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...
Trinucleotide repeats are a subset of a larger class of unstable microsatellite repeats that occur throughout all genomes. The ... This may lead to repeated copying of the repeated sequence, expanding the number of repeats. Additional mechanisms involving ... Trinucleotide repeat disorders, also known as microsatellite expansion diseases, are a set of over 50 genetic disorders caused ... Gao FB, Richter JD (January 2017). "Microsatellite Expansion Diseases: Repeat Toxicity Found in Translation". Neuron. 93 (2): ...
Microsatellites are also known as simple sequence repeats (SSRs). Microsatellite instability structure consists of repeated ... each individual has microsatellites of a set length. The most common microsatellite in humans is a dinucleotide repeat of the ... Microsatellites are repeated sequences of DNA. These sequences can be made of units of 1 to 6 base pairs in length that are ... The majority of repeats occur in untranslated regions, specifically introns. However, microsatellites that occur in coding ...
"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 ...
microsatellite A type of satellite DNA consisting of a relatively short sequence of tandem repeats, in which certain motifs ( ... A direct repeat in which the repeats are immediately adjacent to each other is known as a tandem repeat. dispersive replication ... short tandem repeat (STR) See microsatellite. short interspersed nuclear element (SINE) shotgun sequencing silencer A sequence ... simple sequence repeat (SSR) See microsatellite. single-nucleotide polymorphism (SNP) Any substitution of a single nucleotide ...
microsatellite A type of satellite DNA consisting of a relatively short sequence of tandem repeats, in which certain motifs ( ... short tandem repeat (STR) See microsatellite. short interspersed nuclear element (SINE) shotgun sequencing silencer A sequence ... simple sequence repeat (SSR) See microsatellite. single-nucleotide polymorphism (SNP) Any substitution of a single nucleotide ... trinucleotide repeat Any sequence in which an individual nucleotide triplet is repeated many times in tandem, whether in a gene ...
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 ... Four divergent domains consisted of microsatellite repeats, biased in base composition, with purines on one strand and ... Satellite DNA, together with minisatellite and microsatellite DNA, constitute the tandem repeats. The major satellite DNA ...
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: ...
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- ...
"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 ... Dakin, E E; Avise, J C (2004-08-04). "Microsatellite null alleles in parentage analysis". Heredity. 93 (5): 504-509. doi: ...
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 ...
Microsatellite Minisatellite ProRepeat Satellite DNA Tandem Repeats Database Tandem repeat locus Variable number tandem repeats ... Tandem Repeats over the Edit Distance TandemSWAN Microsatellite repeats finder JSTRING - Java Search for Tandem Repeats in ... The Tandem Repeats Database The Microorganisms Tandem Repeats Database Short Tandem Repeats Database Tandem Repeats in major ... Those with fewer are known as microsatellites or short tandem repeats. When exactly two nucleotides are repeated, it is called ...
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 ...
JSTRING-Java Search for Tandem Repeats In Genomes Microsatellite repeats finder MISA-MIcroSAtellite identification tool MREPATT ... Microsatellite mutation rates vary with base position relative to the microsatellite, repeat type, and base identity. Mutation ... microsatellite mutations lead to the gain or loss of an entire repeat unit, and sometimes two or more repeats simultaneously. ... Microsatellite enrichment). The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/ ...
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 ...
The other significant fraction resides in short tandem repeats (STRs; also called microsatellites) consisting of short ... Variations in the number of STR repeats can cause genetic diseases when they lie within a gene but most of these regions appear ... Telomeric repeat-containing RNA (TERRA) are transcripts derived from telomeres. TERRA has been shown to maintain telomerase ... Highly repetitive DNA consists of short stretches of DNA that are repeated many times in tandem (one after the other). The ...
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 ...
... the repeat is referred to as a short tandem repeat (STR) or microsatellite. When the repeating sequence is 10-60 nucleotides ... Tandem repeats are repeated sequences which are directly adjacent to each other in the genome. Tandem repeats may vary in the ... Inverted repeats occur when a nucleotide sequence is repeated in the inverse direction. For example, a direct repeat of "CATCAT ... Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns of nucleic acids ...
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 ...
Kumar M, Kapil A, Shanker A (November 2014). "MitoSatPlant: mitochondrial microsatellites database of viridiplantae". ... "Accurate prediction of repeat prostate biopsy outcomes by a mitochondrial DNA deletion assay". Prostate Cancer and Prostatic ... Mitochondrial microsatellites database of viridiplantae. MitoZoa 2.0: a database for comparative and evolutionary analyses of ... but slow compared to other DNA regions such as microsatellites) which makes it useful for studying the evolutionary ...
July 2010). "Human Y-chromosome short tandem repeats: a tale of acculturation and migrations as mechanisms for the diffusion of ... of Serbian Populations through Mitochondrial DNA Sequencing and Non-Recombining Region of the Y Chromosome Microsatellites". ... "Y chromosome genetic data defined by 23 short tandem repeats in a Serbian population on the Balkan Peninsula". Annals of Human ...
Smith, S., & Hughes, J. (2008). Microsatellite and mitochondrial DNA variation defines island genetic reservoirs for ... causes a decrease in the reproductive fitness of a population because of a decrease in its heterozygosity from the repeated ...
... tandem repeat sequence - taste bud - TATA box - tax gene product - taxonomy - telophase - tertiary structure - tetrodotoxin - ... microsatellite - microscope - microtiter plate - microtubule-associated protein - mineralocorticoid receptor - minisatellite - ... trinucleotide repeat - triose - tropomyosin - troponin - tryptophan - tubulin - tumor necrosis factors - tumor necrosis factor ... dinucleotide repeat - diploid - disaccharide - dissociation constant - disulfide bond - disulfide bridge - DNA - DNA ...
... has recently been associated with regulating iron metabolism through ubiquitinating the F-box and leucine-rich repeat ... UBE2Q1 and UBE4B in gastric and colorectal carcinomas with microsatellite instability". Pathology. 43 (7): 753-5. doi:10.1097/ ... low-copy repeats in the Prader-Willi/Angelman region encodes a large protein implicated in protein trafficking, which is ...
Shah KA, Shishkin AA, Voineagu I, Pavlov YI, Shcherbakova PV, Mirkin SM (2012) Role of DNA polymerases in repeat-mediated ... Co-organizer, 6th International Conference on Unstable Microsatellites and Human Disease, 3 Costa Rica, 2009 Editor-in-Chief, ... Kononenko AV, Ebersole T, Vasquez KM, Mirkin SM (2018) Mechanisms of genetic instability caused by (CGG)n repeats in an ... Krasilnikova, M M; Samadashwily, G M; Krasilnikov, A S; Mirkin, S M (1998-09-01). "Transcription through a simple DNA repeat ...
"Santos J, Serra L, Solé E, Pascual M. FISH mapping of microsatellite loci from Drosophila subobscura and its comparison to ... repeated protrusion and withdrawal of the proboscis before the male mounted. The tips of the male and female probosces can be ...
July 2010). "Human Y-chromosome short tandem repeats: a tale of acculturation and migrations as mechanisms for the diffusion of ... of Serbian Populations through Mitochondrial DNA Sequencing and Non-Recombining Region of the Y Chromosome Microsatellites". ... 2005). "Genetic variation at nine short tandem repeat loci among islanders of the eastern Adriatic coast of Croatia". Human ... 2022). "Influence of genetic substructuring of statistical forensic parameters on genetic short tandem repeat markers in the ...
A suite of microsatellite markers (short segments of DNA that have a repeated sequence) have been developed to help aid in ... Copulation with a single male may be repeated several times, with a total mating time of up to fourteen hours, while the male ... Vocalizations include purring, a threatening call, and a call of fear, consisting of "repeated loud, coarse inhalations and ... "Characterization of 26 microsatellite marker loci in the fossa (Cryptoprocta ferox)". Conservation Genetics. 10 (5): 1449-1453 ...
The female repeats the process with other brood cells, going progressively deeper into the soil. A higher temperature increases ... Soro, Antonella; Paxton, Robert J. (2009). "Characterization of 14 polymorphic microsatellite loci for the facultatively ... The second brood in New York yields only gynes and males, which breed to repeat the cycle. In Kansas, the first brood is ...
A genome-wide microsatellite genotyping laboratory at the Ottawa Health Research Institute, led by Dennis Bulman, was added. ... January 2005). "Expanded repeat in canine epilepsy". Science. 307 (5706): 81. doi:10.1126/science.1102832. PMID 15637270. S2CID ... The Genetic Analysis area includes capillary-based genotyping (Applied Biosystems TaqMan and SNaPshot, microsatellites), custom ...
The howl consists of a wail repeated 3-4 times on an ascending scale, followed by three short yelps. Jackals typically howl at ... from Serbia as Revealed by Mitochondrial DNA and Nuclear Microsatellite Loci". Biochemical Genetics. 47 (3-4): 241-50. doi: ...
... microsatellite markers or short tandem repeats (STRs), (4) multinucleotide polymorphisms (MNPs), (5) heterozygous sequences, ...
... ranging from 75 to over 11,000 repeats. Like DM1, the size of the microsatellite repeat array lengthens from generation to ... triplet repeats, termed trinucleotide repeat expansion and classifying DM1 as a one of several trinucleotide repeat disorders. ... as the degree of repeat expansion beyond 75 repeats does not affect the age of onset or disease severity. The repeat expansion ... The microsatellite expansion responsible for DM2 is of cytosine-cytosine-thymine-guanine (CCTG) repeats, classifying it as a ...
June 23 - Diwata-2, the second microsatellite under the Philippine Scientific Earth Observation Microsatellite program, is ... September 17: President Duterte repeats his call to shut all mines in the country following deadly landslides, hours after ...
October 2009). "Increased microsatellite instability and epigenetic inactivation of the hMLH1 gene in head and neck squamous ... repeating the process. This exposes large sections of DNA to exonuclease digestion, allowing for quick excision (and later ... Recognizing and repairing mismatches and indels is important for cells because failure to do so results in microsatellite ... Mutations in the human homologues of the Mut proteins affect genomic stability, which can result in microsatellite instability ...
Z-DNA does not contain single base-pairs but rather a GpC repeat with P-P distances varying for GpC and CpG. On the GpC stack ... Triple-stranded DNA structures have been demonstrated in repetitive polypurine:polypyrimidine Microsatellite sequences and ...
This fatal disease can lead to losses as much as 80% after repeated planting cycles. Ganoderma produces enzymes that degrade ... "Identification and development of new polymorphic microsatellite markers using genome assembly for Ganoderma boninense, causal ...
Microsatellite comparisons support the idea that the Hawaiian T. oceanicus colonization originated in the Western islands and ... convergent song loss in Hawaiian crickets is repeated, morphologically varied, and widespread". Ecology. 100 (8): e02694. doi: ...
Three novel microsatellite markers linked to ASIP were isolated from a domestic cat BAC clone containing this gene and were ... After about 20 to 30 minutes, once the female is finished grooming, the cycle will repeat. Because ovulation is not always ...
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 ...
Using Nuclear Microsatellites DNA Markers". International Journal of Forestry Research. 2009: 1-8. doi:10.1155/2009/210179. ... growing in the Kingdom of Saudi Arabia using inter-simple sequence repeat markers". BMC Genetics. 15 (109): 109. doi:10.1186/ ...
These contests involve repeated confrontations between two males using surface splashing, fighting, paired somersaulting, and ... assessed by micro- satellite DNA markers". Molecular Ecology. 7 (5): 627-638. doi:10.1046/j.1365-294x.1998.00373.x. PMID ...
The third set of molars lasted for 10 years, and this process was repeated until the final, sixth set emerged when the animal ... "Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation". Molecular Ecology. 21 (14): ... The resulting offspring would be an elephant-mammoth hybrid, and the process would have to be repeated so more hybrids could be ... "Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation". Molecular Ecology. 21 (14): ...
Kershaw, EE; Chua, SC Jr; Leibel, RL (1995). "Localization of a (CA)n repeat in glucagon-like peptide-1 receptor gene (Glp1r) ... Chua, SC Jr; Hansen, MH; Truett, GE; Leibel, RL (1993). "Utility of a C-jun microsatellite marker in determining gene dosage ... "Genomic structure of the human OB receptor and identification of two novel intronic microsatellites". Genome Res. 6 (12): 1192- ...
... along with inverted-repeat Z-DNA structures within a larger 2.1kb satellite DNA repeat unit. Additionally, H-DNA has been shown ... Triple-stranded DNA has been observed in supercoiled Satellite DNA in regions where microsatellite copy numbers are highly ... Polypurine mirror-repeat H-DNA forming sequences were found neighboring the P1 promoter of the c-MYC gene and are associated ... The transcriptional activity of mutant NSEs can be predicted by the element's ability to form H-DNA and not by repeat number, ...
Repeated sampling in the newly established Tesso Nilo National Park documented a trend of increasing tiger density from 0.90 ... ten mitochondrial DNA haplotypes and 11 out of 108 unique microsatellite alleles. The relatively high genetic variability and ...
Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. ... MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion Science. 2021 Jun 25;372(6549): ... Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. ... Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains ...
Repeat expansions confer WRN dependence in microsatellite-unstable cancers. Authors list. Niek van Wietmarschen Sriram ... Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and ... The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of ... Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from ...
microsatellite repeat expansion disorders; pathophysiology; RNA biology; repeat transcripts; polymeric repeat proteins; RNA ... Short repeated sequences of 3−6 nucleotides are causing a growing number of over 50 microsatellite expansion disorders, which ... Adding to the complexity of pathogenesis, microsatellite repeat expansions are polymorphic and found in coding as well as in ... Here, we will briefly review the pathogenic mechanisms mediated by microsatellite repeat expansions prior to focus on the RNA ...
Fields of Study , genetics , molecular genetics , nucleotide sequences , repetitive sequences , microsatellite repeats ... 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 ... A variety of simple repeat sequences that are distributed throughout the genome. ...
Shortening of microsatellite deoxy(CA) repeats involved in GL331-induced down-regulation of matrix metalloproteinase-9 gene ... Shortening of microsatellite deoxy(CA) repeats involved in GL331-induced down-regulation of matrix metalloproteinase-9 gene ... Shortening of microsatellite deoxy(CA) repeats involved in GL331-induced down-regulation of matrix metalloproteinase-9 gene ... Shortening of microsatellite deoxy(CA) repeats involved in GL331-induced down-regulation of matrix metalloproteinase-9 gene ...
Is the polymorphic microsatellite repeat of the dopamine beta-hydroxylase gene associated with biochemical variability of the ... Dive into the research topics of Is the polymorphic microsatellite repeat of the dopamine beta-hydroxylase gene associated ...
Fragments of Interrupted Repeats Joined by RepeatMasker ID. Microsatellite. hide. dense. squish. pack. full. Microsatellites - ... Simple Repeats. hide. dense. squish. pack. full. Simple Tandem Repeats by TRF. ... Di-nucleotide and Tri-nucleotide Repeats. RepeatMasker Viz.. hide. dense. full. Detailed Visualization of RepeatMasker ...
The Croatian study also reported an association of a GT dinucleotide repeat microsatellite variant (intron 2) in the TLR2 gene ... Investigations of a TNFα microsatellite dinucleotide repeat polymorphism have had conflicting results. ... Thymidylate synthase (TS): The TS enhancer region contains a series of 28 base-pair tandem repeats, most commonly 2 repeats ( ... NOS2: A single study found no association of NOS2 tetra-repeat and penta-repeat polymorphisms with colorectal cancer. Another ...
Forensics- Microsatellite loci, generally known in forensic applications as Short Tandem Repeat (STR) loci, are widely used for ... Microsatellites are tandem repeats of one to six nucleotides scattered throughout the genome. ... In the literature they can also be called simple sequence repeats (SSR), short tandem repeats (STR), or variable number tandem ... are repeated in tandem arrays. This means that the sequences are repeated one right after the other. The lengths of sequences ...
Microsatellite Repeats. 1. 2010. 812. 0.020. Why? Magnetic Resonance Imaging. 1. 2015. 33990. 0.020. Why? ...
KEYWORDS: forensic science, forensic entomology, bed bug, DNA, microsatellite repeats. Read Abstract + ... Autosomal Short Tandem Repeats and an Alu Insertion Polymorphism Are Detectable in Cimex lectularius L. (Hemiptera: Cimicidae) ... Using polymorphic autosomal short tandem repeat (STR) markers commonly employed in forensic investigations and an Alu insertion ...
Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes. GAO, HUAN; CAI, SHENGLI; YAN, BINLUN; CHEN ...
... microsatellite repeats; mitochondria; phylogeography; population genetics; population structure; Hawaii. Abstract:. ... The ... Cryptic Species in the United States Based on Microsatellite Markers ...
Vis forfatter(e) (1997). Complexity of 12q13-22 amplicon in liposarcoma: Microsatellite repeat analysis. Genes, Chromosomes and ... Vis forfatter(e) (2021). The expressed mutational landscape of microsatellite stable colorectal cancers. Genome Medicine. ... Vis forfatter(e) (1999). Characterization of the 17p amplicon inhuman sarcomas - microsatellite marker analysis. International ... Vis forfatter(e) (2017). Multilevel genomics of colorectal cancers with microsatellite instability - clinical impact of JAK1 ...
Elimination of toxic microsatellite repeat expansion RNA by RNA-Targeting Cas9. Cell 2017;170:899-912.doi:10.1016/j.cell. ... 2 while people with a C9orf72 repeat expansion (C9FTD/ALS) can carry hundreds to thousands of repeats.3-6 The repeats are ... repeat-associated non-ATG translation of the repeat expansion leads to the production of dipeptide repeat proteins (DPRs). ... Impeding transcription of expanded microsatellite repeats by deactivated Cas9. Mol Cell 2017;68:479-90.doi:10.1016/j.molcel. ...
A high-resolution map of genes, microsatellite markers, and new dinucleotide repeats from UBE1 to the GATA locus in the region ...
Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PLoS ONE, 8(2), ...
Fragments of Interrupted Repeats Joined by RepeatMasker ID. Microsatellite. hide. dense. squish. pack. full. Microsatellites - ... Simple Repeats. hide. dense. squish. pack. full. Simple Tandem Repeats by TRF. ... Di-nucleotide and Tri-nucleotide Repeats. RepeatMasker Viz.. hide. dense. full. Detailed Visualization of RepeatMasker ...
Several repeat sequences were also discovered, namely, 33 forward, 14 reverse, 3 complement, and 49 microsatellite repeats. ... and two inverted repeat regions. A total of 85 protein-coding, 8 ribosomal RNA, and 36 transfer RNA genes were identified. ...
Microsatellite Repeats Medicine & Life Sciences 41% * Triploidy Medicine & Life Sciences 28% * Zygote Medicine & Life Sciences ... Here, microsatellite markers were employed in a redetermination of the pressures required to generate zebrafish half-tetrads ... Here, microsatellite markers were employed in a redetermination of the pressures required to generate zebrafish half-tetrads ... Here, microsatellite markers were employed in a redetermination of the pressures required to generate zebrafish half-tetrads ...
Microsatellite Repeats 7% * Cluster Analysis 6% * Population 2% Earth & Environmental Sciences. * philopatry 89% ...
An alternative RNA-mediated toxicity arises from microsatellite repeat instability in the human genome. The expanded repeat- ...
Tandem Repeats Finder was used to find tandem repeats while MIcroSAtellite detected the microsatellite DNA (1-6 bp). ... Simple sequence repeats (also known as microsatellites) comprise tandemly repeated genetic loci of 1-6 bp (Tautz and Renz, 1984 ... All mono-nucleotide repeats were consisted of A/T repeats and the di-nucleotide repeats were AT/TA, with G/C only found in the ... repeats in the O. sinensis mt genome, including 30 forward repeats (61-128 bp, in total 2446 bp), 13 palindromic repeats (61-90 ...
Short repeated segments of DNA called microsatellites are especially prone to DNA mismatch errors. Tumors that are mismatch ... For example, a specific microsatellite mutation in the TGFBR2 gene occurs in 60% to 80% of people with mismatch repair- ... A silver lining to microsatellite instability is that it has the potential to create novel proteins, known as neoantigens, that ... Recent data suggests that some people with microsatellite instability-high cancer have evidence of an immune reaction against ...
Mori T et al. Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal ... Munakata K et al. Inflammation-Associated Microsatellite Alterations Caused by MSH3 Dysfunction Are Prevalent in Ulcerative ...
Scores represent the allele calls for each microsatellite locus (i.e. DNA fragment length containing the microsatellite repeats ... Scores represent the allele calls for each microsatellite locus (i.e. DNA fragment length containing the microsatellite repeats ... These data consist of microsatellite genotype scores for all samples of Santa Ana sucker (Catostomus santaanae) used in the ... These data consist of microsatellite genotype scores for all samples of Santa Ana sucker (Catostomus santaanae) used in the ...
Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed ... components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites and has ... components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight ... We genotyped 64 dinucleotide microsatellite repeats in individuals from populations that represent all inhabited continents. ...
The different alleles of each microsatellite were numbered according to their increasing numbers of repeats. The haplotype ... Microsatellite instability in the tumors of the proband and of patient III-1 was indicative of MMR deficiency and thus argued ... Fragment length analysis was also used to determine the number of adenine repeats at the end of the inserted sequence. It ... The proband presented with colorectal cancer (CRC) exhibiting microsatellite instability and apparent isolated loss of PMS2 ...
  • Forensics - Microsatellite loci, generally known in forensic applications as Short Tandem Repeat (STR) loci, are widely used for forensic identification and relatedness testing, and are a predominant genetic marker in this area of application. (mcqsonline.net)
  • therefore we also hypothesize that the predictability of cancerassociated microsatellite loci in germline DNA may support the current hypothesis of a glioma cell of origin. (elsevier.com)
  • In this study, "normal" germline exome sequenced DNA from the 1000 Genomes Project (n=390) were compared with exome sequences from germlines of subjects with WHO grade II and III lower-grade glioma (LGG, n=136) and WHO grade IV glioblastoma (GBM, n=252) from The Cancer Genome Atlas to identify microsatellite loci non-randomly associated with glioma. (elsevier.com)
  • Segregation of microsatellite alleles and residual heterogosity at single loci in homozygous androgenetic common carp (Cyprino carpio L. (wur.nl)
  • Screening with 11 microsatellites also revealed two linkage groups, a segregation distortion at two microsatellite loci, and the possible association of some microsatellites with mass, length, stress-related plasma cortisol levels, and basal plasma glucose levels. (wur.nl)
  • Dive into the research topics of 'Segregation of microsatellite alleles and residual heterogosity at single loci in homozygous androgenetic common carp (Cyprino carpio L.)'. Together they form a unique fingerprint. (wur.nl)
  • Excel coded microsatellite repeat number data for Megalagrion xanthomelas across all loci, populations, and individuals. (datadryad.org)
  • Excel coded microsatellite repeat number data for Megalagrion pacificum across all loci, populations, and individuals. (datadryad.org)
  • Excel coded microsatellite repeat number data for Megalagrion xanthomelas and M. pacificum across all loci, populations, and individuals, with formatting prepared for GenePop. (datadryad.org)
  • Among the 55 primers pairs designed from clones from pathotype 3 of P. sorghi, 36 flanked microsatellite loci containing simple repeats, including 28 (55%) with dinucleotide repeats and 6 (11%) with trinucleotide repeats. (usda.gov)
  • The regions flanking the repeat sequence of published microsatellite loci in Chinook Salmon were also chosen to examine nucleotide variation. (critfc.org)
  • In addition, EST-derived microsatellite loci (also known as simple sequence repeats or SSRs) were isolated and characterized. (eurekamag.com)
  • Wide range of genetic variability supported the utility of these microsatellite loci in measurement of genetic diversity indices in other Indian cattle breeds too. (who.int)
  • Two (A)n microsatellite loci were cloned from the mtDNA of P. cinnamomi. (digglicious.com)
  • Microsatellite marker analysis involves PCR amplification of the microsatellite loci using fluorescently labeled primers that flank the repeated sequence. (digglicious.com)
  • We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. (biomedcentral.com)
  • Here, microsatellite markers were employed in a redetermination of the pressures required to generate zebrafish half-tetrads with currently available equipment. (elsevier.com)
  • Two criteria were used to choose conditions for half tetrad gynogenesis: expected ploidy as confirmed with microsatellite markers and maximal egg viability. (elsevier.com)
  • Genetic diversity within and between European pig breeds using microsatellite markers. (semanticscholar.org)
  • The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. (semanticscholar.org)
  • A multi-farm assessment of Greek black pig genetic diversity using microsatellite molecular markers. (semanticscholar.org)
  • Assessment of genetic diversity, genetic characterization, and usefulness of an individual assignment test for 12 commercial chicken lines using 40 microsatellite markers found that assignment test could correctly allocate individuals at the line level to their origins, with a high accuracy. (semanticscholar.org)
  • Genetic diversity of Brazilian pig breeds evidenced by microsatellite markers. (semanticscholar.org)
  • Insight is provided into the use of microsatellite markers to reveal origin, genetic structure and diversity within and across various domestic pig breeds around the world. (semanticscholar.org)
  • But DNA markers called microsatellites have since been associated with birds of the various species. (answersingenesis.org)
  • This haplotype consisted of five SNP markers and two microsatellites, which all appear to be in strong linkage disequilibrium. (elsevier.com)
  • Thirty-three androgenetic progeny groups of common carp were analysed using 11 microsatellite markers to (i) verify the homozygous status of the 566 androgenetic individuals, (ii) analyse the microsatellite allele segregation, and (iii) study the possible association of microsatellite alleles with phenotypic traits. (wur.nl)
  • In this study, we presented the results of newly developed molecular microsatellites markers to detect the differences of sorghum downy mildew isolates and other related downy mildew isolates of corn, sugarcane, pearl millet and rose at the DNA level. (usda.gov)
  • A total of 260 alleles were obtained using 54 microsatellites primer combinations, with an average of 4.8 polymorphic markers per SSR across 34 Peronosclerospora, Peronospora and Sclerospora spp isolates studied. (usda.gov)
  • The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. (biomedcentral.com)
  • The present study estimates genetic variability with a set of 25 microsatellite markers in a random sample of 50 animals of Tharparkar breed of Indian zebu (Bos indicus) cattle. (who.int)
  • Microsatellites were evaluated as genetic markers for the mitochondrial genome (mtDNA) of Phytophthora cinnamomi for population studies. (digglicious.com)
  • Highly polymorphic microsatellite markers can be used to identify individuals in the population. (digglicious.com)
  • A high-resolution map of genes, microsatellite markers, and new dinucleotide repeats from UBE1 to the GATA locus in the region Xp11.23. (medscape.com)
  • Microsatellite markers clearly separated cv. (tubitak.gov.tr)
  • Using simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs), the genetic diversity of 43 populations of Festuca species from Oruro, La Paz, Potosi and Cochabamba departments was evaluated for the purpose of providing information for effective conservation and breeding. (slu.se)
  • In this study, 42 accessions from in vitro and field populations were genotyped using 11 microsatellite markers and 23 morphological descriptors to assess variability within and between accessions. (iita.org)
  • Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides5. (crick.ac.uk)
  • In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. (crick.ac.uk)
  • Alleles at a specific location (locus) can differ in the number of repeats. (mcqsonline.net)
  • A high heterogeneity of the polymorphic repeats was demonstrated, extending the range of the published alleles from 13 to 22 and allowing a first attempt at making a phenotype/genotype correlation. (elsevier.com)
  • Short repeated sequences of 3−6 nucleotides are causing a growing number of over 50 microsatellite expansion disorders, which mainly present with neurodegenerative features. (whiterose.ac.uk)
  • They form secondary and tertiary structures involving G-quadruplexes and atypical helices in repeated GC-rich sequences. (whiterose.ac.uk)
  • A variety of simple repeat sequences that are distributed throughout the genome. (usda.gov)
  • This means that the sequences are repeated one right after the other. (mcqsonline.net)
  • Tumors exhibit MMR deficiency, which is the consequence of somatic inactivation of the second allele of the affected gene and leads to instability of microsatellite sequences in the tumor genome. (nature.com)
  • Microsatellites" are not complete genomes but short repeated sequences useful for mapping kinship. (answersingenesis.org)
  • Replication slippage also increases DNA content by looping of the synthesized strand during DNA replication , but typically involves short sequence stretches such as microsatellites (short repeated sequences). (encyclopedia.com)
  • MSI tumors are the subset of CRC that are characterized by dysfunction of mismatch repair genes (MMR) causing failure to repair errors in repetitive DNA sequences called microsatellites. (digglicious.com)
  • Microsatellites or STRs are repetitive co-dominant sequences of 2-6 bp of DNA that are present throughout the entire genome. (digglicious.com)
  • Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. (biomedcentral.com)
  • In the literature they can also be called simple sequence repeats (SSR), short tandem repeats (STR), or variable number tandem repeats (VNTR). (mcqsonline.net)
  • MSI is a genomic tumor marker (or biomarker) characterized by the presence of multiple mutations caused by a variance in the length of short DNA sequence repeats in tumors compared with normal tissue. (ahdbonline.com)
  • Microsatellites exist in most biological genomes. (digglicious.com)
  • A total of 24 wheat cultivars and 5 wild progenitors of wheat were examined using 24 simple sequence repeat (SSR) primers with a known physical locus on the A, B, and D genomes of hexaploid wheat. (tubitak.gov.tr)
  • The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg 133 , a key residue whose mutation causes Rett syndrome. (nih.gov)
  • For example, a specific microsatellite mutation in the TGFBR2 gene occurs in 60% to 80% of people with mismatch repair-deficient colorectal cancer. (cancer.gov)
  • Further correlation analyses between YIF1B expression and mutation indicators such as tumor mutation burden (TMB), microsatellite instability (MSI), and mismatch repair (MMR) were also examined by the Spearman test. (silverchair.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)
  • 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)
  • We hypothesized that microsatellite variation could expand the understanding of glioma etiology. (elsevier.com)
  • To date only one GWA-based study of variation in eggplant has been performed [ 16 ] but the present study used a larger number of accessions (191 vs 141 ) and a more densely populated genetic map (384 SNPs (single nucleotide polymorphisms) vs 105 microsatellites) and targeted traits related to anthocyanin accumulation and fruit color. (biomedcentral.com)
  • They are also known as short tandem repeats (STRs). (usda.gov)
  • También se les conoce como repeticiones cortas en tándem (STRs). (bvsalud.org)
  • Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. (nih.gov)
  • Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome. (nih.gov)
  • An alternative RNA -mediated toxicity arises from microsatellite repeat instability in the human genome. (hopkinsmedicine.org)
  • Over the mapped portion of the genome of the cross, the QTL with the greatest effect upon yield was located within a 22 cM region between mlo and the simple sequence repeat HVM67 on chromosome 4(4H). (dundee.ac.uk)
  • Short tandem repeats are abundantly present within the genome. (elsevier.com)
  • Tumors that are mismatch repair-deficient end up accumulating alterations in these microsatellites, a condition known as microsatellite instability . (cancer.gov)
  • What's more, tumors that form in people with Lynch syndrome often have the same microsatellite mutations. (cancer.gov)
  • Here, we report the identification of frequent frameshift mutations in the coding mononucleotide repeat of TFAM in sporadic colorectal cancer (CRC) cell lines and in primary tumors with microsatellite instability (MSI), but not in microsatellite stable (MSS) CRC cell lines and tumors. (elsevier.com)
  • Chicago, IL-Tumors with high microsatellite instability (MSI-H) are predictive of Lynch syndrome. (ahdbonline.com)
  • MSK-IMPACT also incorporates an MSI stratification algorithm that stratifies tumors as being MSI-H, MSI-indeterminate (MSI-I), or microsatellite stable (MSS). (ahdbonline.com)
  • Recent data suggests that some people with microsatellite instability-high cancer have evidence of an immune reaction against several of these shared neoantigens . (cancer.gov)
  • In 2011, researchers from DKFZ-the German Cancer Research Center in Heidelberg, Germany-began clinical testing of a neoantigen vaccine in people who had advanced colorectal cancer that was microsatellite instability-high. (cancer.gov)
  • Based on the results from the Phase 3 KEYNOTE-775/Study 309 trial, KEYTRUDA plus LENVIMA has been approved in the U.S. for patients with advanced endometrial carcinoma that is not microsatellite instability-high or dMMR, who have disease progression following prior systemic therapy in any setting and are not candidates for curative surgery or radiation. (merck.com)
  • Adding to the complexity of pathogenesis, microsatellite repeat expansions are polymorphic and found in coding as well as in non-coding regions of genes. (whiterose.ac.uk)
  • Unwinding of these structures by RNA helicases plays multiple roles in the expression of genes including repeat-associated non-AUG (RAN) translation of polymeric-repeat proteins with aggregating and cytotoxic properties. (whiterose.ac.uk)
  • Microsatellite instability (MSI) is caused by mutations in DNA mismatch repair genes such as MLH1, MSH2, MSH6, and PMS2, and it is found in 10% to 15% of sporadic colorectal cancers (CRCs). (digglicious.com)
  • This is the first report that an anti-cancer agent can inhibit mmp-9 gene expression by inducing microsatellite DNA shortening. (elsevier.com)
  • Several of these microsatellites have been described within the β-globin locus and some could be involved in controlling gene expression. (elsevier.com)
  • Our purpose was to investigate the extent and significance of the (TG)n(CG)m dinucleotide repeat polymorphisms in the two γ-globin gene IVS2s. (elsevier.com)
  • Thus, our in vivo and in vitro data raise the question of a possible contribution of the γ-gene IVS2s polymorphic microsatellites to the variable Hb F synthesis in the major haemoglobinopathies: a well known, puzzling and still unanswered question. (elsevier.com)
  • BACKGROUND: The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. (bvsalud.org)
  • Here, we will briefly review the pathogenic mechanisms mediated by microsatellite repeat expansions prior to focus on the RNA helicases eIF4A, DDX3X and DHX36 which act as modifiers of RAN translation in C9ORF72-linked amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72-ALS/FTD) and Fragile X-associated tremor/ataxia syndrome (FXTAS). (whiterose.ac.uk)
  • In addition, we will contrast these with the roles of other RNA helicases such as DDX19/20, senataxin and others which have been associated with neurodegeneration independently of microsatellite repeat expansions. (whiterose.ac.uk)
  • A microsatellite consists of a specific sequence of DNA bases or nucleotides which contains mono, di, tri, or tetra tandem repeats. (mcqsonline.net)
  • The expressed mutational landscape of microsatellite stable colorectal cancers. (uib.no)
  • Genotyping is the process to identify the genotype of each microsatellite. (digglicious.com)
  • The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair1-4. (crick.ac.uk)
  • Short repeated segments of DNA called microsatellites are especially prone to DNA mismatch errors. (cancer.gov)
  • Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. (nih.gov)
  • Aumento del número de repeticiones de una secuencia genómica de ADN repetida en tándem de una generación a la siguiente. (bvsalud.org)
  • Genotyping of a range of cultivars and sources of Mlo resistance with the HVM67 simple sequence repeat showed that the Derkado HVM67 allele was rare as it was found only in one other cultivar and four land-races or sources of disease resistance. (dundee.ac.uk)
  • Microsatellites are widely used for DNA profiling, also known as "genetic fingerprinting", of crime stains (in forensics) and of tissues (in transplant patients). (digglicious.com)
  • Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. (biomedcentral.com)
  • Microsatellite, as related to genomics, refers to a short segment of DNA, usually one to six or more base pairs in length, that is repeated multiple times in succession at a particular genomic location. (digglicious.com)
  • An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next. (bvsalud.org)
  • They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. (usda.gov)
  • 3. Short sequence (2-5) repeat DNA. (mcqsonline.net)
  • Where does microsatellite DNA present in the chromosome? (digglicious.com)
  • Explanation: Microsatellite DNA is less than 150bp and found in a dispersed condition all over the chromosome. (digglicious.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)
  • Assessing genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses. (semanticscholar.org)
  • Microsatellites are amplified by PCR using fluorescently labeled primers and the amplicons are separated using CE. (digglicious.com)
  • Here, we examine the genetic consequences of fluctuating island areas and connectivity using microsatellite analysis of 2 widespread, endemic Hawaiian damselflies. (datadryad.org)
  • We will further review the RNA helicases DDX5/17, DHX9, Dicer and UPF1 which play additional roles in the dysregulation of RNA metabolism in repeat expansion disorders. (whiterose.ac.uk)
  • Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. (crick.ac.uk)
  • The workflow of microsatellite genotyping generally involves specific primer design, amplification of microsatellites, and Polymorphism testing. (digglicious.com)
  • A microsatellite-based study of genetic diversity on southern African pig populations suggested a true genetic structure with significant differentiation between most populations sampled, but with little differentiation among the commercial SA Landrace and Large White breeds. (semanticscholar.org)