Define Microsatellite repeats. Microsatellite repeats synonyms, Microsatellite repeats pronunciation, Microsatellite repeats translation, English dictionary definition of Microsatellite repeats. n. 1. A short sequence of DNA consisting of multiple repetitions of a set of two to nine base pairs, used as a genetic marker when individuals differ in the...
Hybridisation-capture was used to create 12 unique alpaca DNA libraries each enriched for a different tetranucleotide microsatellite motif. Two hundred and forty nine microsatellites were found, of which 26 were polymorphic (motifs GGAT, GTTT and GCAC). Nine markers were fully characterised on 45 samples. Allele numbers ranged from 6 (Locus P135) to 12 (loci P149 and PCTD17). There was no evidence of linkage disequilibrium at any locus (p = 0.064 - 1). Deviation from Hardy-Weinberg equilibrium was observed in three loci after Bonferroni correction (PCTD17, P135 and P193). Null alleles were detected at loci P147, P193 and P194. Polymorphic information content ranged from 0.48 to 0.82. When combined, the markers had an exclusion probability of 97.7%. Two polymerase chain reaction multiplex sets comprising six and three markers each were optimized. These multiplex sets will be useful for parentage determination, and individually the markers will add to the pool of markers available for mapping of ...
The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. The reported markers provide a novel
An experimental procedure using biotin-labelled probes and streptavidin-bound magnetic beads (FIASCO) was used to produce a microsatellite-enriched library for the collembolan Orchesella villosa. PCR primers were successfully constructed for seven loci containing, respectively, five pure, one interrupted, and one compound dinucleotide microsatellite repeats. As a preliminary test of their variability, we investigated 15 individuals from 5 locations inside a dismissed mining area in southern Tuscany. All microsatellite loci showed high levels of polymorphism. The mean number of different alleles at each locus across populations was 10.1 and observed heterozygosity per locus was 0.13-0.86. Only 2 out of the 7 loci appeared to be in Hardy-Weinberg equilibrium. The potential application of these loci to test the effects of environmental contamination on the genetic structure of exposed populations is discussed.. ...
Figure 1: (a) Microsatellite instability was originally assessed using gel electrophoresis and autoradiographic detection. In the left panel, additional bands (black arrows) in the tumor lane illustrate multiple contracted microsatellite alleles relative to the genomic control lane. In the right panel, an information (heterozygous) microsatellite is shown in the genomic control sample, and a significant loss of signal intensity for the smaller allele is observed in the tumor sample, characteristic of allelic imbalance/loss of heterozygosity (LOH). (b) Microsatellite loci are now commonly assessed using fluorescent PCR amplifications, capillary electrophoresis, and automated sequencing techniques. Laser scanners detect fluorescent PCR products and generate a chromatogram displaying microsatellite allele frequencies. Note in the tumor panel, one of the alleles has undergone contraction, depicting MSI in this tumor specimen. (c) Subcloning and direct sequencing of microsatellite amplifications can ...
The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM) analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence of Mycospherlla graminicola and Fusarium graminearum. A total of 20 new microsatellite primers as easy-to-score markers were developed. Microsatellite primer PCR (MP-PCR) yielded highly reproducible and complex genomic fingerprints, with several bands ranging in size from 200 to 3000 bp. Of the 20 primers tested, only (TAGG)4, (TCC)5 and (CA)7T produced a high number of polymorphic bands from either F. graminearum or F. culmorum. (ATG)5 led to successful amplifications in M. graminicola isolates collected from Germany. Percentage of polymorphic bands among Fusarium species ranged from 9 to 100%. Cluster analysis of banding patterns of the isolates corresponded well to the established species delineations based
Despite the central significance of microsatellite mutations to issues of genomic instability, forensic testing, and population genetic analyses, the rate of origin and spectrum of effects of such mutations are still poorly understood, with many estimates being derived from reporter constructs in yeast cultures (e.g., Henderson and Petes 1992; Strand et al. 1995; Wierdl et al. 1996; Sia et al. 1997). Our long-term series of mutation-accumulation lines of C. elegans and D. pulex provide a useful platform for a more direct evaluation of the properties of microsatellite mutations in two key model organisms.. As in previous studies (Wierdl et al. 1997; Brinkmann et al. 1998; Kayser et al. 2000; Beck et al. 2003; Whittaker et al. 2003; Legendre et al. 2007), we find a strong correlation between allele size (repeat number) and mutation rate in C. elegans (Figure 1). In addition, although the variation of repeat numbers among loci sampled in D. pulex does not permit a formal evaluation of length ...
Objectives: Tumors with high-frequency microsatellite instability (MSI-H) have unique biological behavior and the predictive role of microsatellite instability (MSI) status on survival of colorectal cancer is still debated. The prognostic significance of MSI status in sporadic stage II and III rectal cancer patients needs to be more precisely defined. So we investigated the relationship between MSI status and clinicopathological features and prognosis in these patients. Methods: DNAs from fresh-frozen paired samples of tumors and corresponding normal tissue from 128 stage II and III rectal cancer patients were analyzed for MSI by PCR amplification using markers recommended by a National Cancer Institute workshop on MSI. To assess prognostic significance, Cox proportional hazards modeling was used. Results: Twelve (9.3%) tumors in our study were MSI-H, 28 (21.9%) were low-frequency MSI (MSI-L) and 88 (68.8%) were microsatellite stable (MSS). Most of the MSI-H tumors compared with MSI-L and MSS ...
Inactivation from the DNA mismatch restoration pathway manifests while microsatellite instability, a build up of mutations that drives carcinogenesis. analyzed using immunocytochemical evaluation. SNP karyotyping was utilized to review chromosomal instability. RNA silencing, Traditional western blotting and gene manifestation analysis was utilized to review the functional effects of mutations. Acute myeloid leukemia cell lines (4 of 12, 33%) and main examples (2 of 18, 11%) exhibited microsatellite instability with 925681-41-0 IC50 mono-allelic mutations in and high-risk myelodysplastic symptoms exhibited microsatellite instability. Considerably, all 11 individuals with microsatellite instability experienced cytogenetic abnormalities with 4 of these (36%) having a mono-allelic microsatellite mutation in worth cut offs had been dependant on Bonferronis multiple check correction using the threshold arranged at 0.05. Further information on Design and Strategies can be purchased in the and and in ...
Somatic and germ-line mutations: An understanding of microsatellite mutation patterns is central to their use for the accurate reconstruction of population processes. We have developed and validated an experimental approach to estimate the distribution of mutation sizes for each individual microsatellite locus. These distributions were estimated from somatic mutations observed in the tumor tissue of sporadic patients with colorectal cancer.. It is not known whether such mutations arise from the same events that produce variation in the normal population. Microsatellite instability in some cancer patients may reflect defects in mismatch repair; but, in other patients, it may be a consequence of the higher number of cell divisions that occurs in the tumor compared to the normal tissue. Nevertheless, in the absence of specific mechanistic or genetic information on the source of these mutations, it is still possible to test whether they reflect the mutation process in the general population by using ...
To date, two forms of microsatellite instability (MSI) have been described in human cancer. MSI typical of hereditary nonpolyposis colon cancer (HNPCC), is due to deficient DNA mismatch repair (MMR) and is defined with mono- and dinucleotide repeat microsatellites. A second variety of instability is best seen at selective tetranucleotide repeats (EMAST; elevated microsatellite alterations at select tetranucleotides). While MSI occurs infrequently in bladder cancers, EMAST is common. Sporadic tumours with the largest proportion showing MSI are those found most frequently in HNPCC kindreds. While bladder cancer is not frequently seen in HNPCC, upper urinary tract tumours (UTTs) are. Having previously found a low frequency of MSI in bladder cancer, we sought to determine the relative levels of MSI and EMAST in transitional cell carcinoma (TCC) of the upper and lower urinary tracts. Microsatellite analysis was performed at 10 mono- and dinucleotide and eight tetranucleotide loci, in 89 bladder and 71 UTT
TY - JOUR. T1 - Microsatellite instability and allelic imbalance in primary and secondary colorectal cancer. AU - Schneider, Anne. AU - Rohr, Serge. AU - Kelly, Michael D.. AU - Mitry, Ragai. AU - Pignatelli, Massimo. AU - Dore, Caroline J.. AU - Gaub, Marie Pierre. AU - Jaeck, Daniel. AU - Meyer, Christian. AU - Oudet, Pierre. AU - Habib, Nagy A.. PY - 2000. Y1 - 2000. N2 - Background: Several studies of colorectal cancer have shown an association between the number and type of genomic defects and the stage of disease. A subset of colorectal tumours are due to inactivation of DNA mismatch repair genes and these tumours exhibit microsatellite instability. The aim of the present study was to compare and contrast the genomic defects present in both the primary and metastatic stages of the disease using microsatellite probes. Methods: Modifications of the allelic profiles of 25 microsatellite regions were studied in a total of 85 colorectal tumours using fluorescent polymerase chain reaction (PCR) ...
Microsatellite analysis includes PCR amplification of the microsatellite loci using fluorescently labeled primers; labeled PCR products are then analyzed by capillary electrophoresis (CE) or electrophoresis to separate the alleles by size. We have more than 800 markers to choose from and will be happy to discuss them in more detail with you. We will need 10ul/marker of 30-50ng/ul DNA in Strip tubes.. We ask that all new clients either call or email Ross Wilson to discuss your projects details.. Phone: 214-648- ...
Microsatellite enrichment is a method in molecular biology used for enriching the amount of microsatellite sequences in a DNA sample. This can be achieved by designing oligonucleotide probes that hybridize with the repeats in the microsatellites and then pull out the probe/microsatellite complexes from the solution. This has been shown to be a cost-effective method to sample the genetic diversity in non-model organisms. Kaukinen KH, Supernault KJ, Miller KM (2004). Enrichment of tetranucleotide microsatellite loci from invertebrate species. Journal of Shellfish Research. 23 (2): 621. Jennings, TN; Knaus, BJ; Mullins, TD; Haig, SM; Cronn, RC (2011-06-16). Multiplexed microsatellite recovery using massively parallel sequencing. Molecular ecology resources. 11 (6): 1060-7. doi:10.1111/j.1755-0998.2011.03033.x. PMID 21676207 ...
In 10-20% of patients with colorectal cancer (CRC), carcinogenesis is due to genomic defects in the mismatch repair machinery. Defective DNA repair as a result of germ-line mutations has been linked to sporadic colorectal carcinoma, and also to those carcinomas arising in hereditary non-polyposis colorectal carcinoma (HNPCC) syndrome. In both settings, the mutations and promoter hypomethylation occur mainly in the genes hMLH1 and hMSH2 of the mismatch repair system, and result in loss of their expression.1 Further, defects in the mismatch repair process with subsequent base pair mismatches lead to microsatellite instability (MSI).1 2 Since the failure of the repair system as a cause of genomic instability is associated with a better prognosis1 3 many different microsatellite loci have been used to identify MSI in tumours for diagnostic and prognostic purposes.2 In an attempt to provide uniformity in clinical diagnoses, an international meeting at the National Cancer Institute (NCI) recommended ...
Mismatch repair protein deficiency (MMR-D) and high microsatellite instability (MSI-H) are features of Lynch syndrome-associated colorectal carcinomas and have implications in clinical management. We evaluate the ability of a targeted next-generation sequencing panel to detect MMR-D and MSI-H based on mutational phenotype. Using a criterion of ,40 total mutations per megabase or ,5 single-base insertion or deletion mutations in repeats per megabase, sequencing achieves 92% sensitivity and 100% specificity for MMR-D by immunohistochemistry in a training cohort of 149 colorectal carcinomas and 91% sensitivity and 98% specificity for MMR-D in a validation cohort of 94 additional colorectal carcinomas. False-negative samples are attributable to tumor heterogeneity, and next-generation sequencing results are concordant with analysis of microsatellite loci by PCR. In a subset of 95 carcinomas with microsatellite analysis, sequencing achieves 100% sensitivity and 99% specificity for MSI-H in the ...
The present study deals with the assessment of genetic diversity using microsatellite marker in the fish Labeo gonius from Nanak Sagar and Dhaura reservoirs of Uttarakhand having different morpho-edhaphic features and self- recruiting populations of this fish. These reservoirs are distantly located and distinctly separated without any connection having negligible possibility of gene exchange with each other. Total 12 cross amplified microsatellite primers after using software Primer-BLAST and Primer-3 were screened in all 100 DNA samples of fish collected from both the reservoirs. 12 cross amplified microsatellite primers were screened and successfully amplified. After PCR amplification of microsatellite loci and performing native PAGE using amplified DNA samples as above, POP GENE Version 1.32 was used to calculate Neis observed heterozygosity, expected heterozygosity, Neis genetic diversity, Fixation index (Fis) and Shannons information index (SI) and genetic variability indices viz. Gene flow(Nm),
Read Isolation and characterization of twelve polymorphic microsatellite loci in the buff-throated partridge (Tetraophasis szechenyii), Russian Journal of Genetics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
TY - JOUR. T1 - Kanniadu goats of Tamilnadu, India. T2 - genetic characterisation through microsatellite markers. AU - Thilagam, K. AU - Jayaraj, Rama. AU - Sivaselvam, S N. AU - Karthickeyan, S M. AU - Thangaraju, P. PY - 2006. Y1 - 2006. N2 - Characterisation of Kanniadu goats was done using microsatellite markers. The genomic DNA from 50 unrelated Kanniadu goats were PCR-amplified with a panel of 20 microsatellite markers and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining.The number of alleles ranged from 5 to 14 with allele sizes ranging from 90 to 222bp. The allele frequencies ranged from 0.0106 to 0.4480. Polymorphism information content ranged from 0.5710 to 0.8570. Except four loci, thepopulation was not in Hardy-Weinberg equilibrium. The observed heterozygosity ranged from 0.7142 to 0.9778 while the expected heterozygosity ranged from 0. 6390 to 0.8702, indicating the heterogenous nature of the population distributed in the breeding ...
Genetic diversity and relationships among 38 Iranian durum wheat accessions were analysed using conserved DNA-derived polymorphism (CDDP) and start codon targeted (SCoT) markers. A total of 10 CDDP and 10 SCoT primers were used to estimate genetic polymorphism among 38 durum wheat accessions. Comparatively, both CDDP and SCoT markers proved to be more effective and in terms of percentage of polymorphisms and polymorphic information content value were relatively similar. The average polymorphic information content value of CDDP was 0.39 which was relatively higher than those of SCoT where the respective values of polymorphic information content was 0.35. Using the neighbor joining clustering method, CDDP and SCoT markers were used to generate dendrograms, which revealed that the durum accessions were clustered into three and two major groups, respectively. According to the present results, CDDP markers proved more informative in studying genetic diversity among durum accessions. In both marker ...
Xiao Bingbing, Han Lingxia, Niu Chengming, Si Changde and Han Jianlin. 2010. Population genetic variation in BWEL-SPF chickens inferred from microsatellite DNA markers. China Animal Husbandry and Veterinary Medicine 37(9):106-111 ...
BEHEREGARAY, L. B., SCHWARTZ, T. S., MÖLLER, L. M., CALL, D., CHAO, N. L. and CACCONE, A. (2004), A set of microsatellite DNA markers for the one-lined pencilfish Nannostomus unifasciatus, an Amazonian flooded forest fish. Molecular Ecology Notes, 4: 333-335. doi: 10.1111/j.1471-8286.2004.00687.x ...
Genetic variation in three Iranian pelt sheep breeds namely: Gray Shiraz, Zandi and Karakul were investigated using fifteen microsatellite loci. Genomic DNA was extracted from 360 blood samples by extraction kits and salting-out procedure with some modifications. The total number of alleles ranged from 6 to12 in loci. The fifteen tested loci were all polymorphic in the three breeds. The average direct count of heterozygosity overall loci in each tested breed was more than the expected heterozygosity. Tests of genotype frequencies for deviation from the Hardy-Weinberg equilibrium (HWE) were performed at each locus of overall breeds and revealed significant departure from HWE (P , 0.001) due to heterozygote excess. Polymorphism information content value in Gray Shiraz, Zandi and Karakul were 0.815, 0.808 and 0.808, respectively. Rate of inbreeding within the three breeds was not noticeable (global Fis = - 0.19). Low genetic differentiation was detected by estimation of Fst index between all pairs ...
Defective DNA mismatch repair in human tumors leads to genome-wide instability of microsatellite repeats and a molecular phenotype referred to as microsatellite instability (MSI). MSI has been reported in a variety of cancers and is a consistent feature of tumors from patients with hereditary non-po …
Hybridization and/or incomplete sorting of ancestral polymorphism are commonly implicated to explain discordant phylogenetic analyses of closely related species complexes. One genus in which these phenomena have been suggested to have played major roles based on phylogenetic data is Conradina, a genus of mints (Lamiaceae) endemic to the southeastern USA containing several endangered species. The goals of this study were to use microsatellite data to better understand patterns of genetic structure in Conradina, to test hypotheses of recent or ancient hybridization and incomplete lineage sorting, and to clarify species boundaries. Individuals from 55 populations representing all Conradina species were genotyped using 10 microsatellite loci. Analyses of the patterns of genetic structure in Conradina revealed a clear differentiation of populations following recognized species boundaries, indicating that species have diverged from one another genetically and interspecific hybridization has not ...
Patterns of biodiversity and evolutionary processes controlling them are still poorly studied in desert biomes. Fine-scale markers could help answer some of the pressing research questions for desert biomes and Sahara in particular. Such markers are available for some large mammals and crocodiles, but not for small vertebrates. Here we present a battery of microsatellite loci developed for Agama boulengeri, a promising model to study evolutionary and demographic processes in the Sahara-Sahel. Loci were selected by sequencing enriched DNA libraries with 454 pyrosequencing. A total of 23 polymorphic loci were successfully amplified in four multiplex reactions. Cross-amplification of the microsatellite loci in A. agama and A. boueti was partially successful. These markers are a promising tool for assessing genetic diversity, gene-flow dynamics and demographic patterns in this group. Given the genus Agama is distributed throughout Africa, results presented here might also facilitate studies in other ...
Aberrant Wnt signaling activation occurs commonly in colorectal carcinogenesis, leading to upregulation of many target genes. APC (adenomatous polyposis coli) is an important component of the β-catenin destruction complex, which regulates Wnt signaling, and is often mutated in colorectal cancer (CRC). In addition to mutational events, epigenetic changes arise frequently in CRC, specifically, promoter hypermethylation which silences tumor suppressor genes. APC and the Wnt signaling target gene ITF2 (immunoglobulin transcription factor 2) incur hypermethylation in various cancers, however, methylation-dependent regulation of these genes in CRC has not been studied in large, well-characterized patient cohorts. The microsatellite instability (MSI) subtype of CRC, featuring DNA mismatch repair deficiency and often promoter hypermethylation of MutL homolog 1 (MLH1), has a favorable outcome and is characterized by different chemotherapeutic responses than microsatellite stable (MSS) tumors. Other epigenetic
Microsatellite instability has been observed in both sporadic and hereditary forms of colorectal cancer. In the hereditary form, this instability is generally due to germline mutations in mismatch repair (MMR) genes. However, only one in ten patients with sporadic tumours exhibiting microsatellite i …
Microsatellite loci mutate at an extremely high rate and are generally thought to evolve through a stepwise mutation model. Several differentiation statistics taking into account the particular mutation scheme of the microsatellite have been proposed. The most commonly used is R(ST) which is independent of the mutation rate under a generalized stepwise mutation model. F(ST) and R(ST) are commonly reported in the literature, but often differ widely. Here we compare their statistical performances using individual-based simulations of a finite island model. The simulations were run under different levels of gene flow, mutation rates, population number and sizes. In addition to the per locus statistical properties, we compare two ways of combining R(ST) over loci. Our simulations show that even under a strict stepwise mutation model, no statistic is best overall. All estimators suffer to different extents from large bias and variance. While R(ST) better reflects population differentiation
Alterations at microsatellite DNA markers in cells exfoliated in urine have been correlated to the presence of bladder cancer. To check the feasibility of such noninvasive analysis to routinely diagnose bladder cancers, we have developed a highly sensitive method using fluorescent PCR to search for DNA microsatellite alterations in urine sediment compared with a blood paired sample. One hundred eighty-three patients were included in our study. This population comprised 103 bladder cancers (64 pTa stages), the complement representing controls and other benign or malignant diseases. Results of the analysis at 17 loci in a blinded study were compared with cystoscopy and/or pathology. The high reproducibility of this technique and the analysis of 26 control patients allowed us to determine for each microsatellite a cutoff characterizing a significant allelic imbalance. For bladder cancer detection, the overall sensitivity of the test was 84%. Using this procedure, we identified alterations in 81%, ...
In order to identify polymorphic microsatellite markers and evaluae genetic variation within Baluchi sheep population, nineteen microsatellite loci were studied. Whole Blood samples were collected from 156 sheep at north eastern animal breeding station of Iran (Abbasabad-Mashhad). DNA was extracted by salting-out procedure with some modifications. Polymerase chain reactions were ...
Dec 21, 2009. From 7-18 December 2009, the project RER/5/015 Supporting Early Warning and Surveillance of Avian Influenza Infection in Wild and Domestic Birds and Assessing Genetic Markers for Bird Resistance, held a Regional Training Course on Genomic DNA Preparation, Microsatellite Analyses and Sequencing, at the IAEA and FAO Agriculture and Biotechnology Laboratory in Seibersdorf, Austria.. This IAEA Technical Cooperation Programme in Europe initiated a new regional programme to establish early bird-flu diagnosis and assessment of genetic markers for Avian Influenza reistsance with nuclear molecular methods in the region to prevent spread of Avian Influenza for better animal health and economic benefits.. The purpose of the training course was to enhance knowledge on highly pathogenic avian influenza (advanced molecular genetic tools by use of nuclear and nuclear related and molecular technologies), in genomic DNA preparation, microsatellite analyses and sequencing, with the ultimate goal to ...
To facilitate large-scale genetic mapping of the human genome, we have developed chromosome-specific sets of microsatellite marker loci suitable for use with a fluorescence-based automated DNA fragment analyser. We present 254 dinucleotide repeat marker loci (80% from the Genethon genetic linkage map) arranged into 39 sets, covering all 22 autosomes and the X chromosome. The average distance between adjacent markers is 13 centiMorgans, and less than 4% of the genome lies more than 20 cM from the nearest marker. Each set of microsatellites consists of up to nine marker loci, with allele size ranges that do not overlap. We selected marker loci on the basis of their reliability in the polymerase chain reaction, polymorphism content, map position and the accuracy with which alleles can be scored automatically by the Genotyper(TM) program ...
Laboratory and field protocols, and scripts used in the LEGAL laboratory.. For scripts check out our GitHub repository.. For PDF versions of protocols also check out our GitHub repository.. ...
Comparing different methods of estimating the genetic diversity could define their usefulness in plant breeding programs. In this study, a total of 18 morphological traits and 20 simple sequence repeat (SSR) loci were used to study the morphological and genetic diversity among 20 maize hybrids selected from different countries, and to classify the hybrids into groups based on molecular profiles and morphological traits. To collect morphological data, a field experiment was carried out using an RBCD design with three replications in Moghan, Ardabil, Iran. The highest estimates for genetic coefficients of variation were observed in anthesis-silking interval, followed by grain yields, leaf chlorophyll rates, kernel row numbers, and ear heights. The total number of PCR-amplified products was 84 bands, all of which were polymorphic. Among the studied primers,NC009,BNLG1108,BNLG1194,PHI026 and PHI057 showed the maximum polymorphism information content(PIC) and the greatest diversity. To determine the genetic
AIMS: To detect microsatellite abnormalities in the primary tumours and plasma of patients with breast carcinoma. METHODS: Plasma was obtained from 17 breast carcinoma patients before surgery. Corresponding tumour and benign lymph node (control) samples for each of the carcinoma patients were obtained from paraffin blocks. DNA was extracted from the plasma samples and the paraffin embedded tissue using previously described methods. RESULTS: The 17 primary tumours showed two examples of loss of heterozygosity and three examples of microsatellite instability; the 17 plasma samples showed three and one, respectively. Many of the longer microsatellites (over 200 base pairs) were difficult to amplify from plasma. The investigations suggested that this was because of the highly fragmented nature of plasma DNA. Only one example of loss of heterozygosity and one example of microsatellite instability showed a concordant pattern in both primary tumour and plasma. These were both in the same patient. ...
In total, 41 different microsatellite variants have been typed in one or more of four different sets of recombinant inbred (RI) mouse strains. Microsatellite variants were selected that were located in chromosomal regions previously lacking markers. These markers extend the regions swept in these RI strains.
Parentage Testing Procedures - DNA - $35. A DNA profile-which provides allele sizes for all microsatellite markers-is obtained, and parentage analysis is performed. A variety of sample types can be utilized for routine testing, including blood, hair, semen, buccal swabs and FTA cards. Non-routine sample types include bone, teeth, saliva, dried blood, urine and feces. DNA is extracted from the samples, and microsatellite marker analysis begins with the PCR procedure. In this process a computer program compares the DNA profile of the offspring to those of the presumed parents. A parentage analyst reviews the results and sends the final report. If a listed parent or parents are excluded, additional analysis is performed including retesting of samples and the possible use of additional DNA markers to confirm the exclusion.. *If there is any question about a kid(s) sire, i.e. more than one buck in a doe pen, All kids will be required to have a DNA test completed as well as at least one of the bucks ...
Hi bionetters I am doing research on the occurrence and polymorphism of microsatellites in co nifers. I havent found a lot of polymorphisms in GT/CA repeats or CT/GA. Howev er, I have an AT/AT microsatellite that shows a high rate of variability. There are a few problems with it though. 1) I originally isolated it as a CA-repeat that was followed by a stretch of TA s. I amplified it from the genomic DNA and found that all the products I obtain ed are shorter than the original. Then I cloned the PCR amplified fragments and sequenced them. To my surprise, the CA/GT microsatellite was not present. What was left was a stretch of TAs. Am I amplifying a microsatellite family and is the CA/GT + TA member that I cloned only a minority???? I am not so sure since I havent obtained more than 2 alleles from a single tree up to now. 2) When I PCR the plasmids containing the different AT stretches, I obtain two or more distinct bands as a result. Instability of the TA repeat in the plasmid /bacterial host ...
TY - JOUR. T1 - Band-specific localization of the microsatellite at D13S71 by microdissection and enzymatic amplification. AU - Spielvogel, H.. AU - Hennies, H. C.. AU - Claussen, U.. AU - Washington, S. S.. AU - Chakravarti, A.. AU - Reis, A.. PY - 1992/6/1. Y1 - 1992/6/1. N2 - Microsatellite DNA consists of tandemly repeated simple DNA sequence motifs, the number of these repeats being polymorphic. These recently described polymorphisms are ubiquitously distributed throughout the human genome and are highly informative, making them ideal markers for linkage analysis. Physical localization of these microsatellites is an important prerequisite for aligning physical and genetic maps. We have physically mapped the microsatellite at D13S71, which has previously been assigned to chromosome 13. Band-specific mapping of D13S71 to the distal part of band 13q32, near 13q33, was achieved by microdissection of GTG-banded chromosomes and subsequent enzymatic amplification with a heminested PCR approach. ...
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Genomic copy number changes are frequently found in cancers and they have been demonstrated to contribute to carcinogenesis; and it is widely accepted that tumors with microsatellite instability (MSI) are genetically stable and mostly diploid. In the present study we compared the copy number alterations and the gene-expression profiles of microsatellite stable (MSS) and MSI colorectal tumors. A total number of 31 fresh-frozen primary tumors (16 MSS and 15 MSI) were used. Twenty-eight samples (15 MSS and 13 MSI) were analyzed with metaphase comparative genomic hybridization (CGH), nine of which plus one additional sample (4 MSS and 6 MSI) were further analyzed by cDNA-based array-CGH. Gene expression analysis was performed with six samples [3 MSS and 3 MSI, four of these used in metaphase CGH (mCGH) analysis] to identify differentially expressed genes possibly located in the lost or amplified regions found by CGH, stressing the biological significance of copy number changes. Metaphase and ...
Immunotherapy has achieved long-term durable responses for multiple types of previously difficult-to-treat solid cancers, such as lung cancer and melanoma.40 MSI-H tumors cancer have been approved for the application of ICI such as pembrolizumab.3 Nivolumab (anti-PD1) plus ipilimumab (anti-CTLA-4) has demonstrated high response rates, improving progression-free survival and overall survival at 12 months, and is a promising treatment option for patients with dMMR MSI-H metastatic colorectal cancer.41 In contrast, MSS colon cancer seems to obtain limited benefits from immunotherapy. Chalabi et al42 tested ipilimumab plus nivolumab in early stage dMMR and pMMR colon cancers. Major pathological responses were observed in 7/7 (100%) dMMR tumors, with 4/7 (57%) complete responses, and no major pathological responses were found in pMMR tumors. Interestingly, significant increases in T-cell infiltration, particularly in CD8+ T cells, were seen post-treatment in both pMMR and dMMR tumors, indicating the ...
OBJECTIVE: To compare the potential of two diagnostic methods for detecting recurrence of urothelial cell carcinoma (UCC) of the bladder, by (i) detecting alterations in microsatellite DNA markers and loss of heterozygosity (LOH), and (ii) detecting aberrant gene hypermethylation, as UCC has a high recurrence rate in the urinary tract and the disease can invade muscle if new tumours are overlooked. PATIENTS AND METHODS: Over 1 year, urine samples were retrieved from 40 patients already diagnosed with bladder UCC (30 pTa, two pTis, eight pT1). Samples were collected 6 months after bladder tumour resection, during the follow-up schedule. We used samples to analyse nine microsatellite markers and the methylation status of 11 gene promoters. Receiver operating characteristic curves were generated and Bayesian statistics used to create an interaction network between recurrence and the biomarkers. RESULTS: During the study, 15 of the 40 patients (38%) had a tumour recurrence and 14 were identified by
Crohn disease (CD) is a chronic relapsing inflammatory condition of the gastrointestinal tract. Recently, polymorphisms in NOD2 (CARD15), a gene mapping to the chromosome 16 IBD1 susceptibility locus, have been associated with susceptibility to CD. One group identified the gene by using classic positional cloning methods. Here, we report linkage and fine mapping analyses using 27 microsatellite markers encompassing the IBD1 susceptibility locus in 131 CD affected sibling pairs, and a simplex family cohort. No evidence for linkage was observed, and microsatellite markers close to NOD2 did not show association. However, significant association was confirmed in 294 CD trios for the NOD2 variants Arg702Trp and Leu1007fsinsC. Our fine mapping study of the IBD1 locus did not enable us to identify NOD2 as a CD gene, despite the presence of association with disease-causing alleles. This study illustrates the difficulties facing microsatellite linkage and linkage disequilibrium mapping methods for identifying
Profound MSI is a hallmark of hereditary nonpolyposis colon carcinoma (HNPCC) and is also found in a proportion of sporadic HNPCC-spectrum tumors, such as endometrial carcinoma.21 The underlying cause of MSI is a defect in mismatch repair, which results in tumorigenesis through an accumulation of somatic mutations in genes important for regulating cell cycle, growth, or apoptosis. A lower level of MSI occurs in tumors that are outside the HNPCC spectrum. Previous studies of endothelial cells microdissected from plexiform lesions of PAH lungs have shown monoclonal expansion in 17 of 22 lesions (77%) from 4 patients and microsatellite mutation rates ranging from 21% for BAX to 50% for BAT26.13,15 This suggested that endothelial cell expansion in plexiform lesions is akin to neoplasia and might result from an accumulation of somatic mutations, either through MSI or other mutational mechanisms. We have now conducted similar analyses in a series of FPAH cases in whom BMPR2 has been fully ...
Microsatellite combines several features of an ultimate molecular marker and they are used increasingly in various plant genetic studies and applications. Characterization of mungbean genotypes on the basis of DNA fingerprinting has become an efficient tool to link genotypic variation. This work is reporting the utilization of a small set of five previously developed mungbean microsatellite (SSR) markers for the identification and discrimination of six HYVs and 36 landraces. All five microsatellite markers were found to be polymorphic. Variation was found in number of alleles, allele frequency, observed and expected heterozygosity. Using five primers across 42 genotypes a total of 20 alleles with an average number of 4 alleles per locus were found of which GBssr-MB91 showed highest number of alleles (6) (size ranging from 135 to 152 bp) followed by 4 alleles (from 160 to 176 bp and 175 to 195 bp) and 3 alleles (from 264 to 282 bp and 283 to 304 bp) were detected at the loci LR7322B, LR7323A, LR7323B and
A total of 83 prostate adenocarcinomas was evaluated for allelic loss on chromosome 10 by analysis of loss of polymorphic microsatellite repeats. Initially, 64 stage B carcinomas were analyzed at 12 loci on chromosome 10. Nine cases showed loss of chromosome 10 sequences, with a fractional allelic loss of 20%. These nine cases were then analyzed at an additional 19 loci to define better the regions of loss. Four areas of loss were identified, including 10p (2 of 64 cases), 10q23.1 (7 of 64 cases), 10q23.3 (4 of 64 cases), and 10q26 (2 of 64 cases). Three loci in these regions, D10S111, D10S185, and D10S192, were then analyzed in 19 advanced (stage C and D) carcinomas. Seven (37%) of 19 advanced carcinomas showed allelic loss at one or more of these loci. A statistically significant increase in the fractional allelic loss at both D10S111 (10p) and D10S185 (10q23.1) was observed. Thus, a complex pattern of loss is seen on chromosome 10 in prostate carcinoma, with regions of loss on 10p and 10q, ...
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 ...
Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. We designed |13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at
TY - JOUR. T1 - Novel Polymorphic Microsatellite Markers for Panulirus ornatus and their Cross-species Primer Amplification in Panulirus homarus. AU - Delghandi, Madjid. AU - Afzal, Hasifa. AU - Al Hinai, Manal Saif Nasser. AU - Al-Breiki, Rafaida Dhuhai Gharib. AU - Jerry, Dean R.. AU - Dao, Hoc Tan. PY - 2016/10/1. Y1 - 2016/10/1. N2 - Polymorphic microsatellite loci were isolated for Panulirus ornatus using 454 GS-FLX Titanium pyrosequencing. Fifteen markers containing perfect di-, tri-, tetra-, and penta-nucleotide motifs were consistently co-amplified in five multiplexes in a panel of 91 randomly selected samples. Observed number of alleles varied from 2 to 14 per locus. Observed and expected heterozygosity ranged from 0.090 to 0.79 and 0.08 to 0.87, respectively. Ten loci deviated from Hardy-Weinberg equilibrium after sequential Bonferroni correction. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between 11 loci. ...
TY - JOUR. T1 - Microsatellite DNA markers for the study of horseshoe crab (Limulus polyphemus) population structure. AU - King, Tim L.. AU - Eackles, Michael S.. PY - 2004/9. Y1 - 2004/9. N2 - Twenty-two microsatellite DNA loci were identified and characterized for horseshoe crabs (Limulus polyphemus) collected from two Atlantic coast and one Gulf of Mexico site. These markers revealed a high degree of genetic diversity (8-35 alleles per locus), heterozygosity (25.0% to 100.0%), and allelic heterogeneity (69.8% of comparisons). Considerable regional differentiation was observed as genetic distances (chord) ranged between 0.25 and 0.45, and all FST values (0.014-0.092) were significant. These preliminary findings are consistent with patterns of regional differentiation observed using allozyme variation and contradictory to findings of limited gene flow reported for sequence variation at the mitochondrial DNA COI region.. AB - Twenty-two microsatellite DNA loci were identified and characterized ...
Relatively few studies have investigated the genetic population structure of sea anemones. This is particularly true for sea anemones that host some of the most iconic fishes on coral reefs, the anemonefishes. One of the main reasons for this knowledge gap is the lack of appropriate genetic markers. We developed and characterized a total of 47 novel polymorphic microsatellite markers for four host sea anemone species from the Indo-Pacific: Entacmaea quadricolor (n = 16 microsatellite markers), Heteractis magnifica (n = 8), Stichodactyla mertensii (n = 13), and Stichodactyla gigantea (n = 10). Here, we report genetic diversity statistics from two different sampling locations for each anemone species. Overall, we found that most markers were highly polymorphic. On average, we found a mean of seven alleles per locus. Observed and expected heterozygosities displayed high variation among loci, ranging from 0.033 to 0.980 and from 0.038 to 0.927, respectively. Only four loci showed deviations of ...
TY - JOUR. T1 - Genetic structure of Tellicherry goats (capra hircus) based on microsatellite markers. AU - Jayaraj, Rama. AU - Sivaselvam, S N. AU - Subramanian, A. AU - Kumarasamy, P. AU - Karthickeyan, S M. AU - Thangaraju, P. PY - 2006. Y1 - 2006. N2 - Tellicherry goats were characterized by FAO recommended microsatellite markers. All 21 loci were highly polymorphic with PIC values ranging from 0.5785 to 0.8349. Significant differences (P,0.01) were noticed between observed and expected proportions of genotypes at 14 loci in the Tellicherry population studied. The highest expected heterozygosity value was 0.8504 and lowest was 0.6445 in this breed. AB - Tellicherry goats were characterized by FAO recommended microsatellite markers. All 21 loci were highly polymorphic with PIC values ranging from 0.5785 to 0.8349. Significant differences (P,0.01) were noticed between observed and expected proportions of genotypes at 14 loci in the Tellicherry population studied. The highest expected ...
Microsatellite markers from a transcriptome sequence library were initially isolated, and their genetic variation was characterized in a wild population of the mud crab (Scylla paramamosain). We then tested the association between these microsatellite markers and the growth performance of S. paramamosain. A total of 129 polymorphic microsatellite markers were identified, with an observed heterozygosity ranging from 0.19 to 1.00 per locus, an expected heterozygosity ranging from 0.23 to 0.96 per locus, and a polymorphism information content (PIC) ranging from 0.21 to 0.95 per locus. Of these microsatellite markers, 30 showed polymorphism in 96 full-sib individuals of a first generation family. Statistical analysis indicated that three microsatellite markers were significantly associated with 12 growth traits of S. paramamosain. Of these three markers, locus Scpa36 was significantly associated with eight growth traits, namely, carapace length, abdomen width (AW), body height (BH), fixed finger length of
The Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. edulis, the most important commercial Passiflora species, are still incipient. In spite of many recognized applications of microsatellite markers in genetics and breeding, their availability for passion fruit research remains restricted. Microsatellite markers in P. edulis are usually limited in number, show reduced polymorphism, and are mostly based on compound or imperfect repeats. Furthermore, they are confined to only a few Passiflora species. We describe the use of NGS technology to partially assemble the P. edulis genome in order to develop hundreds of new microsatellite markers. A total of 14.11 Gbp of Illumina paired-end sequence reads were analyzed to detect simple sequence repeat sites in the sour passion fruit genome. A sample of 1300 contigs containing perfect repeat microsatellite
The oval squid Sepioteuthis lessoniana is one of the most economically important squid species in Japan; however, its population structure is poorly understood due to the lack of hypervariable markers. Such information is critical for managing sustainable fisheries, as well as for ensuring the existence of wild S. lessoniana stocks. Eleven candidate microsatellite loci were isolated from a small insert genomic DNA library. Polymorphisms in these 11 loci were screened in 24 wild individuals. The number of alleles per locus was found to range from 5 to 19 alleles, and the observed heterozygosity ranged from 0.292 to 0.958. No evidence for linkage disequilibrium was detected among all the loci. The genotypic proportions conformed to Hardy-Weinberg equilibrium, except at one locus. In conclusion, these polymorphic microsatellite loci may be used to develop a genetic framework to manage S. lessoniana in the future.
Evans, K. M. , Bates, S. S. , Medlin, L. and Hayes, P. K. (2004): . Microsatellite marker development and genetic variation in the toxic marine diatom Pseudo-nitzschia multiseries (Bacillariophyceae). , Journal of Phychology ...
The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic
The Use of DNA Microsatellite Markers for Genetic Diversity Identification of Soybean (Glycine max (L) Meriil.) as a Supplementary Method in Reference Collections Management
A total of 10,089 simple sequence repeat (SSR) loci were identified from 81,072 Illumina-based transcriptomic unigenes of white calla lily (Zantedeschia aethiopica), an evergreen ornamental plant of Zantedeschia section Zantedeschia, cultivated worldwide. Of these SSRs, dinucleotide repeats were the most common type (63.43%), followed by trinucleotide repeats (35.02%). Microsatellite motifs AG/CT and AGG/CCT separately predominated in dimeric and trimeric repeat motifs. PCR primer pairs were successfully designed for 5104 SSR loci with appropriate flanking sequences. To validate the usefulness of SSRs in white calla lily, 153 perfect markers (repeat length ≥20 bp) were selected, of which 120 yielded stable and repeatable products, while the remaining failed to generate any clear DNA products. Twenty-seven SSR markers were then randomly selected to assess genetic diversity in 16 white calla lily accessions and cross-species transferability in 16 colored calla lily cultivars of Zantedeschia ...
Mercurialis annua is a wind-pollinated annual plant that has long been used as a model for the study of ploidy and sexual-systems evolution. However, no molecular markers are yet available for genetic studies of its diploid populations. Here, we develop and characterize a set of eight polymorphic microsatellite markers for diploid dioecious M. annua. Following an SSR-enrichment protocol, 13 microsatellite markers were proposed, eight of which yielded successful amplification and polymorphism. We screened the eight microsatellite loci in 100 individuals. The number of alleles per marker ranged from 6 to 12, and observed heterozygosity ranged from 0.57 to 0.76. To estimate potential allele scoring errors, these individuals offspring were genotyped for the same loci, and error rates were estimated from parentage analyses. Error rates ranged from 0 to 6.8%. Cross-amplification tests were performed for congeneric M. huetti and M. canariensis, with successful amplification for
MTILENI, B.J. et al. A comparison of genetic diversity between South African conserved and field chicken populations using microsatellite markers. S. Afr. j. anim. sci. [online]. 2010, vol.40, n.5, pp.462-466. ISSN 2221-4062.. The objective of the study was to determine genetic diversity within South African indigenous chicken populations and the effectiveness of the current conservation flocks in capturing the available diversity in the founder populations. Two chicken populations, Venda (VD_C) and Ovambo (OV_C) conservation flocks (n = 56) from the Animal Production Institute in Irene and two founder population from which these conservation flocks were sampled; Venda (VD_F) and Ovambo (OV_F) field populations (n = 72) were genotyped for 29 autosomal microsatellite markers. All microsatellites typed were found to be polymorphic. A total of 213 alleles were observed for all four populations. The mean number of alleles per population ranged from 3.52 ± 1.09 (VD_C) to 6.62 ± 3.38 (OV_F). Mean ...
In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers ...
A Phase III Study of Pembrolizumab (MK-3475) vs. Chemotherapy in Microsatellite Instability-High (MSI-H) or Mismatch Repair Deficient (dMMR) Stage IV Colorectal Carcinoma (KEYNOTE-177)
The whole broodstock of two Hungarian common carp farms-80 and 196 individuals-was analyzed by using random amplified polymorphic DNA (RAPD) assay and microsatellite analysis. Ten polymorphic RAPD markers and four microsatellites were selected to genotype both of the stocks. As expected, microsatellite analysis revealed more detailed information on genetic diversities than RAPD assay. Results obtained with both types of DNA markers showed lack of major differences between the genetic structure of the two stocks: heterozygosity values and allele frequencies were very similar. Dendrograms created from both sets of data did not show grouping of individuals according to stocks. Genotypes from the two stocks were also compared to those from a limited number of samples collected from other hatcheries and two rivers. Allele frequencies in the groups were similar, with the exception of wild carps. An interesting observation was that three private microsatellite alleles were found in the eight wild carp ...
Title: Microsatellite Instability (MSI) as Genomic Marker in Endometrial Cancer: Toward Scientific Evidences. VOLUME: 10 ISSUE: 14. Author(s):A. Tinelli, V. Mezzolla, G. Leo, M. Pisano, F. Storelli, G. Alemanno, A. Malvasi, S. Tommasi, G. Ronzino and V. Lorusso. Affiliation:Department of Gynecology and Obstetric, Division of Experimental Endoscopic Surgery, Imaging, Minimally Invasive Therapy&Technology, Vito Fazzi Hospital, P.zza Muratore, 73100 Lecce, Italy.. Keywords:Endometrial cancer, microsatellite instability, MSI, HNPCC, endometrial hyperplasia, Lynch sindrome, genomics, proteomics, laparoscopy, endoscopy, Genomic Marker, tumors, menopause, hyperestrogenism, Lynch Syndrome, Hereditary NonPolyposis Colorectal Cancer, DNA replication, neoplastic transformations, gynecological cancers, malignant uterine cancers, uterine tumors, MisMatch Repair genes, MMR genes, replication errors in repeats, adenomas, Familiar Adenomatous Polyposis, breast cancer, National Cancer Institute, ...
Seagrasses are one of the most productive and economically important habitats in the coastal zone, but they are disappearing at an alarming rate, with more than half the worlds seagrass area lost since the 1990s. They now face serious threat from climate change, and there is much current speculation over whether they will survive the coming decades. The future of seagrasses depends on their ability to recover and adapt to environmental change-i.e. their resilience. Key to this, is understanding the role that genetic diversity plays in the resilience of this highly clonal group of species. To investigate population structure, genetic diversity, mating system (sexual versus asexual reproduction) and patterns of connectivity, we isolated and characterised 23 microsatellite loci using next generation sequencing for the Australian seagrass species, Zostera muelleri (syn. Z. capricorni), which is regarded as a globally significant congeneric species. Loci were tested for levels of variation based ...
Thirteen new microsatellite loci were isolated and tested on two land snail species, Trochulus villosus and T. sericeus (Pulmonata: Hygromiidae), resulting in a set of eight polymorphic markers for each species. The expected heterozygosity was high for all loci and species (between 0.616 and 0.944). Such levels of variability will allow detailed insights into the population genetic structure of some Trochulus species.
Cowpea [Vigna unguiculata (L.) Walp] is an important grain legume crop grown for its protein rich grains. It is an inexpensive source of protein in the diets of people in sub-Saharan Africa. The International Institute of Tropical Agriculture (IITA) has been working on the improvement of cowpea for more than 30 yr. Over 60 countries receive cowpea cultivars improved by IITA for testing and adoption where needed. Many of these cultivars have identical parentage but look very different morphologically when grown in the field. Forty-six microsatellite DNA markers were used to evaluate genetic similarities among 90 cowpea breeding lines developed at IITA. Twenty-seven primer pairs could amplify polymorphic single-locus microsatellites from all of these materials. Two to seven alleles per primer were detected with a polymorphic information content varying from 0.02 to 0.73. By means of only five polymorphic microsatellite primers, 88 of the 90 cowpea lines could be distinguished. A dendrogram based ...
Anmarkrud, Jarl Andreas; Kleven, Oddmund; Bachmann, Lutz & Lifjeld, Jan Terje (2008). Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10. BMC Evolutionary Biology. ISSN 1471-2148. 8(138) . doi: 10.1186/1471-2148-8-138 Vis sammendrag BACKGROUND Microsatellites are frequently used genetic markers in a wide range of applications, primarily due to their high length polymorphism levels that can easily be genotyped by fragment length analysis. However, the mode of microsatellite evolution is yet not fully understood, and the role of interrupting motifs for the stability of microsatellites remains to be explored in more detail. Here we present a sequence analysis of mutation events and a description of the structure of repeated regions in the hypervariable, pentanucleotide microsatellite locus HrU10 in barn swallows (Hirundo rustica) and tree swallows (Tachycineta bicolor). RESULTS In a large-scale parentage analysis in barn ...
Jabon merah (Anthocephalus macrophyllus Roxb) is an endemic tree to Sulawesi having high economic value. It has rarely been investigated, either in genetic population or genetic consevation aspects. The information regarding genetic diversity is very important in order to gain more understanding for breeding and conservation strategies. Genetic diversity is used as material selection of expected genotype. The study was aimed to determine genetic diversity of Jabon merah from Sulawesi provenances that will be used in further development of this species. Leaf samples were collected from 108 families of Jabon merah belong to Sulawesi provenances. Four out of ten microsatellite markers that had high polymorphism were used for amplifying the 108 DNA samples. Results showed alleles number and mean of allele were 3 to 4 alleles and 3,5, respectively. Moreover, PIC mean of the evaluated loci was 3,7. The analysis of genetic relationship showed that the 108 families had moderate level of genetic ...
Anopheles culicifacies sensu lato is an important vector of malaria in Southeast Asia contributing to almost 70% of malaria cases in India. It exists as morphologically similar sibling species A, B, C, D and E with varied geographical distribution patterns. Vector control measures have been difficult for this important vector as the sibling species have developed varying levels of resistance to the currently used insecticides. In view of the importance of this vector, we developed and validated a set of microsatellite markers and the same were used to analyze the population genetic structure of five different geographical populations of An. culicifacies A. Anopheles culicifacies A samples were collected from different localities across India, and genotyping was performed using eight microsatellite markers on ABI Prism 310 Genetic Analyzer. Several statistical analyses were performed to ascertain the genetic diversity that exists within and between the populations. The markers were found to be moderately
TY - JOUR. T1 - Mismatch repair deficiency in hematological malignancies with microsatellite instability. AU - Gu, Liya. AU - Cline-Brown, Brandee. AU - Zhang, Fujian. AU - Qiu, Lu. AU - Li, Guo Min. N1 - Funding Information: We thank Steve Presnell and Cecilia Ramilo for helpful comments on the manuscript. This work was supported in part by grants CA85377 (from the National Cancer. PY - 2002. Y1 - 2002. N2 - Mutations in human mismatch repair (MMR) genes are the genetic basis for certain types of solid tumors displaying microsatellite instability (MSI). MSI has also been observed in hematological malignancies, but whether these hematological malignancies are associated with MMR deficiency is still unclear. Using both biochemical and genetic approaches, this study analysed MMR proficiency in 11 cell lines derived from patients with hematological malignancies and demonstrated that six out of seven hematological cancer cell lines with MSI were defective in strand-specific MMR. In vitro ...
In an analysis of the PETACC-8 trial reported by Taieb et al in JAMA Oncology, BRAF V600 and KRAS mutations were associated with shorter disease-free and overall survival in patients with microsatellite-stable colon cancer-but not in those with tumors with microsatellite instability-in the setting of adjuvant therapy. The PETACC-8 trial showed that the addition of cetuximab to FOLFOX4 (leucovorin, fluorouracil, and oxaliplatin) did not improve disease-free survival in patients with KRAS exon 2 wild-type disease.. Study Details. The analysis included patients with available tumor blocks from among the total of 2,599 patients in the trial. Microsatellite instability was found in 9.9% (177 of 1,791; microsatellite-stable tumors in 1,614 [90.1%]), KRAS mutation was found in 33.1% (588 of 1,776), and BRAF V600E mutation was found in 9.0% (148 of 1,643) of cases.. Outcome by Mismatch Repair and Mutation Status. In multivariate analysis, no significant prognostic effect for disease-free survival or ...
Background: Germline mutations in DNA mismatch repair (MMR) genes cause Lynch syndrome colon and extra-colonic cancers. Less understood is the risk of colon cancer associated with common polymorphisms in MMR genes and the potential interacting role of lifestyle factors known to damage DNA. Methods: We examined whether MLH1 (-93G,A and Ile219Val) and MSH6 (Gly39Glu) polymorphisms were associated with risk of colon cancer in data from 1,609 colon cancer cases and 1,972 controls. Genotype data were further stratified by microsatellite instability status, smoking, alcohol, Western-diet, alcohol, and obesity, to investigate potential heterogeneity.. Results: The MSH6 39Glu allele was associated with increased risk of colon cancer among men (Gly/Glu or Glu/Glu vs Gly/Gly odds ratio (OR): 1.27; 95% confidence interval (CI): 1.04-1.54). Neither MLH1 polymorphism was associated with colon cancer risk overall. When stratified by microsatellite stability status, however, the MLH1 -93 A allele was ...
Alemu, T. 2004. Genetic characterization of indigenous goat populations of Ethiopia using Microsatellite DNA markers. PhD thesis. Haryana, India: National Dairy Research Institute, Deemed University ...
Read Molecular structure of the allelic variants of (AAT)n microsatellite locus Du47D in the parthenogenetic species Darevskia unisexualis and bisexual parental species D. valentini and D. raddei, Russian Journal of Genetics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
In this study, we developed 134 novel polymorphic polynucleotide-repeat microsatellite markers for silver carp (Hypophthalmichthys molitrix) and characterized 40 loci for polymorphism and genetic diversity in a test population. The number of alleles per locus ranged from 3 to 19 (mean 9.4), and the average observed and expected heterozygosities were 0.74-0.76, respectively. Thirty-five loci were highly informative (PIC > 0.5) in silver carp population. After Bonferroni adjustments, no pairs of loci showed evidence of significant linkage disequilibrium, and none of the loci significantly deviated from the Hardy-Weinberg equilibrium. All 134 silver carp microsatellite loci could be successfully amplified in bighead carp (Hypophthalmichthys nobilis) with 65 loci being polymorphic, indicating a high transferability of these microsatellites across species. This set of novel highly polymorphic polynucleotide-repeat microsatellites would be powerful tools for population and conservation genetics ...
Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units) are present within exonic sequences of ,350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement with previous computational analyses of germ-line biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA ...
TY - JOUR. T1 - Allelic imbalance and microsatellite instability in resected Dukes D colorectal cancer. AU - Kochhar, Ruby. AU - Halling, Kevin C.. AU - McDonnell, Shannon. AU - Schaid, Daniel J.. AU - French, Amy J.. AU - OConnell, Michael J.. AU - Nagorney, David M.. AU - Thibodeau, Stephen N.. PY - 1997/4/1. Y1 - 1997/4/1. N2 - Hepatic resection is the treatment of choice for selected patients with liver metastases from colorectal cancer (CRC). Although the 5-year survival rate among patients after liver resection is 25-45%, 55-75% of patients die from progressive disease. The purpose of this study was to characterize molecular genetic alterations, including microsatellite instability and allelic imbalance, in patients with potentially curative resected liver metastases from CRC and to correlate these molecular features with clinical and pathologic characteristics. We examined DNA from formalin-fixed, paraffin-embedded archival tumor specimens from 141 surgically resected hepatic metastases ...
Fruit breeding programs usually use controlled hand pollination among cultivars and advanced selections for obtaining segregating populations to select new cultivars. In sweet cherries, however, sometimes in controlled pollination few hybrids are obtained. Caging whole trees with bees and flowers of the pollinating cultivar is sometimes used to obtain larger hybrid populations. To generate large segregating populations for the Chilean Sweet Cherry Breeding Program (run by the Consortium of BioFrutales S.A. and Instituto de Investigaciones Agropecuarias), the initial strategy was to harvest seeds from open pollinated self-incompatible cultivars maintained at the germplasm collection orchard of Univiveros, one of the leading fruit tree nurseries in Chile. While the female parent is known, the male parent is unknown. The pollen source will depend on the cultivars present in the area, the flowering time and the compatibility of the cultivars involved. In order to identify pollinators of the ...
In the present study, seven populations of J. regia were characterized using 11 highly polymorphic microsatellite markers. The average number of alleles per locus was 5.73, much higher than 1.3 and 3.9 detected in J. regia with RAPDs (Nicese et al., 1998) and ISSRs (Potter et al., 2002), respectively. For all loci, the observed numbers of alleles was lower than that reported in J. nigra (Victory et al., 2006), the species from which the markers were originally developed (Woeste et al., 2002). This may be because of the large number of samples and populations analyzed in previous J. nigra studies or because SSRs may show a decrease in allele number when applied in related species (Ana et al., 2000). For most of the loci, the length ranges of the amplification products obtained here were wider than those detected in J. nigra (Victory et al., 2006), a bias reported in other species as well (Donini et al., 1998).. Although a great number of population genetic studies have been conducted on Juglans ...
The SSR enriched library was constructed from the genotype TMV2 following by modified method of Fischer and Bachmann [23]. This library was enriched for CA and CT SSR repeat motifs. From this library, 3,072 clones were picked from 32 96-well plates. Hybridization of these clones with digoxigenin-labeled SSR probes (CA and CT) provided 720 (23.4%) putatively positive clones. Sequencing of these clones indicated the insert size in the range of 50 bp to 792 bp with an average size of 309 bp. Majority of clones (43.9%) contained the insert of moderate size (200 bp-400 bp) while 34.6% clones contained small inserts (50 bp-200 bp) and 21.5% clones contained inserts of , 500 bp.. Analysis of sequence data mentioned above with Tandem Repeat Finder (TRF) had 490 (68%) clones which contained one or more SSRs. The efficiency of the enrichment procedure for the constructed library was higher as compared to other SSR isolation studies of groundnut. Like the present study, 61% of clones were found to contain ...
PV mediated by simple sequences or microsatellites is a common feature of many bacteria, but, in Hi, a conspicuous feature is the predominance of tetranucleotide repeat tracts. In this report, we show that mutation of Hi polI, but not of seven other Hi genes, whose products are involved in MMR or other pathways of DNA repair or recombination, increases PV rates mediated by a tetranucleotide repeat tract. Conversely, loss of MMR activity, but not of polI activity, increased PV rates mediated by a dinucleotide repeat tract. This is the first report of a trans‐acting factor that alters PV rates in Hi, and also demonstrates that this bacterial species has apparently uncoupled the hypermutability of tetranucleotides that mediate PV from some important MMR functions. In the context of the biology of commensal and virulence behaviour of pathogenic bacteria, these findings are of particular interest because it has been proposed that mutations in MMR genes are an important source of adaptive evolution ...
TY - JOUR. T1 - Accuracy and sensitivity of DNA pooling with microsatellite repeats using capillary electrophoresis. AU - Breen, G AU - Sham, P AU - Li, T AU - Shaw, D AU - Collier, D A AU - St Clair, D PY - 1999. Y1 - 1999. N2 - DNA pooling is a genetic screening method that combines DNA from many individuals in a single polymerase chain reaction (PCR) reaction to generate a representation of allele frequencies. The substantial saving in effort with DNA pooling over individual genotyping facilitates linkage disequilibrium scanning of the human genome using many thousands of genetic markers, and is applicable to mapping of complex diseases such as schizophrenia. However, the literature to date has not addressed several crucial technical aspects of DNA pooling. These include: DNA quantification; the choice of electrophoresis methods; sensitivity (the minimum reliably detectable difference between poets); and methods of dealing with plus-A stutter. We have examined these points and make ...
Background: Colorectal malignancies with high microsatellite instability (MSI-H), either hereditary (Lynch syndrome) or sporadic, demonstrate better prognosis and altered response to 5FU chemotherapy. It is now recommended to perform MSI testing for all new cases of colorectal cancer regardless of being categorized as hereditary or sporadic. For MSI detection, immunohistochemistry or PCR-based protocols using a cohort of various sets of STR markers are recommended. Here we aimed to evaluate a simplified protocol using just a single STR marker, MT1XT20 mononucleotide repeat, for detection of MSI in Lynch syndrome patients. A Promega five-marker MSI testing panel and immunohistochemistry (IHC) were used as the gold standard in conjunction with MT1XT20. Materials and Methods: Colorectal patients with a positive history of familial cancers were selected by evaluating medical records. Based on Amsterdam II criteria for Lynch syndrome 20 families were short listed. DNA was extracted from formalin ...
TY - JOUR. T1 - Microsatellite analysis of childhood brain tumors. AU - Blaeker, Hendrik. AU - Rasheed, B. K.Ahmed. AU - McLendon, Roger E.. AU - Friedman, Henry S.. AU - Batra, Surinder K.. AU - Fuchs, Herbert E.. AU - Bigner, Sandra H.. PY - 1996/1. Y1 - 1996/1. N2 - Loss of heterozygosity at specific chromosomal locations has been taken as evidence of a tumor suppressor gene located in that area. We performed a genomic allelotyping study on 46 childhood brain tumors of different histopathological types in order to identify and confirm common areas of deletion in different tumor types. Two hundred microsatellite DNA probes equally distributed over the 22 autosomes were applied, covering the genome in steps of approximately 25 cM. Our results confirm frequent loss of heterozygosity of chromosome arms 9q, 10q, 11p, 11q, 16q, and 22q in high- grade gliomas, medulloblastomas, and ependymomas. In addition, we found a new region of loss on chromosome segment 2p21-23 affected predominantly in high- ...
The Guineagrass (Panicum maximum Jacq.) is one of the most important tropical forage grasses, but genetic knowledge and tools regarding this species are still limited. Therefore, 20 novel polymorphic microsatellite markers were developed, validated, and employed in estimating genetic relationships among 25 P. maximum genotypes selected from a Brazilian germplasm collection. In addition, they were tested for cross-species amplification in four other forage grass species. The number of alleles observed for each locus ranged from 4 to 12 (average 6.7). The values of polymorphism information content (PIC) varied from 0.41 to 0.83 (average 0.61) and the discriminating power (D) ranged from 0.53 to 0.98 (average 0.72). Cross-amplification demonstrated the potential transferability of these microsatellites to four tropical forage grass species. Cluster analysis based on the unweighted pair group method revealed three distinct groups: two clusters consisted of P. maximum genotypes and a third cluster, ...
Citation: Arias De Ares, R.S., Stetina, S.R., Tonos, J.L., Scheffler, J.A., Scheffler, B.E. 2010. Microsatellites Reveal Genetic Diversity in Reniform Nematode Populations. National Cotton Council Beltwide Cotton Conference, New Orleans, Louisiana, January 4-7, 2010 Interpretive Summary: Technical Abstract: Reniform nematode (Rotylenchulus reniformis) is the predominant parasitic nematode of cotton in the Mid South area of the United States. To document genetic variability within this species, we developed microsatellite-enriched libraries and designed 192 simple sequence repeats (SSR) markers for reniform nematode. The markers were tested on six reniform nematode cultures that originated in Texas, Louisiana, Mississippi and Georgia. Based on performance we selected 156 SSR markers for reniform nematode, 88 of which were polymorphic across the six reniform nematode populations. The most frequent motif was the dinucleotide AG. The polymorphic information content of the markers ranged from 0.00 to ...
Freeman, JS and Potts, BM and Shepherd, M and Vaillancourt, RE (2006) Parental and consensus linkage maps of Eucalyptus globulus using AFLP and microsatellite markers. Silvae Genetica, 55 (4-5). pp. 202-217. ISSN 0037-5349 ...
Diversity in crops provides opportunity for plant breeders to develop new and improved cultivars with desirable characteristics, genetic improvement for existing varieties thus meet subsistence food requirement. DNA marker is reliable in genetic diversity study due to variations at sequence level, not influenced by environment and its expression in all tissues. Marker used in our study is Inter Simple Sequence Repeats (ISSR) for 30 different accessions of white yam including dwarf, semi dwarf and tall. Cluster analysis was done based on Euclidean distance of 30 accessions for ISSR, Dendrogram showed the partition of most of the dwarf and tall genotypes in to two different clusters and semi dwarf comes under the dwarf cluster. The ISSR primers produced an average of six polymorphic alleles with a mean Hobs and PIC values of 0.738 and 0.707 respectively. The higher PIC and Hobs values obtained in the present study for ISSR markers indicate high variability of population studied. Hence, ISSR markers can be
use str analysis in a sentence, and str analysis meaning 1. The power of STR analysis comes from looking at multiple STR loci simultaneously. 2. The true power of STR analysis is in its statistical power of discrimination. click for more sentences of str analysis...