• The 17 Y-STR loci included in the AmpFLSTR Yfiler PCR Amplification Kit were analyzed in 98 unrelated healthy males from Apulia (Southern Italy). (nih.gov)
  • We identified 24 unique individuals from 234 feces collected at nine microsatellite loci. (nature.com)
  • Microsatellite markers, or short tandem repeats (STR), are polymorphic DNA loci containing repeated nucleotide sequences, typically from 2 to 7 nucleotides per unit. (igbiosystems.com)
  • Short tandem repeats (STRs), also called microsatellites, are polymorphic DNA loci present throughout the genome and used for linkage mapping studies, association studies, and identification of organisms. (igbiosystems.com)
  • The microsatellite haplotypes within HG were constructed using 7 STR loci. (blogspot.com)
  • Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. (biomedcentral.com)
  • To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. (biomedcentral.com)
  • Analyzing approximately 1.6 million STR loci, we estimate the empirical de novo STR mutation rate to be 5.24 × 10 −5 mutations per locus per generation. (biomedcentral.com)
  • It is possible that each of these mechanisms contributes to the high mutation rate of STRs, but strand slippage is the mechanism proposed for generating most observed mutations in STR loci [ 19 ]. (biomedcentral.com)
  • Due to the repetitive structure of STRs and their high mutability, sequencing and genotyping these loci is difficult, especially using short-read sequencing data. (biomedcentral.com)
  • Some of these tools are designed to detect STR expansions at disease-related loci, while others detect expansions and contractions of STRs genome-wide but are constrained by sequencing read length and the STR motif size. (biomedcentral.com)
  • It was shown that these 5 microsatellite loci were polymorphic and could differ among the investigated populations. (sibran.ru)
  • The success of sequence mapping pattern from STR loci are TPOX, THO1, and CS1PO according to each GC content. (unair.ac.id)
  • We investigated the patterns of mate choice in 26 wild-living breeding pairs of gray wolf (Canis lupus) that were identified through noninvasive genetic methods and genotyped at 3 MHC class II and 12 autosomal microsatellite (STR) loci. (datadryad.org)
  • Fitness values were positively correlated with heterozygosity of the breeders at both MHC and STR loci, whereas they decreased with relatedness at STRs. (datadryad.org)
  • The 2X STR Master Mix allows for even and reliable multiplex PCR analysis of microsatellite loci. (mclab.com)
  • In addition to these points, Y-STR loci are linked, meaning that evaluation of haplotype probabilities are either based on overly simplified counting methods or computationally costly genetic models, neither of which extend well to the evaluation of mixed Y-STR data. (edu.au)
  • We developed NanoSTR for detection of target STR loci based on the length-number-rank (LNR) information of reads. (researchsquare.com)
  • Although NanoSTR needs further optimization and development, it is useful as an analytical method for the detection of STR loci by nanopore sequencing. (researchsquare.com)
  • These highly individual-specific number of repeats and the abundance of motifs have contributed to the polymorphism of STR loci. (researchsquare.com)
  • On average, STR loci occur every 15 kb in the human genome. (researchsquare.com)
  • Prior to the application of any DNA based identification method, it is essential to estimate the allele frequencies and forensic statistical parameters of targeted STR loci in each population in order to provide a more precise reference database for forensic investigation. (edu.au)
  • In this study, we are presenting an analysis of GlobalFiler STR loci on 209 unrelated individuals from Serbia. (edu.au)
  • By using a panel of 24 microsatellite loci previously developed and adapted to the genus Papio I could show that the cross-species amplification of microsatellites allows for the fast and easy generation of nuclear genetic data in geladas. (uni-goettingen.de)
  • The resulting panel of 42 microsatellite loci can be applied to all catarrhine primates and facilitates the fast and accurate generation of nuclear genetic data from various sample sources including such with low-quality DNA. (uni-goettingen.de)
  • 2004). Characterization and haplotype analysis of 10 novel Y-STR loci in Chinese Han population. (geneticsmr.com)
  • 2009). Decreased rate of evolution in Y chromosome STR loci of increased size of the repeat unit. (geneticsmr.com)
  • Variation in short tandem repeat sequences - a survey of twelve microsatellite loci for use as forensic identification markers. (geneticsmr.com)
  • The vast amount of data emerging for thousands of microsatellite markers across organisms makes microsatellite analysis a widely accepted tool for linkage and association studies, and also for identifying individual organisms (i.e., human identification or HID). (igbiosystems.com)
  • To date, highly variable markers such as microsatellites have only been developed for the photobionts of two lichen species, namely Lobaria pulmonaria (L.) Hoffm. (bioone.org)
  • We show that the assignment power of a large STR multiplex can be outperformed by an optimised SNPs panel having five times more markers. (europa.eu)
  • To assess if the behavioral difference between the family and kenneled dogs could be due to genetic divergence of these two populations and/or to lower genetic diversity of the kenneled dogs, we analyzed their genetic structure using 11 microsatellite markers. (frontiersin.org)
  • In genetic diversity studies, the most frequently used markers are microsatellites. (intechopen.com)
  • A battery of 14 microsatellite markers was used to carry out parentage tests of 256 progeny individuals including two independent samples of selected trees and one control unselected sample, all derived from 6-year-old forest stands in eastern Brazil. (springer.com)
  • Brondani RPV, Brondani C, Tarchini R, Grattapaglia D (1998) Development and mapping of microsatellite based markers in Eucalyptus. (springer.com)
  • Right now, parentage testing is done by an analysis of microsatellite markers (STR testing). (wbfsh.com)
  • The transition from microsatellite to SNP markers in parentage testing is not trivial and will require some efforts. (wbfsh.com)
  • Today, most studbooks use microsatellite markers for parentage testing. (wbfsh.com)
  • Markers tested by SNP chips can also be used for parentage testing, but the transition from microsatellite to SNP markers will require some efforts. (wbfsh.com)
  • We identified six regions on chromosomes 2, 3, 4, 7, 11 and 14 as candidates to contain genes involved in breast cancer susceptibility, and additional fine mapping genotyping using microsatellite markers around linkage peaks confirmed five of them, excluding the region on chromosome 3. (biomedcentral.com)
  • Genomewide linkage scans have traditionally been performed using low-density maps of microsatellite markers with a spacing of about 10 cM across the genome [ 1 ]. (biomedcentral.com)
  • We show the existence of different candidate regions linked to a small number of families, and a power improvement by using SNPs instead of microsatellite markers. (biomedcentral.com)
  • Five microsatellite markers ( BWF1, Cisco-90, Cisco-126, Cisco-157, Cisco-200 ) had a good representation in populations of vendace from five Latvian lakes (Sventes, Raznas, Nirzas, Dridzas, Stirnu) and were used for genetic analysis of these populations. (sibran.ru)
  • Microsatellite markers are very valuable in population genetics, conservation genetics, and phylogenetic research. (vajiramandravi.com)
  • In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. (biomedcentral.com)
  • These sequences, also called microsatellites, are a class of genetic markers consisting of tandem sequence repeats with a size of two to seven base pairs. (genomia.cz)
  • Method and Materials: This study was conducted by analysing DNA damage patterns using CODIS STR (Short Tandem Repeat) markers to effect the decay process. (unair.ac.id)
  • We tested for deviations from random mating and evaluated the covariance of genetic variables at functional and STR markers with fitness proxies deduced from pedigree reconstructions. (datadryad.org)
  • NanoSTR showed high performance for detection of target STR markers. (researchsquare.com)
  • Because of their high diversity, wide distribution, and high polymorphism, STRs are considered as the second generation of genetic markers after restriction fragment length polymorphisms (RFLP). (researchsquare.com)
  • The method uses statistical analysis methods such as multisampling and the length-number-rank (LNR) information of reads for the genotyping and correction of STR markers with improved accuracy (Fig. 1). (researchsquare.com)
  • In wildlife studies, the current markers of choice are often still microsatellites. (uni-goettingen.de)
  • A large number of microsatellite genetic markers have been identified in the human leukocyte antigen (HLA) region. (geneticsmr.com)
  • microsatellite A type of satellite DNA consisting of a relatively short sequence of tandem repeats, in which certain motifs (ranging in length from one to six or more bases) are repeated, typically 5-50 times. (wikipedia.org)
  • Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
  • They are also known as short tandem repeats (STRs) or simple sequence repeats (SSRs). (vajiramandravi.com)
  • The number of repeats at a certain microsatellite locus might vary greatly between people in a population because microsatellite DNA is highly variable. (vajiramandravi.com)
  • The alleles of STR locus change according to the number of repeats of the given sequence motive. (genomia.cz)
  • This laboratory is one of the few in Spain that has Quality Certification based on UNE-EN ISO 9001:2015 Standards, and with ENAC accreditation based on UNE-EN ISO/IEC 17025:2017 standards for the "Genetic profile identification, identity and parentage verification using microsatellite analysis (Short tandem repeats or STRs) and AME marker by means of PCR and capillary electrophoresis" for equines. (usprea.com)
  • Short tandem repeats (STRs) are widely present in the human genome. (researchsquare.com)
  • Short tandem repeats (STRs), also known as microsatellites, are repetitive DNA sequences consisting of 1-6-bp motifs present in a genome. (researchsquare.com)
  • Autosomal short tandem repeats (STRs) have been widely used in forensic investigations. (edu.au)
  • Public databases were screened to develop ultra-efficient microsatellite (STR) and single nucleotide polymorphism (SNP) panels for parentage assignment. (europa.eu)
  • Search for the polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and copy number variation (CNV). (hinv.jp)
  • Therefore, STR detection has been widely used in forensic identification, paternity testing, species polymorphism identification, and genetic disease diagnosis (1)(2)(3)(4) . (researchsquare.com)
  • 2004). Study of polymorphism at new Y-STR DYS605 in a Chinese Han population of Shanxi. (geneticsmr.com)
  • Allele frequencies for each Y-STR locus in pooled sample and estimated value of gene diversity (GD) were evaluated. (nih.gov)
  • Often Y-STR profiles are used when autosomal profiling has failed to yield an informative result. (edu.au)
  • For all of these reasons Y-STR data analysis has not seen the same advances as autosomal STR data. (edu.au)
  • The 6-dye GlobalFiler™ PCR Amplification kit (ThermoFisher Scientific) comprises 21 autosomal STRs have already been proven to be able to provide reliable DNA profiling results and enhance the power of discrimination between individuals. (edu.au)
  • Microsatellites are small DNA sequences made up of repeating units. (vajiramandravi.com)
  • To determine the genetic profile, tandem repetitive sequences (STR) are used. (genomia.cz)
  • Microsatellite DNA is utilised in genetic analysis, more specifically in molecular genetics and genomics. (vajiramandravi.com)
  • Brinkmann B, Klintschar M, Neuhuber F, Huhne J, Rolf B (1999) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. (springer.com)
  • NanoSTR can be used for STR detection and genotyping based on long-read data from nanopore sequencing with improved accuracy and efficiency compared with other existing methods, such as Tandem-Genotypes and TRiCoLOR. (researchsquare.com)
  • There are a few methods for STR identification based on nanopore sequencing, and the representative software are Tandem-Genotypes (11) , NanoSatellite (12) , STRique (13) , etc. (researchsquare.com)
  • Tandem-Genotypes requires data preprocessing steps such as LAST alignment and establishment of a genomic background database, and histograms are needed to assist STR genotyping. (researchsquare.com)
  • We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants. (biomedcentral.com)
  • Phylogenetic analysis showed that TR 34 /L98H/S297T/F495I isolates from 2 patients with pulmonary aspergillosis (isolates B44 and B51 in 2012, isolates E071, E073, and E074 in 2015) ( Figure ) belonged to a local microsatellite genotype widely distributed in the environment of Taiwan ( 3 ), indicating that this clone has locally evolved and adapted to the environment. (cdc.gov)
  • Their high heterozygosity has made STRs a valuable tool in forensics. (biomedcentral.com)
  • Based on analysis of microsatellite haplotypes within main Y- chromosomal haplogroups, molecular diversity within monophyletic lineages were calculated and phylogenetic trees for most common haplogroups were reconstructed. (blogspot.com)
  • This method adds to the toolbox for nanopore-based STR analysis and expands the applications of nanopore sequencing in scientific research and clinical scenarios. (researchsquare.com)
  • For example, NanoSatellite directly analyzes STRs based on electric current distribution, and the accuracy of analysis depends heavily on the stability of the sequencing current and the precision of the basecalling model. (researchsquare.com)
  • The second study presented here deals with several problems that have been identified in the past for the analysis of microsatellites. (uni-goettingen.de)
  • We are performing our standard fragment analysis services utilizing an ABI 3730xl protocol that has been specifically developed and optimized for Microsatellite and MLPA applications. (harvard.edu)
  • 2001). DNA commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs. (geneticsmr.com)
  • 2006). DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. (geneticsmr.com)
  • Studies have confirmed that STRs are associated with more than 30 diseases, and they have also been used in forensic identification and paternity testing. (researchsquare.com)
  • Population genetics: Microsatellite DNA can be used to study the genetic diversity of populations. (vajiramandravi.com)
  • Taylor, D , Bright, J-A & Buckleton, J 2016, ' Using probabilistic theory to develop interpretation guidelines for Y-STR profiles ', Forensic Science International: Genetics , vol. 21, pp. 22-34. (edu.au)
  • abstract = "Y-STR profiling makes up a small but important proportion of forensic DNA casework. (edu.au)
  • 13 seabream and 14 seabass STRs mapped in different linkage groups were selected to be amplifiable in a single tube. (europa.eu)
  • The results were compared with those obtained previously using a 10 cM microsatellite scan (STR-GWS) and we found lower or not significant linkage signals with STR-GWS data compared to SNP data in all cases. (biomedcentral.com)
  • Alternatively, significant linkage may have been missed as a result of sub-optimal coverage of the genome by the STR marker set used, which may not have extracted all the inheritance information contained in the dataset. (biomedcentral.com)
  • 1 medical azoles (itraconazole, voriconazole, posaconazole, and isavuconazole) were defined as azole-resistant A. fumigatus and examined for resistance mechanisms, microsatellite-based phylogenetic relatedness, and growth rates following previously described methods ( 3 , 4 ). (cdc.gov)
  • Genetic relatedness among Aspergillus fumigatus isolates based on microsatellite genotyping, Taiwan. (cdc.gov)
  • Researchers can analyse the genetic structure, population dynamics, and evolutionary relationships among various species of animals by analysing microsatellite DNA. (vajiramandravi.com)
  • Further, microsatellites are often not species-specific and can be amplified across species boundaries. (uni-goettingen.de)
  • This allows for the fast and easy implementation of a microsatellite panel in closely related species with comparatively little effort. (uni-goettingen.de)
  • To test the ease of implementation for a microsatellite panel in a cross-species approach and whether the usage of microsatellites can provide a sufficient amount of data, I conducted a study in geladas to investigate their population genetic structure. (uni-goettingen.de)
  • Additionally, the situation in non-human catarrhine primates is further complicated as many different microsatellite panels have been analyzed across and within species. (uni-goettingen.de)
  • Therefore, I present the development and validation of a microsatellite panel that can be universally applied to all catarrhine species incorporated into a genotyping-by-sequencing approach. (uni-goettingen.de)
  • In practice, however, the high error rate and special data characteristics of long-read sequencing have limited the efficient identification of STR polymorphisms, and therefore, further evaluation of the analytical methods is required (9)(10) . (researchsquare.com)
  • Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. (biomedcentral.com)
  • STRs are distributed throughout the genome and are located in both coding and non-coding regions [ 2 ]. (biomedcentral.com)
  • Genetic mapping: Microsatellite DNA can be used to map the location of genes in the genome. (vajiramandravi.com)
  • Microsatellites are widespread throughout most organisms' genomes and tend to have higher mutation rates than other regions. (wikipedia.org)
  • A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) to estimate Y-STR mutation rates. (nih.gov)
  • We present here a probabilistic model for the interpretation of Y-STR data. (edu.au)
  • Due to the fact that probabilistic systems for Y-STR data are still some way from reaching active casework, we also describe how data can be analysed in a continuous way to generate interpretational thresholds and guidelines. (edu.au)
  • However, there are few methods for STR detection based on nanopore sequencing due to the challenges posed by the sequencing principles and the data characteristics of nanopore sequencing. (researchsquare.com)
  • In terms of data characteristics, NanoSTR effectively avoids the non-random sequencing errors and unexpected insertions-deletions (indels) associated with nanopore sequencing (8)(9) and thus improves the efficiency of sequencing data utilization, the detection rate of STR genotypes, and the accuracy of STR profiling. (researchsquare.com)
  • For selected applications (Microsatellite and MLPA), we also offer the final data interpretation as an add-on service for samples labeled with 6-FAM. (harvard.edu)
  • On-site data interpretation (Microsatellite and MLPA applications only! (harvard.edu)
  • Git repository for the paper : Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural networks. (lirmm.fr)
  • Overall, this thesis highlights the applicability of microsatellites in wildlife studies and specifically provides a new tool to analyze nuclear genetic variation in non-human catarrhine primates. (uni-goettingen.de)
  • 2009). The effects of Asian population substructure on Y STR forensic analyses. (geneticsmr.com)
  • Forestry Institute, Lithuanian Research Centre for Agriculture and Forestry, Liepu Str. (mdpi.com)
  • Microsatellites are highly abundant in eukaryote genomes, the majority is located in the non-coding parts of the genomes and therefore assumed to evolve neutrally without selection pressure. (uni-goettingen.de)
  • 2004). A comprehensive survey of human Y-chromosomal microsatellites. (geneticsmr.com)
  • Studies have shown that STRs represent a source of phenotypic variations in more than 30 Mendelian diseases, such as neurological disorders (5)(6) . (researchsquare.com)
  • Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information. (biomedcentral.com)