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).
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.
Repetitive Sequences, Nucleic Acid
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).
Polymerase Chain Reaction
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.
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.
Molecular Sequence Data
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.
Sequence Analysis, DNA
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.
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).
Tandem Repeat Sequences
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.
Loss of Heterozygosity
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.
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.
Trinucleotide Repeat Expansion
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
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.
Base Pair Mismatch
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.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
DNA Mismatch Repair
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)
Repetitive Sequences, Amino Acid
Colorectal Neoplasms, Hereditary Nonpolyposis
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.
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.
DNA Sequence, Unstable
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 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.
Inverted Repeat Sequences
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.
DNA Repeat Expansion
An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next.
Adaptor Proteins, Signal Transducing
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
Chromosomes, Human, Pair 3
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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)
Microsatellite repeats - definition of Microsatellite repeats by The Free Dictionary
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...
Characterization and multiplex genotyping of alpaca tetranucleotide microsatellite markers
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 ...
Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes ...
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
Isolation of novel microsatellite loci in Orchesella villosa (Arthropoda, Collembola). | IRIS Università degli Studi di Siena
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.. ...
Microsatellite Instability in Sarcoma: Fact or Fiction? : Figure 1
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 ...
IJMS | Free Full-Text | Characterization of Novel Di-, Tri-, and Tetranucleotide Microsatellite Primers Suitable for Genotyping...
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
The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex | Genetics
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 ...
Microsatellite instability did not predict individual survival in sporadic stage II and III rectal cancer patients
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 ...
Distinct patterns of microsatellite instability are seen in tumours of the urinary tract. - Surgical Intervention Trials Unit
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
Microsatellite instability and allelic imbalance in primary and secondary colorectal cancer<...
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 Marker Analysis: DNA Genotyping Core, UT Southwestern, Dallas, TX
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 - Wikipedia
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 ...
CIENCIASMEDICASNEWS: Detection of Mismatch Repair Deficiency and Microsatellite Instability in Colorectal Adenocarcinoma by...
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 ...
Assessment of Genetic Diversity in Labeo gonius (Hamilton, 1822) through Microsatellite Marker in Nanak Sagar and Dhaura...
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),
Isolation and characterization of twelve polymorphic microsatellite loci in the buff-throated partridge (Tetraophasis...
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.
Kanniadu goats of Tamilnadu, India: genetic characterisation through microsatellite markers<...
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 ...
Environ Exp Biol (2016) 14: 63-68
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 ...
Population genetic variation in BWEL-SPF chickens inferred from microsatellite DNA markers
A set of microsatellite DNA markers for the one-lined pencilfish Nannostomus unifasciatus, an Amazonian flooded forest fish -...
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 among pelt sheep population using microsatellite markers | African Journal of Biotechnology
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 ...
MLH1 promoter methylation and gene silencing is the primary cause of microsatellite instability in sporadic endometrial cancers
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 …
Using patterns of genetic structure based on microsatellite loci to test hypotheses of current hybridization, ancient...
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 ...
Development of 23 microsatellite loci for Boulengers agama (Agama boulengeri) with partial cross-amplification in other Agama...
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 ...
Promoter methylation of ITF2 , but not APC , is associated with microsatellite instability in two populations of colorectal...
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
Serval - Statistical properties of population differentiation estimators under stepwise mutation in a finite island model.
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%, ...
Genetic Variation among Baluchi Sheep Population Using Microsatellite Markers - Isfahan University of Technology - Journal...
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 ...
Our Work: RER/5/015: RTC in Genomic DNA Preparation and Microsatellite Analyses
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 ...
Chromosome-Specific Microsatellite Sets for Fluorescence-Based, Semiautomated Genome Mapping - UQ eSpace
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.. ...
Genetic Diversity Analysis of Maize Hybrids Through Morphological Traits and Simple Sequence Repeat Markers
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
Microsatellite abnormalities in plasma of patients with breast carcinoma: concordance with the primary tumour. | Journal of...
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. ...
Typing recombinant inbred mouse strains for microsatellite markers. by B A. Taylor and P C. Reifsnyder
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.
MDGA Member UC Davis Testing Guide
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 ...
Band-specific localization of the microsatellite at D13S71 by microdissection and enzymatic amplification<...
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. ...
Population structure in a comprehensive genomic data set on human microsatellite variation. - PubMed - NCBI
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Genome-wide differences between microsatellite stable and unstable colorectal tumors : Carcinogenesis - oi
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 ...
Analysis of the molecular nature associated with microsatellite status in colon cancer identifies clinical implications for...
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 ...
A comparison of the performance of microsatellite and methylation urine analysis for predicting the recurrence of urothelial...
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
Investigation of Second Genetic Hits at the BMPR2 Locus as a Modulator of Disease Progression in Familial Pulmonary Arterial...
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 ...
Development and mapping of microsatellite (SSR) markers in wheat
Microsatellite DNA markers are consistently found to be more informative than other classes of markers in hexaploid wheat. The objectives of this research were to develop new primers flanking wheat microsatellites and to position the associated loci on the wheat genome map by genetic linkage mapping …
Genetic Diversity Analysis and DNA Fingerprinting of Mungbean (<i>Vigna radiata</i> L.) Genotypes Using SSR Markers :: Science...
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, ...
Form Success | Thermo Fisher Scientific - US
Discover our solutions for capillary electrophoresis. Applied Biosystems genetic analysis systems are a trusted standard for Sanger sequencing and fragment analysis by capillary electrophoresis-proven through decades of results, including the first sequencing of the human genome and the discovery of genes implicated in diseases like cystic fibrosis.. Explore applications, instrumentation, reagents, consumables, and software designed to respond to the unlimited potential of scientific inquiry.. Sanger sequencing applications. Sanger sequencing is the gold standard for sequencing technology since it provides a high degree of accuracy, long-read capabilities, and the flexibility to support a diverse range of applications in many research areas.. Fragment analysis applications. Learn more about the applications fragment analysis enables, from microsatellite marker analysis in cell line authentication (CLA) to multiplex ligation-dependent probe amplification (MLPA) assay in inherited disease ...
Search | Korea Science
Knowledge of genetic diversity and of the genetic relationships among elite breeding materials has had a significant impact on the improvement of crops. In maize, this information is particularly useful in i) planning crosses for hybrid and line development, ii) in assigning lines to heterotic groups and iii) in plant variety protection. We have used the SSR technique to study the genetic diversity and genetic relationships among 76 Korean waxy corn accessions, representing a diverse collection from throughout Korea. Assessment of genetic diversity among members of this group was conducted using 30 microsatellite markers. Among these 30 microsatellite markers, we identified a total of 127 alleles (with an average of 4.2 and a range of between 2 and 9 alleles per locus). Gene diversity at these 30 microsatellite loci varied from 0.125 to 0.795 with an average of 0.507. The cluster tree generated with the described microsatellite markers recognized two major groups with 36.5% genetic similarity. ...
Isolation and characterization of 13 polymorphic nuclear microsatellite primers for the widespread Indo-Pacific three-spot...
A set of 13 simple sequence repeat markers was developed from D. trimaculatus genomic DNA, tested for D. auripinnis and characterized using 40 individuals per species. All the loci were polymorphic with a number of alleles ranging from three to 30. Observed heterozygosities varied from 0.23 to 0.89 for D. trimaculatus and from 0.11 to 0.85 for D. auripinnis. Early results show that these will be powerful markers for the study of ecological and evolutionary mechanism in this coral reef fish species complex ...
Identification and Characterization of Microsatellites in Expressed Sequence Tags and Their Cross Transferability in Different...
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75.
Bioline International Official Site (site up-dated regularly)
and thus are genetically linked. The primers used to generate polymorphic bands were 3-anchored inter-simple sequence repeat primers which identified genomic microsatellites with a repeated motif of 3 nucleotides in length. The primers were used singly to amplify genomic segments which were flanked by inversely orientated, closely spaced, identical microsatellite sequences. One of the polymorphic bands, a 900 base pair band, was completely linked to the Sr39 and Lr35 rust resistance genes in the segregating population used in this study. After cloning and sequencing this polymorphic band, the inter-simple sequence repeat marker was converted to a sequence characterized amplified region marker by designing primer sets which amplify a single, easily resolved band from DNA of plants with Sr39/Lr35 genes. This marker is present in six wheat lines carrying the Sr39 and Lr35 genes on the translocated chromosome segment from Ae. speltoides, The marker has facilitated efforts to breed Canada Prairie ...
Publication : USDA ARS
Citation: Kottapalli, K., Burow, M., Burow, G.B., Burke, J.J., Puppala, N. 2007. Molecular characterization of the US peanut mini core collection using microsatellite markers. Crop Science. 47(4):1718-1727. Interpretive Summary: Peanut is the second-most important legume crop in the United States. A limitation to increased peanut productivity is that peanut improvement is hampered by relatively low genetic variability in the germplasm commonly used by breeding programs. To facilitate accessibility to diverse germplasm sources for breeding applications, a core subset of the United States Department of Agriculture (USDA) peanut germplasm was previously established that later on was refined to develop a mini core collection consisting of 112 accessions. In this study we determined the genetic diversity of the US peanut minicore collection at the molecular level using microsatellites or simple sequence repeat markers. Microsatellites are well known for their potentially high information content and ...
Centre for Cellular and Molecular Biology
Discovered the functionality of microsatellites (simple sequence repeats) among non-coding DNA. Discovered the gene CPA1, which ...
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- ...
Between the strand-biased microsatellite repeats and G:C mononucleotide repeats, all sequence variations retained one or two ... The most prevalent repeated sequences in the embedded microsatellite regions were CCT:AGG, CTT:AAG, CTTT:AAAG, and CCCT:AGGG. ... Variations among cloned RU sequences were characterized by the number of microsatellite repeats, and also by the lengths of C ... Four divergent domains consisted of microsatellite repeats biased in composition with purines on one strand and pyrimidines on ...
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: ...
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: ...
Balai Penelitian Ternak, Ciawi, Bogor
2001.Characterization of duck microsatellite repeat sequences. JARQ 35(4): 217-219. (in Indonesian) Sari L, Purwadaria T. 2004 ...
Vasopressin receptor 1A
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 ...
2013-08-12). "Table 3: Complete Data Set of Y-Chromosomal HGs, Numbers of Repeats at 10 Microsatellite Loci, and Descriptions ...
Zenklusen JC, Bièche I, Lidereau R, Conti CJ (December 1994). "(C-A)n microsatellite repeat D7S522 is the most commonly deleted ...
Human genetic variation
Short tandem repeats (about 5 base pairs) are called microsatellites, while longer ones are called minisatellites. The Out of ... 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 ...
Slipped strand mispairing
Genomic regions with a high proportion of repeated DNA sequences (tandem repeats, microsatellites) are prone to strand slippage ... In long repeats, expansions may involve two or more units. For example, insertion of a single repeat unit in GAGAGA expands the ... For example, a transversion could change the simple two- base repeat [GA]10 to [GA]4GATA[GA]2. This could then be expanded to[ ... The combination of SSM events with point mutation is thought to account for the evolution of more complex repeat units. ...
Patel MS, Mankoo BS, Brickell PM (Apr 1992). "A polymorphic microsatellite repeat is located close to the promoter region of ...
Eukaryotic chromosome fine structure
Short repeats of nucleotides. Microsatellite: Very short repeats of nucleotides. Some trinucleotide repeats are found in coding ... Repeated sequences are of two basic types: unique sequences that are repeated in one area; and repeated sequences that are ... This region is a microsatellite, but its function is more specific than a simple tandem repeat. Throughout the eukaryotic ... They can be classified based on the length of the repeat as: SINE: Short interspersed sequences. The repeats are normally a few ...
Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) are a type of MSI where loci containing AAAG or ... Nakajima E, Orimo H, Ikejima M, Shimada T (1996). "Nine-bp repeat polymorphism in exon 1 of the hMSH3 gene". Jpn. J. Hum. Genet ... This leads to a heightened rate of microsatellite instabilities and increased rates of somatic mutations. This effect is ... 2000). "Association between single nucleotide polymorphisms in the hMSH3 gene and sporadic colon cancer with microsatellite ...
... 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) ... Repeat turnover therefore appears to be controlled by recombinational activity in DNA that flanks the repeat array and results ... and that was subsequently identified as large centromeric tandem repeats. When shorter (10-30-bp) tandem repeats were later ...
DNA based markers- microsatellites otherwise known as simple sequence repeats (SSR) were therefore used for the diversity ... The next 400 million years included repeated, massive biodiversity losses classified as mass extinction events. In the ...
Smaller k-mers also have the problem of not being able to resolve areas in the DNA where small microsatellites or repeats occur ... This is because most of the k-mers will sit in the repeated region and may just be discarded as repeats of the same k-mer ... Larger k-mer sizes help alleviate the problem of small repeat regions. This is due to the fact that the k-mer will contain a ... This is because smaller k-mers will tend to sit entirely within the repeat region and is therefore hard to determine the amount ...
Surfactant protein C
1995). "Mapping of the pulmonary surfactant SP5 (SFTP2) locus to 8p21 and characterization of a microsatellite repeat marker ...
Paternal age effect
Brinkmann B, Klintschar M, Neuhuber F, Huhne J, Rolf B (1998). "Mutation Rate in Human Microsatellites: Influence of the ... Structure and Length of the Tandem Repeat". Am J Hum Genet. 62 (6): 1408-1415. doi:10.1086/301869. PMC 1377148 . PMID 9585597. ... such as telomeres and microsatellites), caused by cellular copying errors DNA point mutations, caused by cellular copying ...
DNA Specimen Provenance Assignment
A panel of 16 microsatellite short tandem repeat (STR) markers that recognizes highly variable loci of human DNA is used in a ... 1999). "The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing ... 81265 Comparative analysis using Short Tandem Repeat (STR) markers; patient and comparative specimen, and 81266 Comparative ... analysis using Short Tandem Repeat (STR) markers; each additional specimen. Current Procedural Terminology (CPT®) copyright ...
It contains the microsatellite (short tandem repeat) profiles of 7121 individuals from various parts of the world residing or ...
A short tandem repeat is a microsatellite, consisting of a unit of two to thirteen nucleotides repeated hundreds of times in a ... having a certain number of repeats at one locus does not change the likelihood of having any number of repeats at any other ... This method uses highly polymorphic regions that have short repeated sequences of DNA (the most common is 4 bases repeated, but ... A Short Tandem Repeat (STR) analysis is one of the most useful methods in molecular biology which is used to compare specific ...
Molecular-weight size marker
Microsatellites Also known as SSR (simple sequence repeats) or STR (short tandem repeats), microsatellites differ from ... Microsatellites are most commonly used in population genetics. Microsatellites have a high and complex mutation rate, which is ... Minisatellites are short sequences of tandem repeats, approximately 10-60 base pairs. Minisatellites can be used in DNA ... This property of microsatellites allows for easy isolation. ...
... microsatellite markers or short tandem repeats (STRs), (4) multinucleotide polymorphisms (MNPs), (5) heterozygous sequences, ...
This gene has microsatellite repeats which are associated with the age-at-onset of insulin-dependent diabetes mellitus (IDDM) ...
... genomics The commonly used markers include Simple sequence repeats (or microsatellites), single nucleotide polymorphisms (SNP ... So we want to keep genetic background of the recipient genotypes, which is done by 4-6 rounds of repeated backcrosses while ...
Single or repeated krlee or similar component of calls used in other circumstances, but this can be very variable. Alarm calls ... Hailer, F., Gautschi, B., & Helander, B. (2005). Development and multiplex PCR amplification of novel microsatellite markers in ... Studies of microsatellite and mitochondrial DNA in white-tailed eagles from north-central Europe have shown that the recovering ... This may be repeated or gain intensity until they are talon-grappling or "mutual cartwheeling", consisting of the pair locking ...
分子演化 - 维基百科，自由的百科全书
... tandem repeat），可再依單元序列的長短分為衛星序列（satellite）、小衛星序列（minisatellite）和微衛星序列（microsatellite）；分佈較為分散的是
... making repeated treatments unnecessary. This approach to locust control was used in Tanzania in 2009 to treat around 10,000 ... A worldwide survey in a pest plagued by microsatellite null alleles". Molecular Ecology. 17 (16): 3640-3653. doi:10.1111/j.1365 ...
Pang H, Soejima M, Koda Y, Kimura H (2005). "A novel tetrameric short tandem repeat located in the 3' flanking region of the ... within the microsatellite genetic map of chromosome 19". Cytogenet. Cell Genet. 71 (2): 158-62. doi:10.1159/000134098. PMID ...
A Xenon Resistojet Propulsion System for Microsatellites (Surrey Space Centre, University of Surrey, Guildford, Surrey) ... Aerobraking allows a spacecraft to reduce the high point of an elliptical orbit by repeated brushes with the atmosphere at the ...
Evolution - Simple English Wikipedia, the free encyclopedia
Dodd's experiment has been easy for others to repeat. It has also been done with other fruit flies and foods. ... Microsatellite variation and evolution of human lactase persistence. Human Genetics 117(4): 329-339. ...
Automatic identification system
A repeat indicator that was designed to be used for repeating messages over obstacles by relay devices. ... ORBCOMM and Luxspace launched the Vesselsat AIS microsatellites, one in an equatorial orbit and the other in a polar orbit ( ...
Over 41,000 goats were removed during the initial hunting effort (1971-82). This process was repeated until only the " ... Ciofi, Claudio; Milinkovitch, Michel C.; Gibbs, James P.; Caccone, Adalgisa; Powell, Jeffrey R. (2002). "Microsatellite ... and the repeated action over many generations has formed half-sphere depressions in the rock. ...
For other abnormalities, the colonoscopy can be repeated after 1 year. Routine PET or ultrasound scanning, chest X-rays, ... a survey of current practices and re-evaluation of the role of microsatellite instability testing". Modern Pathology. 31 (11): ... If a villous polyp, a polyp ,1 centimeter or high grade dysplasia is found, it can be repeated after 3 years, then every 5 ... Mismatch repair (MMR) deficient tumours are characterized by a relatively high amount of poly-nucleotide tandem repeats. ...
Trinucleotide repeats are classified as insertion mutations and sometimes as a separate class of mutations. ... This can often happen in microsatellite regions due to the DNA polymerase slipping. Insertions can be anywhere in size from one ...
This led to repeated misrepresentations or misconceptions in journalistic accounts on the topic. Popular science presentations ... a study of Y chromosome microsatellites.", Mol Biol Evol, 16 (12): 1791-98, doi:10.1093/oxfordjournals.molbev.a026091, PMID ... But the concept of Eve caught on with the public and was repeated in a Newsweek cover story (11 January 1988 issue featured a ...
Geneetiliselt muundatud toit - Vikipeedia
"A single domestication for maize shown by multilocus microsatellite genotyping". 2002. Proceedings of the National Academy of ... ingl The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system, CRISPR) on bakteriaalsest ...
... mutation rates vary with base position relative to the microsatellite, repeat type, and base identity. ... Microsatellite enrichment). The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/ ... microsatellite mutations lead to the gain or loss of an entire repeat unit, and sometimes two or more repeats simultaneously. ... Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as ...
It was proposed as a distinct subspecies on the basis of mtDNA and micro-satellite sequences that differs from the Indochinese ... It was found to have similar repeat composition to other cat genomes and an appreciably conserved synteny. ...
Tandem repeats. *Satellite DNA. *Variable number tandem repeat/Minisatellite. *Short tandem repeat/Microsatellite ( ... De novo repeat identification. De novo repeat identification is an initial scan of sequence data that seeks to find the ... This method works best for tandem repeats, but can be used for dispersed repeats as well. However, it is a slow process, making ... Some k-mer approach programs use the k-mer as a base, and extend both ends of each repeated k-mer until there is no more ...
Xenoma, a enciclopedia libre
Li, YC; Korol, AB, Fahima, T, Beiles, A, Nevo, E (2002 Dec). "Microsatellites: genomic distribution, putative functions and ... "Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes". Microbiology and Molecular Biology Reviews 72 (4): ... Schlötterer, C (2000 Dec). "Microsatellite analysis indicates genetic differentiation of the neo-sex chromosomes in Drosophila ... "Characterization and Repeat Analysis of the Compact Genome of the Freshwater Pufferfish Tetraodon nigroviridis". Genome ...
Ebolusyon, ang malayang ensiklopedya
... at isang pagkakaibang microsatellite sa mga populasyon sa Europe, Japan, Australia, middle East at Atlantic islands. ... pilohenetiko ay lumalapat din sa sobrang lawak na uri ng mga walang silbing elementong sekwensiya kabilang ang repeats, ...
... microsatellite and mitochondrial DNA) study to date (2016) which found high divergence between Rocky Mountain and Sierra Nevada ... horns can frequently exhibit damage from repeated clashes. Females exhibit a stable, nonlinear hierarchy that correlates ...
Methods frequently include using microsatellites to determine gene flow and hybridization between populations. The development ... Metapopulation structure and the repeated extinctions and recolonizations can significantly affect a population's genetic ...
... inferred with mtDNA and microsatellite loci". Molecular Phylogenetics and Evolution. 53 (2): 556-564. doi:10.1016/j.ympev. ... Competitions were held where bets were placed on which caged chaffinch would repeat its song the greatest number of times. The ...
Somatic evolution in cancer
Within these new patches (sub-clones), the process may have been repeated multiple times, indicated by the still smaller ... 2004). "Frequent inactivation of PTEN by promoter hypermethylation in microsatellite instability-high sporadic colorectal ... Microsatellite shifts and instability, loss of heterozygosity (LOH), Copy number variation (detected both by ... taking repeated tumor biopsies from patients as they develop resistance to these drugs would help to understand the tumor ...
Within these new patches (sub-clones), the process may be repeated multiple times, indicated by the still smaller patches ... "Increased microsatellite instability and epigenetic inactivation of the hMLH1 gene in head and neck squamous cell carcinoma". ... Of polyps less than 10mm in size, found during colonoscopy and followed with repeat colonoscopies for 3 years, 25% were ...
This process is repeated many times, and is usually repeated a higher number of times when used with ancient DNA. Some issues ... Microsatellite DNA, single nucleotide polymorphisms (SNPs), and insertion/deletion polymorphisms (INDELS) have shown that Nilo- ... "low diversity of lineage-associated Y-chromosomal short tandem repeat (Y-STR) haplotypes" provide evidence for a "recent ...
RGS12 - ويكيبيديا
... genes with somatic frameshift mutations within coding mononucleotide repeats in colorectal tumors with high microsatellite ...
... and the results for microsatellite short tandem repeat sequences (Y-STRs). The UEP results represent the inheritance of events ...
This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and ... The high variance of R1a1 in India (table 12), the spatial frequency distribution of R1a1 microsatellite variance clines (fig. ... which increases the likelihood of diversification and microsatellite variation. According to Sengupta et al. (2006), "[ ... "The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time" ...
STR is short tandem repeats which are short DNA regions in the genome and are 2-6 base pairs in length. STR is common in ... Statistical analyses are used in assignment tests based on an individual's microsatellites or Amplified Fragment Length ... Friction ridge paths and the details in small areas of friction ridges are unique and never repeated. ... "nature never repeats," originating from the father of social statistics, Lambert Adolphe Jacques Quetelet. The belief was ...
Males repeat cycles of patrolling and perching as long as the male remained in the territory and was not disturbed by other ... "Isolation and cross-species characterization of polymorphic microsatellites for the orchid bee Eulaema meriana (Hymenoptera: ...
Microsatellite repeats - definition of Microsatellite repeats by The Free Dictionary
Microsatellite repeats synonyms, Microsatellite repeats pronunciation, Microsatellite repeats translation, English dictionary ... definition of Microsatellite repeats. n. 1. A short sequence of DNA consisting of multiple repetitions of a set of two to nine ... redirected from Microsatellite repeats). Also found in: Medical.. Related to Microsatellite repeats: Simple Sequence Repeat mi· ... Microsatellite repeats - definition of Microsatellite repeats by The Free Dictionary https://www.thefreedictionary.com/ ...
WikiGenes - Microsatellite Repeats
Associations of Microsatellite Repeats with chemical compounds. *We present microsatellite DNA evidence for the hypothesis that ... Gene context of Microsatellite Repeats. *In yeast, mutations in several genes, including RTH and MSH3, cause microsatellite ... High impact information on Microsatellite Repeats. *A microsatellite, DG10S478, within intron 3 of the transcription factor 7- ... diagnostic and therapeutic context of Microsatellite Repeats. *Haplotyping for these highly polymorphic microsatellites in ...
microsatellite repeat provided by a negative link the hallmark T(H)1 cytokine « FAROUCHE OMBRÉ
... that contains a CA microsatellite repeat that is highly polymorphic, with up to 6 alleles with 12 homozygotic CA repeats ... microsatellite repeat provided by a negative link the hallmark T(H)1 cytokine. , ...
Frontiers | GTn Repeat Microsatellite Instability in Uterine Fibroids | Genetics
In humans, COL1A2 contains two microsatellite loci: one located at the 5-flanking region is composed of poly CA and poly CG; ... Among the 15 haplotypes, 12 have a mutation at position 2284C,G and 7 at position 2292C,G. Insertions of repeated dinucleotide ... Methods: In this study, repeated dinucleotide GTn of intron 1 COL1A2 was highlighted in 55 patients with uterine fibroids (UF ... Results: Based on reference microsatellite pattern (GT)14CT(GT)3CT(GT)3, 15 haplotypes were found. ...
PRIME PubMed | Evaluation of tumor microsatellite instability using five quasimonomorphic mononucleotide repeats and pentaplex...
Evaluation of tumor microsatellite instability using five quasimonomorphic mononucleotide repeats and pentaplex PCR. Download ... T25 repeat in the 3 untranslated region of the CASP2 gene: a sensitive and specific marker for microsatellite instability in ... Detection of microsatellite instability in endometrial cancer: advantages of a panel of five mononucleotide repeats over the ... Evaluation of tumor microsatellite instability using five quasimonomorphic mononucleotide repeats and pentaplex PCR.. ...
Microsatellite repeats | definition of Microsatellite repeats by Medical dictionary
What is Microsatellite repeats? Meaning of Microsatellite repeats medical term. What does Microsatellite repeats mean? ... Looking for online definition of Microsatellite repeats in the Medical Dictionary? Microsatellite repeats explanation free. ... microsatellite. (redirected from Microsatellite repeats). Also found in: Dictionary.. Related to Microsatellite repeats: Simple ... and identify microsatellite repeats. Microsatellites were identified as motifs repeated at least five times.. Development and ...
Microsatellite Short Tandem Repeat (STR) Analysis | Thermo Fisher Scientific
If the repeat is equal to or less than 6 bases, NTRs are named microsatellites, also known as short tandem repeats (STRs). One ... are repeating sequences of multi-base segments of DNA. ... One common example of a microsatellite is a (CA)n repeat, where ... If the repeat is equal to or less than 6 bases, NTRs are named microsatellites, also known as short tandem repeats (STRs). ... Because microsatellites are polymorphic DNA loci present throughout the genome, microsatellite genotyping is a widely accepted ...
IJMS | Free Full-Text | Tetra-Repeat Microsatellite Markers for the Masu Salmon (Oncorhynchus masou masou) and Its Application...
454 pyrosequencing was used to discover repeat motifs, and seven polymorphic microsatellite-primer sets were identified. The ... These microsatellites can be utilized in studies of genetic structure, genetic diversity, and intra- and inter-subspecific ... We developed tetranucleotide-repeat microsatellite markers for the masu salmon (Oncorhynchus masou) complex. ...
Microsatellite instability, MLH-1 promoter hypermethylation, and frameshift mutations at coding mononucleotide repeat...
Microsatellite instability was infrequent in this series of ovarian tumors, and it was limited to endometrioid and clear cell ... Microsatellite instability analysis was assessed by evaluating three (CA)n dinucleotide repeats (D2S123, D5S346, D17S250) and ... Microsatellite instability, MLH-1 promoter hypermethylation, and frameshift mutations at coding mononucleotide repeat ... Results: Microsatellite instability was identified in only 2 of the 52 (3.8%) tumors of the initial series (1 endometrioid and ...
Genotyping Two Promoter Polymorphisms in the MIF Gene: A −794 CATT5-8 Microsatellite Repeat and a −173 G/C SNP | SpringerLink
Leng L., Siu E., Bucala R. (2020) Genotyping Two Promoter Polymorphisms in the MIF Gene: A −794 CATT5-8 Microsatellite Repeat ... Genotyping Two Promoter Polymorphisms in the MIF Gene: A −794 CATT5-8 Microsatellite Repeat and a −173 G/C SNP. ... Zhong X, Leng L, Beitin A et al (2005) Simulaneous detection of microsatellite repeats and SNPs in the macrophage migration ... A variable nucleotide tandem repeat at position −794 comprises five to eight CATT repeats (referred to henceforth by numbers ...
Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability |...
Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability. ... Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability ... Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability ... Fremeshift mutations in coding mononucleotide repeats of AXIN2 and RIZ in gastric cancers with microsatellite instability ...
Microsatellite Instability Causes Repeat Expansion and WRN Dependence | Cancer Discovery
The length of the CTLA-4 microsatellite (AT)(N)-repeat affects the risk for type 1 diabetes
... Lowe, Michael R.; Graham, J; Sund ... The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3 untranslated sequence of the CTLA-4 gene to ... The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3 untranslated sequence of the CTLA-4 gene to ... The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3 untranslated sequence of the CTLA-4 gene to ...
Author: 'Coelho, Nelson C.' / Journal: Conservation genetics / Subject: loci and microsatellite repeats - PubAg Search Results
... microsatellite repeats Remove constraint Subject: microsatellite repeats Start Over ... Macrocystis pyrifera; alleles; ecology; genomic libraries; loci; macroalgae; microsatellite repeats; population genetics; ... We report the isolation and characterization of 16 microsatellite loci to study the population genetics of the giant kelp, ... Markers were obtained by screening a genomic library enriched for microsatellite motifs. Of the 37 primer pairs defined, 16 ...
Microsatellites or Short Tandem Repeats (STR) - Scena Criminis
Microsatellites or Short Tandem Repeats (STR). Microsatellites or Short Tandem Repeats (STR). 11 March 2015. da admin Leave a ... Short Tandem Repeats (STRs) are regions of the genome composed of approximately 1-5 bases and repeated up to 17 times. STR ... two or more adjacent repeats) or complex (several different length repeats). They are found on 22 autosomal chromosomes as well ... Though there have been thousands of short tandem repeats found in the human genome, only a small number are utilised in ...
An A13 repeat within the 3′-untranslated region of epidermal growth factor receptor (EGFR) is frequently mutated in...
N2 - Colorectal cancers (CRC) with microsatellite instability (MSI) have clinical, pathologic, genetic, and epigenetic features ... title = "An A13 repeat within the 3′-untranslated region of epidermal growth factor receptor (EGFR) is frequently mutated in ... T1 - An A13 repeat within the 3′-untranslated region of epidermal growth factor receptor (EGFR) is frequently mutated in ... An A13 repeat within the 3′-untranslated region of epidermal growth factor receptor (EGFR) is frequently mutated in ...
The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function
Microsatellites containing more than 9 GGAA repeats are very significantly enriched in EWS-FLI1 immunoprecipitates. Moreover, ... Importantly, in vivo EWS-FLI1-bound microsatellites are significantly associated with EWS-FLI1-driven gene activation. Put ... in reporter gene experiments, the transcription activation is highly dependent upon the number of repeats that are included in ... together, these results point out the likely contribution of microsatellite elements to long-distance transcription regulation ...
Microsatellite instability - Wikipedia
Microsatellites are also known as simple sequence repeats (SSRs). Microsatellite instability structure consists of repeated ... Microsatellites are repeated sequences of DNA. These sequences can be made of repeating units of one to six base pairs in ... each individual has microsatellites of a set length. The most common microsatellite in humans is a dinucleotide repeat of the ... The majority of repeats occur in untranslated regions, specifically introns. However, microsatellites that occur in coding ...
Microsatellite - Wikipedia
Microsatellite mutation rates vary with base position relative to the microsatellite, repeat type, and base identity. ... Microsatellite enrichment). The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/ ... microsatellite mutations lead to the gain or loss of an entire repeat unit, and sometimes two or more repeats simultaneously. ... Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as ...
Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing | BMC Genomics |...
Microsatellite repeat discovery. SPUTNIK detected 10,272 repeats of between two and five bases with five or more repeat units ... Microsatellite repeat discovery. Microsatellite markers remain an informative and cost-effective tool for small scale ... To detect repeats which may be screened to find polymorphic microsatellite markers in the great tit, a modified version of ... Microsatellites detected in the great tit transcriptome. an excel table listing repeats detected in the great tit assembly. ...
Subject: 'genetic analysis' / Publication Year: 2019 / Subject: genetic analysis and microsatellite repeats - PubAg Search...
... microsatellite repeats Remove constraint Subject: microsatellite repeats Start Over ... genetic analysis, etc ; cucumbers; fruit quality; fruits; inbred lines; loci; marker-assisted selection; microsatellite repeats ... genetic analysis, etc ; Lycaon pictus; dogs; genetic variation; heterozygosity; inbreeding; microsatellite repeats; national ... genetic analysis, etc ; endangered species; genetic variation; genotyping; heterozygosity; microsatellite repeats; pioneer ...
Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma. -...
Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma.. ... Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma ... Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma ... Tumors not expressing MSH3 show elevated microsatellite alterations at selected tetranucleotide repeats (EMAST). EMAST ...
Detection of monoclonal microsatellite alterations in atypical breast hyperplasia
... J Clin Invest. 1996 Sep 1;98(5):1095-100. doi ... To investigate this question, we used a series of 15 microsatellite loci to analyze 15 separate AH lesions microdissected from ... 59 yrs, P , 0.05) and that a subset of monoclonal lesions (4/6) demonstrated microsatellite alterations at more than one locus ... We found that a significant subset (6/15, or 40%) of these AH lesions demonstrated evidence of monoclonal microsatellite ...
Frameshift mutations at coding mononucleotide repeat microsatellites in endometrial carcinoma with microsatellite instability |...
Frameshift mutations at coding mononucleotide repeat microsatellites in endometrial carcinoma with microsatellite instability. ... Frameshift mutations at coding mononucleotide repeat microsatellites in endometrial carcinoma with microsatellite instability ... Overall, frameshift mutations at i or more of these mononucleotide repeat microsatellites were found in 17 of 24 MI+ tumors ( ... Overall, frameshift mutations at i or more of these mononucleotide repeat microsatellites were found in 17 of 24 MI+ tumors ( ...
Cancer-Specific Retargeting of BAF Complexes by a Prion-like Domain. - PubMed - NCBI
YUHSpace: Frameshift Mutations at Coding Mononucleotide Repeats of the hRAD50 Gene in Gastrointestinal Carcinomas with...
Frameshift Mutations at Coding Mononucleotide Repeats of the hRAD50 Gene in Gastrointestinal Carcinomas with Microsatellite ... Microsatellite instability (MSI) and frameshift mutations in genes containing nucleotide repeats have been reported in a subset ... Frameshift Mutations at Coding Mononucleotide Repeats of the hRAD50 Gene in Gastrointestinal Carcinomas with Microsatellite ... Frameshift Mutations at Coding Mononucleotide Repeats of the hRAD50 Gene in Gastrointestinal Carcinomas with Microsatellite ...
Basic molecular genetics for epidemiologists | Journal of Epidemiology & Community Health
... single repeat mutations in microsatellites. Diseases such as myotonic dystrophy and Huntingtons disease are caused by repeat ... REPEAT EXPANSION. Mutation in a repeat tract that increases the number of repeats by a large amount and that may cause a ... MICROSATELLITE (SYNOMYN, SHORT TANDEM REPEAT, STR). DNA segment consisting in the repetition 5-50 times of a motif 1-6 ... DNA polymerases tend to "slip" when copying microsatellite tracts, adding or subtracting repeat units. Given their high ...
June 2009 - Volume 41 - Issue 4 : Pathology - Journal of the RCPA
Frameshift mutation at mononucleotide repeat inERCC5in gastric carcinomas with microsatellite instability. Kim, Min Sung; Yoo, ... High throughput detection of microsatellite instability (MSI) in sporadic colorectal cancer by MSI COPPER denaturing high ...
Microsatellites /Tandem Repeats database. Genome: Halothermothrix orenii H 168. This database allows retrieval of precomputed ... Percentaje of mismatches allowed within the tandem repeats: 0 , 0.1 , 0.2 Position. Sequence. ... It also allows to easily design primers for amplification of a DNA fragment containing the tandem repeat. The primers may be ...
Microsatellites /Tandem Repeats database. Genome: Melissococcus plutonius ATCC 35311. This database allows retrieval of ... Percentaje of mismatches allowed within the tandem repeats: 0 , 0.1 , 0.2 Position. Sequence. ... It also allows to easily design primers for amplification of a DNA fragment containing the tandem repeat. The primers may be ... precomputed tandem repeats from the selected genome. ...
LociMarkersPolymorphismGenomeMutationsGenesElevated microsatellite alterations at select tetranucleotidesMismatch repairAllelesCarcinomas with microsatelliteMarkerMolecularTandemly repeatedTumoursGeneGeneticsHeterozygosityHumansChromosomesDinucleotide repeatsSequenceSTRsPolymerase chain reAlleleChromosomalTrinucleotide repeatsGenomesColorectal cancerSpeciesAbundantIntronFrameshift mutationsTetranucleotidePolymorphic microsatellitesMotifTumor microsatelliteLocusUnstableTandem repeatPromoterAlterationsGenomic library enrichedRepetitiveProteinInstability-highMarker analysisAnalysis
- Isolation of novel microsatellite loci in Orchesella villosa (Arthropoda, Collembola). (unisi.it)
- PCR primers were successfully constructed for seven loci containing, respectively, five pure, one interrupted, and one compound dinucleotide microsatellite repeats. (unisi.it)
- All microsatellite loci showed high levels of polymorphism. (unisi.it)
- 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. (brill.com)
- Cross-amplification of the microsatellite loci in A. agama and A. boueti was partially successful. (brill.com)
- Microsatellite analysis was performed at 10 mono- and dinucleotide and eight tetranucleotide loci, in 89 bladder and 71 UTT TCC. (ox.ac.uk)
- 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. (edu.au)
- 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. (edu.au)
- Each set of microsatellites consists of up to nine marker loci, with allele size ranges that do not overlap. (edu.au)
- False-negative samples are attributable to tumor heterogeneity, and next-generation sequencing results are concordant with analysis of microsatellite loci by PCR. (blogspot.com)
- 8.Mittal, N. & Dubey, A.K. Microsatellite markers - A new practice of DNA based markers in molecular genetics. (pharmatutor.org)
- 14.B. Pokhriyal, K. Thorat, D.A. Limaye, Y.M. Joshi, V.J. Kadam and Dubey R. Microsatellite Markers- A novel Tool in Molecular Genetics. (pharmatutor.org)
- 15.Kimberly A., Selkoe and Robert J. Toonen Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers, Ecology Letters. (pharmatutor.org)
- The major characteristic that makes microsatellites as useful and powerful genetic tool is the extensive length polymorphism that first of all reflects allelic variation in the number of the tandemly arranged perfect repeats. (pharmatutor.org)
- 13.Grover, A. & Sharma, P.C. Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution? (pharmatutor.org)
- The association of the mutation pattern and microsatellite status was analyzed by a random forest algorithm in The Cancer Genome Atlas (TCGA) and validated by our in-house dataset (39 tumor mutational burden (TMB)-low MSS colon cancer, 10 TMB-high MSS colon cancer, 15 MSI colon cancer). (bmj.com)
- 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. (blogspot.com)
Elevated microsatellite alterations at select tetranucleotides1
- elevated microsatellite alterations at select tetranucleotides). (ox.ac.uk)
- 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. (ox.ac.uk)
- CIENCIASMEDICASNEWS: Detection of Mismatch Repair Deficiency and Microsatellite Instability in Colorectal Adenocarcinoma by Targeted Next Generation Sequencing. (blogspot.com)
- 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. (blogspot.com)
Carcinomas with microsatellite1
- In a subset of 95 carcinomas with microsatellite analysis, sequencing achieves 100% sensitivity and 99% specificity for MSI-H in the combined training and validation set. (blogspot.com)
- Microsatellite are generally considered as the most powerful genetic marker. (pharmatutor.org)
- However, the molecular nature of microsatellite instability is not well elucidated. (bmj.com)
- Methods We examined the immune microenvironment of colon cancer using assessments of the bulk transcriptome and the single-cell transcriptome focusing on molecular nature of microsatellite stability (MSS) and microsatellite instability (MSI) in colorectal cancer from a public database. (bmj.com)
- Microsatellites consist of tandemly repeated sequence, no more than 6 bases long. (pharmatutor.org)
- 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) technology and subsequent direct analysis on an automatic sequencer. (edu.kz)
- Results: Six of 39 primary tumours showed microsatellite instability compared to 0 of 29 liver metastases (P = 0.03). (edu.kz)
- Distinct patterns of microsatellite instability are seen in tumours of the urinary tract. (ox.ac.uk)
- Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal ( Phoca hispida saimensis ), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland. (biomedcentral.com)
- Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites ( F ST = 0.107) than in maternally inherited mtDNA ( F ST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females. (biomedcentral.com)
- A robust microsatellite status-related gene signature was built to predict the prognosis and differentiate between MSI and MSS tumors. (bmj.com)
- A neural network using the expression profile of the microsatellite status-related gene signature was constructed. (bmj.com)
- The microsatellite status-related gene signature is better at predicting the prognosis of patients with colon cancer and response to the combination of immune checkpoint inhibitor-based immunotherapy and anti-VEGF therapy. (bmj.com)
- Hellemans, B. & Volckaert, F.A.M. Microsatellites and their genomic distribution, evolution, function and applications: A review with special reference to fish genetics. (pharmatutor.org)
- Microsatellite diversity within the subspecies ( H E = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. (biomedcentral.com)
- Since most microsatellites show a substantial level of polymorphism between individuals, microsatellites are extensively used for physical mapping in humans ( 28 ). (asm.org)
- For example, fragile-X syndrome , the most common type of inherited mental retardation in humans, is caused by the repetition of up to 1,000 copies of a CGG repeat in a gene on the X chromosome . (britannica.com)
- The telomeres at the ends of the chromosomes, thought to be involved in ageing / senescence , consist of repetitive DNA, with the hexanucleotide repeat motif TTAGGG in vertebrates. (wikipedia.org)
- Taken together with previously published studies, our results suggest that the amplification of microsatellite repeats is tightly associated with the differentiation and heterochromatinization of sex-specific chromosomes in sauropsids as well as in other taxa. (edu.au)
- In order to provide additional chromosomal landmarks to discriminate the A m and A chromosomes, the microsatellite repeats (GAA) n , (CAG) n , (CAC) n , (AAC) n , (AGG) n and (ACT) n were tested as FISH probes. (elsevier.com)
- The 2A m and 2A chromosomes were differentiated by the signals given by the (GAA) n , (CAG) n and (AAC) n repeats, while only (GAA) n discriminated the chromosomes 3A m and 3A. (elsevier.com)
- As potential landmarks for identifying the A m chromosomes, SSR repeats will facilitate the introgression of T. monococcum chromatin into wheat. (elsevier.com)
- Different Y chromosomes can carry varying numbers of repeats at a set of specific STRs, called a Y-STR haplotype. (le.ac.uk)
- To evaluate MSI, a reference panel was proposed at an international consensus meeting, comprised of 2 mononucleotide (BAT-25, BAT-26) and 3 dinucleotide repeats. (unboundmedicine.com)
- Microsatellite instability analysis was assessed by evaluating three (CA)n dinucleotide repeats (D2S123, D5S346, D17S250) and two mononucleotide tracts (BAT 25 and BAT 26). (nih.gov)
- Dinucleotide repeats are associated with human diseases such as Norrie's disease  , and the expansion of trinucleotide repeats is often associated with neurodegenerative disease and chromosomal fragility , such as Huntington's disease and fragile X syndrome , respectively  . (bioinformatics.org)
- The aim of our study was to relate the polymorphic (AT)(n) microsatellite in the 3' untranslated sequence of the CTLA-4 gene to diabetes risk. (lu.se)
- Although no relationship between EGFR overexpression and the length of a CA dinucleotide repeat in intron 1 was observed, a variant A13/A14 repeat sequence within the 3′-untranslated region (3′-UTR) of the EGFR gene was identified, which was mutated by either mononucleotide or dinucleotide adenosine deletions in 64% of MSI cell lines and 69% of MSI colon tumors. (elsevier.com)
- For example, the sequence TATATATATA is a dinucleotide microsatellite, and GTCGTCGTCGTCGTC is a trinucleotide microsatellite (with A being Adenine , G Guanine , C Cytosine , and T Thymine ). (wikipedia.org)
- Microsatellites are also known as simple sequence repeats (SSRs). (wikipedia.org)
- Discovered the functionality of microsatellites (simple sequence repeats) among non-coding DNA. (wikipedia.org)
- One microsatellite marker in the EF3 promoter sequence of C. albicans was previously reported ( 4 ). (asm.org)
- Descriptors are usually used along with the words sequence , repeat , tract or run . (bioinformatics.org)
- This rearrangement is a series of multiple repeats, forming a minisatellite-like structure that comprises five direct tandem repeats of a 23-bp sequence. (plantcell.org)
- Transient assays demonstrated that the 23-bp sequence motif is a target of the MYB10 protein itself, and the number of repeat units correlates with an increase in transactivation by MYB10 protein. (plantcell.org)
- The sequence of TteREP1 is related to the TcREP-class of repeats found in several other trichostrongyloid species including Trichostrongylus colubriformis and Haemonchus contortus. (elsevier.com)
- Destabilization of tetraplex structures of the fragile X repeat sequence (CGG)n is mediated by homolog-conserved domains in three members of the hnRNP family. (semanticscholar.org)
- Posted January 21, 2010) For 627 HGDP microsatellites, these files provide sequence properties, such as the structure of the repeat motif and the GC content of the flanking region. (stanford.edu)
- The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). (ucsc.edu)
- Microsatellites are regions of DNA where a short sequence is repeated in tandem with the number of repeats present varying among individuals. (usda.gov)
- Polymerase chain reaction (PCR) and DNA sequence analysis indicated that intact repeats of three, four, or five GAAAAT units were responsible for observed allele size differences. (usda.gov)
- or a tandem repeat (TR) is a concatenation of the same nucleotide sequence, called a unit. (psu.edu)
- Flow cytometry, chromosome counts and SSR marker (Simple Sequence Repeats) analysis facilitated the identification of six different haploid lines (2n = x = 9), one aneuploid line (2n = 2x+4 = 22) and one doubled haploid plant (2n = 2x = 18) of 'Clemenules' clementine. (nih.gov)
- In this study, we analyzed the influence of fragmentation and environmental changes on the population genetic structure of C. (P.) staigi using inter-simple sequence repeat polymorphisms, and the consequences for management and conservation. (fao.org)
- This simple sequence repeat (SSR) was found to completely cosegregate with the ska phenotype. (jax.org)
- STRs used in forensic science tend to be tetra- and penta-nucleotide repeats, as they are both robust, suffer less environmental degradation, and provide a high degree of error free data. (scenacriminis.com)
Polymerase chain re1
- Polymerase chain reaction-based assays can reveal these novel microsatellites and provide evidence for the presence of MSI. (wikipedia.org)
- We found that a significant subset (6/15, or 40%) of these AH lesions demonstrated evidence of monoclonal microsatellite alterations, both length variation and allele loss. (nih.gov)
- a3) Patient showing a novel allele in tumoral sample indicating the presence of microsatellite instability (marker D11S1391 - case 15). (nih.gov)
- This repeat contains nine adenines in NOD/ShiLtJ, A/HeJ, A/WySnJ, and SKH2/J and 10 adenines in A/J, and NZB/B1NJ, and likely enhances the hearing loss associated with the Cdh23 ahl allele (Johnson et al . (jax.org)
- One of these offspring did not receive the entire chromosomal segment or 'haplotype' (123‐C-G-T) associated with the parent introducing the mutation into the population due to a recombination event that shuffled the 126 allele at the microsatellite locus with the C-G-T subhaplotype. (els.net)
- The two offspring from both matings receive the disease mutation, G. Note that all the diseased individuals share the basic core C-G-T haplotype, but in the first mating, the repeat allele 126 is coinherited with this haplotype, whereas the repeat allele 123 is coinherited with this haplotype in the second mating. (els.net)
- Microsatellites in different eukaryotic genomes: survey and analysis. (bioinformatics.org)
- The microsatellite instability (MSI) phenotype is a characteristic of the hereditary nonpolyposis colorectal cancer syndrome as well as approximately 15% of sporadic colon and gastric tumors. (unboundmedicine.com)
- Microsatellite instability is found most often in colorectal cancer, other types of gastrointestinal cancer, and endometrial cancer. (cancer.gov)
- However, among eukaryote species, microsatellite repeats are more abundant and longer in vertebrates than invertebrates (Chambers and MacAvoy 2000). (thefreedictionary.com)
- Most eukaryotes have microsatellites, with the notable exception of some yeast species. (wikipedia.org)
- The microsatellite was the first sex-linked microsatellite from a lepidopteran species, and had the unusual property of being highly conserved among related crop pest species. (usda.gov)
- The most abundant SSR tracts are the homopolymer repeats poly(dA).poly(dT) and poly(dG).poly(dC). (bioinformatics.org)
- In this study, repeated dinucleotide GT n of intron 1 COL1A2 was highlighted in 55 patients with uterine fibroids (UF). (frontiersin.org)
- Microsatellite instability positive ECs frequently are associated with frameshift mutations in coding mononucleotide tracts in IGFIIR, BAX, hMSH6, and hMSH3. (nih.gov)
- We classified 7(7.3%) of 96 human gastric cancers (HGCs) as MSI-H. Screening this group of HGCs for frameshift mutations in coding mononucleotide repeats of AXIN2 and RIZ, we detected one sample harboring a frameshift mutation (1bp deletion) in exon7 of AXIN2 and four samples with frameshift mutations (1bp deletion) in the (A)9 tract of RIZ, and no mutations were found in the (A)8 tract. (aacrjournals.org)
- Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma. (cdc.gov)
- Of the 37 primer pairs defined, 16 amplified clean polymorphic microsatellites and are described. (usda.gov)
- We show that the repeat motif is capable of binding MYB10 protein in electrophoretic mobility shift assays. (plantcell.org)
- Anthropometric measures and the risk of endometrial cancer, overall and by tumor microsatellite status and histological subtype. (nextbio.com)
- As expected for a haploid fungus, a single band was observed for each microsatellite locus for all isolates. (asm.org)
- A variable nucleotide tandem repeat at position −794 comprises five to eight CATT repeats (referred to henceforth by numbers from 5 to 8, rs5844572). (springer.com)
- The CCTG repeat in the PSTPIP1 promoter may play a role in the pathogenesis of AA and of CD. (cdc.gov)
- This report summarizes the results of our efforts to generate useful induced mutants of the Philippine banana cultivars, 'Latundan' and 'Lakatan' through irradiation, and to evaluate the usefulness of DNA marker techniques, such as RAPD, microsatellites or SSR, and AFLP, to characterize the genomic alterations in induced mutants of the two Philippine banana cultivars. (fao.org)
- Microsatellite alterations are also present in the less aggressive types of adult T-cell leukemia-lymphoma. (nih.gov)
- Microsatellite alterations are important genetic events in cancer development and these alterations have been reported in the aggressive types of ATL. (nih.gov)
- In this study we investigated the role of the microsatellite alterations in the pathogenesis mediated by HTLV-1 in the different types of ATL. (nih.gov)
- None of the smoldering patients with microsatellite alterations progressed to aggressive ATL. (nih.gov)
- These results indicate that microsatellite alterations may participate in the development of the less aggressive types of ATL. (nih.gov)
Genomic library enriched1
- A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. (biomedcentral.com)
- Therefore, microsatellite marker analysis with multiplex PCR and automated procedures has a high throughput and should be suitable for large epidemiologic studies of C. albicans . (asm.org)
- In 2005 leaf samples were collected from the 52 still remaining accessions for a microsatellite (SSR) DNA marker analysis. (fao.org)
- This work was supported by National Institutes of Health grants AR049610 and HL130669 to R.B. We are grateful to the staff of the W. M. Keck Foundation DNA Sequencing Facility at Yale School of Medicine for their assistance in developing the microsatellite fragment analysis and TaqMan assay protocols. (springer.com)
- 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)
- Polymorphic microsatellite marker (PMM) analysis detected a total of 22 different allelic types for 35 isolates of P. marneffei with a high discriminatory power ( D = 0.956). (asm.org)