direct repeat Local direct simple repeats Local direct repeats Local direct repeats with spacer Inverted repeats Global inverted repeat Local inverted repeat Inverted repeat with spacer Palindromic repeat Mirror and everted repeats Repetitive DNA is hard to sequence using next-generation sequencing techniques: sequence assembly from short reads simply cannot determine the length of a repetitive part. (wikipedia.org)
  • Destabilization of tetraplex structures of the fragile X repeat sequence (CGG)n is mediated by homolog-conserved domains in three members of the hnRNP family. (semanticscholar.org)
  • A total of 141,737 SSR (simple sequence repeats) motifs were identified via analysis of 883 Mb of the crab genomic DNA information, including mono-, di-, tri-, tetra-, penta- and hexa-nucleotide repeat motifs. (mdpi.com)
  • Posted January 21, 2010) For 627 HGDP microsatellites, these files provide sequence properties, such as the structure of the repeat motif and the GC content of the flanking region. (stanford.edu)
  • or a tandem repeat (TR) is a concatenation of the same nucleotide sequence, called a unit. (psu.edu)
  • Microsatellites are regions of DNA where a short sequence is repeated in tandem with the number of repeats present varying among individuals. (usda.gov)
  • Flow cytometry, chromosome counts and SSR marker (Simple Sequence Repeats) analysis facilitated the identification of six different haploid lines (2n = x = 9), one aneuploid line (2n = 2x+4 = 22) and one doubled haploid plant (2n = 2x = 18) of 'Clemenules' clementine. (nih.gov)
  • In this study, we analyzed the influence of fragmentation and environmental changes on the population genetic structure of C. (P.) staigi using inter-simple sequence repeat polymorphisms, and the consequences for management and conservation. (fao.org)
  • If the prototypical cohanim Y chromosome arose fairly recently, then the number of microsatellite repeats should be relatively similar among all the cohanim. (thefreedictionary.com)
  • Furthermore, comparative analysis of sex chromosome homology and chromosomal distribution of microsatellite repeats between two closely related chelid turtles, C. longicollis and E. macquarii, identified different ancestry and differentiation history. (edu.au)
  • Another type of marker on the Y chromosome consists of short units of DNA (typically 3 or 4 bases long) that are repeated in tandem several times (see diagram above). (le.ac.uk)
  • The first trinucleotide repeat disease to be identified was fragile X syndrome, which has since been mapped to the long arm of the X chromosome. (wikipedia.org)
  • The second DNA-triplet repeat disease, fragile X-E syndrome, was also identified on the X chromosome, but was found to be the result of an expanded CCG repeat. (wikipedia.org)
  • Microsatellites, transposable elements and the X chromosome. (ajtmh.org)
  • In continuing efforts to characterize genetic differences within the North American population, we identified a microsatellite located on the sex chromosome. (usda.gov)
  • For example, fragile-X syndrome , the most common type of inherited mental retardation in humans, is caused by the repetition of up to 1,000 copies of a CGG repeat in a gene on the X chromosome . (britannica.com)
  • Unlike the internally-repeated patterns of the SSRs, there is nothing obvious about the structure of these repeated flanking regions. (biomedcentral.com)
  • SSRs are composed of short (1 to 5 bp), tandemly repeating units that are exact in identity and repetition. (bioinformatics.org)
  • Since most microsatellites show a substantial level of polymorphism between individuals, microsatellites are extensively used for physical mapping in humans ( 28 ). (asm.org)
  • Other microsatellites are located in regulatory flanking or intronic regions of genes, or directly in codons of genes - microsatellite mutations in such cases can lead to phenotypic changes and diseases, notably in triplet expansion diseases such as fragile X syndrome and Huntington's disease . (wikipedia.org)
  • This study describes the analysis of MSI-positive colorectal (39 cases) and gastric carcinomas (36 cases) for the presence of frameshift mutations of the six genes known to be involved in DNA repair and containing mononucleotide repeats in their coding region. (yonsei.ac.kr)
  • Trinucleotide repeat (TNR) expansions are present in a wide range of genes involved in several neurological disorders, being directly involved in the molecular mechanisms underlying pathogenesis through modulation of gene expression and/or the function of the RNA or protein it encodes. (frontiersin.org)
  • The change in length of these tandem repeats is termed MSI and is often associated with defects in DNA repair genes ( 1 , 2 ). (aacrjournals.org)
  • These are caused by a CAG repeat expansion in protein-coding portions, or exons, of specific genes. (wikipedia.org)
  • Although these diseases share the same repeated codon (CAG) and some symptoms, the repeats are found in different, unrelated genes. (wikipedia.org)
  • It has been noted that genes containing pathogenic CAG repeats often encode proteins that themselves have a role in the DNA damage response and that repeat expansions may impair specific DNA repair pathways. (wikipedia.org)
  • 8882 Nucleic Acids Research, 2013, Vol. 41, No. 19 mononucleotide repeats at the TSS occurs due to the presence of CpG islands =-=(39)-=- around the TSSs of most mammalian genes (40). (psu.edu)
  • PCR primers flanking microsatellite repeats were designed by the program PRIMERSELECT (Lasergene, Madison, WI). (thefreedictionary.com)
  • The four microsatellites that cosegregated with the original gene were reamplified as anticipated, whereas a suspicious 230-bp product obtained when using the MZEGPA1 primers could not be reamplified. (nih.gov)
  • It also allows to easily design primers for amplification of a DNA fragment containing the tandem repeat. (ehu.es)
  • PCR primers flanking the microsatellite repeats were designed with one primer in the set fluorescently labeled. (asm.org)
  • Which of the flowing sets of primers would be used to amplify the CAG repeat in the brackets ([CAG] n )? (proprofs.com)
  • A section of DNA in which a unit of one to five nucleotides is repeated a variable number of times. (thefreedictionary.com)
  • A microsatellite is a tract of tandemly repeated (i.e. adjacent) DNA motifs that range in length from one to six or up to ten nucleotides (the exact definition and delineation to the longer minisatellites varies from author to author), [1] [2] and are typically repeated 5-50 times. (wikipedia.org)
  • Repeat units of four and five nucleotides are referred to as tetra- and pentanucleotide motifs, respectively. (wikipedia.org)
  • Another PCR-based method is the analysis of microsatellites, defined as tandemly repetitive stretches of two to five nucleotides. (asm.org)
  • Trinucleotide repeat disorders, also known as microsatellite expansion diseases, are a set of over 50 genetic disorders caused by trinucleotide repeat expansion, a kind of mutation in which repeats of three nucleotides (trinucleotide repeats) increase in copy numbers until they cross a threshold above which they become unstable. (wikipedia.org)
  • Lack of meiotic crossover and fixation of nucleotides flanking the repeat may contribute to success of interspecies PCR amplification. (usda.gov)
  • Microsatellites in different eukaryotic genomes: survey and analysis. (bioinformatics.org)
  • Trinucleotide repeats are a subset of a larger class of unstable microsatellite repeats that occur throughout all genomes. (wikipedia.org)
  • Together with these regulatory roles, a structural role of repeated DNA in shaping the 3D folding of genomes has also been proposed. (wikipedia.org)
  • Microsatellites were identified as motifs repeated at least five times. (thefreedictionary.com)
  • A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 1-6 or more base pairs ) are repeated, typically 5-50 times. (wikipedia.org)
  • Similarly, insects have shorter repeat motifs in their telomeres that could arguably be considered microsatellites. (wikipedia.org)
  • Here, we describe chromosomal mapping of 18 microsatellite repeat motifs in eight species of Sauropsida. (edu.au)
  • The average number of repeat motifs amplified was 23. (biomedcentral.com)
  • Among di-nucleotide repeats, the most frequent repeats were AC motifs, accounting for 67.55% of the total number. (mdpi.com)
  • Frameshift mutations at coding mononucleotide repeats (IGFIIR, TGF beta II, BAX, hMSH6, and hMSH3) were investigated by single-strand conformation polymorphism analysis and DNA sequencing. (nih.gov)
  • For five of these putative microsatellites, the segregation in a maize restriction fragment length polymorphism mapping population was analyzed. (nih.gov)
  • Frameshift mutations at coding mononucleotide repeats were detected by single strand conformation polymorphism analysis and DNA sequencing. (uniroma1.it)
  • A tetranucleotide repeat polymorphism in the fourth [corrected] intron of the aromatase P450 gene was longer among the lean (187 base pairs) than the rest of the women. (kb.se)
  • These variants are SOD2 Val-9Ala , GPX1 Pro198Leu , and the GPX1 GCG repeat polymorphism. (aacrjournals.org)
  • STRs used in forensic science tend to be tetra- and penta-nucleotide repeats, as they are both robust, suffer less environmental degradation, and provide a high degree of error free data. (scenacriminis.com)
  • Zhong X, Leng L, Beitin A et al (2005) Simulaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor ( MIF ) gene by thin-film biosensor chip and application to rural field studies. (springer.com)
  • Renner P, Roger T, Bochud PY et al (2011) A functional microsatellite of the macrophage migration inhibitory factor gene associated with meningococcal disease. (springer.com)
  • This study suggests that the 3'-end (AT)(n) repeat region of the CTLA-4 gene represents a recessive risk factor for type 1 diabetes. (lu.se)
  • Moreover, in reporter gene experiments, the transcription activation is highly dependent upon the number of repeats that are included in the construct. (plos.org)
  • Importantly, in vivo EWS-FLI1-bound microsatellites are significantly associated with EWS-FLI1-driven gene activation. (plos.org)
  • Although the first microsatellite was characterised in 1984 at the University of Leicester by Weller, Jeffreys and colleagues as a polymorphic GGAT repeat in the human myoglobin gene, the term "microsatellite" was introduced later, in 1989, by Litt and Luty. (wikipedia.org)
  • GT microsatellite repeats in the heme oxygenase-1 gene promoter associated with abdominal aortic aneurysm in Croatian patients. (cdc.gov)
  • The number of (GT)(n) repeats in the heme oxygenase-1 (HO-1) gene promoter modulates transcription of this enzyme, which might have anti-inflammatory, antioxidant, antiapoptotic, and antiproliferative effect. (cdc.gov)
  • The genetic cause of DM type 1 (DM1) is a CTG repeat expansion (CTG exp ) in the 3′ untranslated region of the DM protein kinase ( DMPK ) gene. (nature.com)
  • Is the polymorphic microsatellite repeat of the dopamine beta-hydroxylase gene associated with biochemical variability of the catecholamine pathway in schizophrenia? (uhi.ac.uk)
  • Fingerprint Dive into the research topics of 'Is the polymorphic microsatellite repeat of the dopamine beta-hydroxylase gene associated with biochemical variability of the catecholamine pathway in schizophrenia? (uhi.ac.uk)
  • Patients carry from 230 to 4000 CGG repeats in the gene that causes fragile X syndrome, while unaffected individuals have up to 50 repeats and carriers of the disease have 60 to 230 repeats. (wikipedia.org)
  • citation needed] Some of the problems in trinucleotide repeat syndromes result from causing alterations in the coding region of the gene, while others are caused by altered gene regulation. (wikipedia.org)
  • This is likely explained by the addition of CAG repeats in the affected gene as the gene is transmitted from parent to child. (wikipedia.org)
  • For example, Huntington's disease occurs when there are more than 35 CAG repeats on the gene coding for the protein HTT. (wikipedia.org)
  • The fragile X mental retardation 1 (FMR1) gene contains a CGG repeat within its 5' untranslated region (5'UTR) that, when expanded to 55-200 CGG repeats (premutation allele), can result in the late-onset neurodegenerative disorder, fragile X-associated tremor/ataxia syndrome. (semanticscholar.org)
  • Women with opposite phylogenetic characteristic have a short microsatellite (168 base pairs) in this gene locus. (kb.se)
  • We provide a mathematical basis for suggesting a measure of genetic distance between populations based on microsatellite variation. (genetics.org)
  • The density of different repeats, however, showed significant variation. (elsevier.com)
  • With the exception of tandem repeats involved in human neurodegenerative diseases, repeat variation was often believed to be neutral with no phenotypic consequences. (mdpi.com)
  • Contrary to initial suggestions, tandem repeat variation can have useful phenotypic consequences. (mdpi.com)
  • Third, we find that microsatellite variation differs among species within classes, possibly relating to population dynamics. (bioone.org)
  • Eighth, at the species level, microsatellite and allozyme heterozygosity covary and therefore inferences based on large-scale studies of allozyme variation may also reflect microsatellite genetic diversity. (bioone.org)
  • Originally discovered by Barbara McClintock, dispersed repeats have been increasingly recognized as a potential source of genetic variation and regulation. (wikipedia.org)
  • We used variation in repeat number of the microsatellite to identify genetic differences between European corn borer populations, and infer relationships to other species. (usda.gov)
  • To understand how the authors correlated variation microsatellites to variations in morphology, let's first try to understand how microsatellites are formed. (anthropology.net)
  • This report summarizes the results of our efforts to generate useful induced mutants of the Philippine banana cultivars, 'Latundan' and 'Lakatan' through irradiation, and to evaluate the usefulness of DNA marker techniques, such as RAPD, microsatellites or SSR, and AFLP, to characterize the genomic alterations in induced mutants of the two Philippine banana cultivars. (fao.org)
  • We also describe a novel 146-bp repeat element, TteREP1, which is linked to two-thirds of the microsatellites sequenced and is associated with marker development failure. (elsevier.com)
  • Therefore, microsatellite marker analysis with multiplex PCR and automated procedures has a high throughput and should be suitable for large epidemiologic studies of C. albicans . (asm.org)
  • The discriminatory power of this single microsatellite marker was 0.86. (asm.org)
  • Polymorphic microsatellite marker (PMM) analysis detected a total of 22 different allelic types for 35 isolates of P. marneffei with a high discriminatory power ( D = 0.956). (asm.org)
  • Genetic analysis (via chromosomal segregation and microsatellite marker-based recombination) of various wild-type strains exhibiting relative susceptibility or tolerance to the lethal toxic effects of arsenite identified a limited X-chromosomal region (16D-F) able to confer a differential response phenotype. (nih.gov)
  • Identification of a polymorphic Plasmodium vivax microsatellite marker. (ajtmh.org)
  • In 2005 leaf samples were collected from the 52 still remaining accessions for a microsatellite (SSR) DNA marker analysis. (fao.org)
  • Cells with MSI accumulate unstable, structure-forming (TA) n repeats resolvable by the helicase WRN. (aacrjournals.org)
  • Historically, tandem repeats have been designated as non functional "junk" DNA, mostly as a result of their highly unstable nature. (mdpi.com)
  • We conclude that, although allele frequencies derived from microsatellite pooling are distorted, differences of 5% or greater between pools can be reliably detected. (elsevier.com)
  • To evaluate MSI, a reference panel was proposed at an international consensus meeting, comprised of 2 mononucleotide (BAT-25, BAT-26) and 3 dinucleotide repeats. (unboundmedicine.com)
  • Dinucleotide repeats are associated with human diseases such as Norrie's disease [7] , and the expansion of trinucleotide repeats is often associated with neurodegenerative disease and chromosomal fragility , such as Huntington's disease and fragile X syndrome , respectively [8] . (bioinformatics.org)
  • The role of molecular microsatellite identity testing to detect sampling errors in prenatal diagnosis. (biomedsearch.com)
  • We classified 7(7.3%) of 96 human gastric cancers (HGCs) as MSI-H. Screening this group of HGCs for frameshift mutations in coding mononucleotide repeats of AXIN2 and RIZ, we detected one sample harboring a frameshift mutation (1bp deletion) in exon7 of AXIN2 and four samples with frameshift mutations (1bp deletion) in the (A)9 tract of RIZ, and no mutations were found in the (A)8 tract. (aacrjournals.org)
  • Seventh, there is a directional mutation toward an increase in microsatellite length. (bioone.org)
  • Low ONW1 mutation rate was inferred from population data, and attributed to reduced number of cell divisions during oogenesis, low repeat numbers, or short array length. (usda.gov)
  • More than 35,000 single nucleotide polymorphisms and 10,000 microsatellite repeats were identified. (biomedcentral.com)
  • In addition to the above features, single-nucleotide polymorphisms, microsatellites, transposable elements and inverted repeats that could contribute to toxin diversity were observed. (biomedcentral.com)
  • However, among eukaryote species, microsatellite repeats are more abundant and longer in vertebrates than invertebrates (Chambers and MacAvoy 2000). (thefreedictionary.com)
  • Most eukaryotes have microsatellites, with the notable exception of some yeast species. (wikipedia.org)
  • The microsatellite was the first sex-linked microsatellite from a lepidopteran species, and had the unusual property of being highly conserved among related crop pest species. (usda.gov)
  • PCR amplification is carried out on the region containing the CAG repeat, shown below. (proprofs.com)
  • The reproducibility of length polymorphisms was confirmed by using different DNA preparations from the same isolate or by repeated runs from the same DNA preparation. (asm.org)
  • We describe here a single fluorescent multiplex system comprising 5 quasimonomorphic mononucleotide repeats for the detection of MSI tumors. (unboundmedicine.com)
  • In contrast, all MSI tumors showed allelic size variations in 3 or more of the microsatellites. (unboundmedicine.com)
  • Tumors not expressing MSH3 show elevated microsatellite alterations at selected tetranucleotide repeats (EMAST). (cdc.gov)
  • Kaplan-Meier plots of cumulative recurrence-free survival and overall survival in elevated microsatellite alterations at selected tetranucleotide repeats (EMAST)-positive tumors compared with non-EMAST tumors. (cdc.gov)
  • Overall, frameshift mutations at i or more of these mononucleotide repeat microsatellites were found in 17 of 24 MI+ tumors (70.8%) but in none of the 10 MI negative neoplasms. (uniroma1.it)
  • Colon tumors harboring MSI more frequently present with proximal location, large tumor size, decreased likelihood of metastasis, less advanced stage at diagnosis, and better prognosis compared with microsatellite-stable (MSS) colon cancers ( 4 , 5 ). (aacrjournals.org)
  • Tri- and hexa-nucleotide repeats are more abundant in exons, whereas other repeats are more abundant in non-coding regions. (elsevier.com)
  • The most abundant SSR tracts are the homopolymer repeats poly(dA).poly(dT) and poly(dG).poly(dC). (bioinformatics.org)
  • Expected heterozygosity ranged from 0.462 to 0.666 and did not correlate with the repeat array length. (ajtmh.org)
  • The discovery that trinucleotide repeats could expand during intergenerational transmission and could cause disease was the first evidence that not all disease-causing mutations are stably transmitted from parent to offspring. (wikipedia.org)
  • Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma. (cdc.gov)
  • Of the 37 primer pairs defined, 16 amplified clean polymorphic microsatellites and are described. (usda.gov)
  • Anthropometric measures and the risk of endometrial cancer, overall and by tumor microsatellite status and histological subtype. (nextbio.com)
  • Microsatellites and their longer cousins, the minisatellites , together are classified as VNTR (variable number of tandem repeats ) DNA. (wikipedia.org)
  • The LTR contained a variable region ranging from a simple TC repeat (TC) 11 to more complex repeats of TC/CA, (TC) 1230, (CA) 1822 and was up to 146 bp in length. (edu.kz)
  • Latin prefixes mono- , di- , tri- , etc. might also be added to the root words mer and nucleotide to describe a simple repeat. (bioinformatics.org)
  • The data shown in this track are a subset of the Simple Repeats track, selecting only those repeats of period 2 and 3, with 100% identity and no indels and with at least 15 copies of the repeat. (ucsc.edu)
  • The Simple Repeats track is created using the Tandem Repeats Finder . (ucsc.edu)
  • A variable nucleotide tandem repeat at position −794 comprises five to eight CATT repeats (referred to henceforth by numbers from 5 to 8, rs5844572). (springer.com)
  • Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. (thefreedictionary.com)
  • We show that the repeat motif is capable of binding MYB10 protein in electrophoretic mobility shift assays. (plantcell.org)
  • CNS expression of murine fragile X protein (FMRP) as a function of CGG-repeat size. (semanticscholar.org)
  • The expanded repeat-containing RNAs could potentially induce neuron toxicity by disrupting protein and RNA homeostasis through various mechanisms. (hopkinsmedicine.org)
  • A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. (biomedcentral.com)
  • And, trinucleotide tract elongation can lead to tandem amino acid repeats. (bioinformatics.org)
  • In a coding region, CAG codes for glutamine (Q), so CAG repeats result in a polyglutamine tract. (wikipedia.org)
  • There are several known categories of trinucleotide repeat disorder. (wikipedia.org)
  • Trinucleotide repeat disorders generally show genetic anticipation: their severity increases with each successive generation that inherits them. (wikipedia.org)
  • Trinucleotide repeat expansions may occur through strand slippage during DNA replication or during DNA repair synthesis. (wikipedia.org)
  • Tracking Expansions of Stable and Threshold Length Trinucleotide Repeat Tracts In Vivo and In Vitro Using Saccharomyces cerevisiae. (harvard.edu)
  • This work was supported by National Institutes of Health grants AR049610 and HL130669 to R.B. We are grateful to the staff of the W. M. Keck Foundation DNA Sequencing Facility at Yale School of Medicine for their assistance in developing the microsatellite fragment analysis and TaqMan assay protocols. (springer.com)
  • Although it is becoming clear that such repeats are important in genomic organization and function and may be associated with disease conditions, their systematic analysis has not been reported. (elsevier.com)
  • A population conazole resistance alone is of concern, but widespread genetic analysis of microsatellites showed the existence of azole cross-resistance would be devastating. (cdc.gov)
  • In a tandem array it may have very short repeating units, 2-10 base pairs in the case of microsatellite DNA , or slightly longer ones, 10-100 base pairs in the case of minisatellite DNA. (encyclopedia.com)

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