scholarly journals The Landscape of Human STR Variation

2014 ◽  
Author(s):  
Thomas F. Willems ◽  
Melissa Gymrek ◽  
Gareth Highnam ◽  
The Genomes Project ◽  
David Mittelman ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Phase 1 ◽  
Genetic Diseases ◽  
Point Mutations ◽  
Graphical Interface ◽  
Loss Of Function ◽  
Human Reference Genome ◽  
Str Loci ◽  
Classical Point ◽  
Short Tandem

Short Tandem Repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across over 1,000 individuals in phase 1 of the 1000 Genomes Project. This process nearly saturated common STR variations. After employing a series of quality controls, we utilize this call set to analyze determinants of STR variation, assess the human reference genome?s representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations. The resource is publicly available at http://strcat.teamerlich.org/ both in raw format and via a graphical interface. 

scholarly journals Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 381 ◽  
Author(s):  
Olivier Tytgat ◽  
Yannick Gansemans ◽  
Jana Weymaere ◽  
Kaat Rubben ◽  
Dieter Deforce ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Massively Parallel Sequencing ◽  
Flow Cell ◽  
Nanopore Sequencing ◽  
Flow Cells ◽  
Pattern Complexity ◽  
Str Loci ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies ◽  
Short Tandem

Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost, but genotyping is inaccurate, partially due to the occurrence of homopolymers in STR loci. The goal of this study was to apply the latest progress in nanopore sequencing by Oxford Nanopore Technologies in the field of STR genotyping. The experiments were performed using the state of the art R9.4 flow cell and the most recent R10 flow cell, which was specifically designed to improve consensus accuracy of homopolymers. Two single-contributor samples and one mixture sample were genotyped using Illumina sequencing, Nanopore R9.4 sequencing, and Nanopore R10 sequencing. The accuracy of genotyping was comparable for both types of flow cells, although the R10 flow cell provided improved data quality for loci characterized by the presence of homopolymers. We identify locus-dependent characteristics hindering accurate STR genotyping, providing insights for the design of a panel of STR loci suited for nanopore sequencing. Repeat number, the number of different reference alleles for the locus, repeat pattern complexity, flanking region complexity, and the presence of homopolymers are identified as unfavorable locus characteristics. For single-contributor samples and for a limited set of the commonly used STR loci, nanopore sequencing could be applied. However, the technology is not mature enough yet for implementation in routine forensic workflows.

scholarly journals SHORT TANDEM REPEATS (STRs) AS A PRIMARY METHOD FOR PERSONAL IDENTIFICATION (A Case Report)

2013 ◽  
Vol 1 (1) ◽  
Author(s):  
Johannis Mallo
Keyword(s):  
Police Officers ◽  
Tandem Repeats ◽  
Personal Identification ◽  
Str Loci ◽  
Indonesian Population ◽  
Buccal Swabs ◽  
Paternity Index ◽  
Left And Right ◽  
Dna Pcr ◽  
Short Tandem

Abstrak: Mayat seorang perempuan tak dikenal yang ditemukan di daerah Malalayang dibawa oleh polisi ke Rumah Sakit Umum Pusat Prof.dr.R.D Kandou. Mayat tersebut telah mengalami proses awal pembusukan. Selain itu pihak kepolisian mengalami kesulitan untuk menentukan identitas mayat tersebut serta menemukan keluarganya. Demi pengungkapan kejadian yang menyebabkan kematian perempuan tak dikenal ini, terlebih dahulu polisi harus dapat menentukan identitas mayat. Melalui data medis yang dikumpulkan dari proses autopsi forensik, digabungkan dengan daftar orang hilang yang dibuat oleh kantor kepolisian Sektor Malalayang dan Kepolisian Kota Besar Manado, ditemukan kecocokan data yang merujuk pada seorang perempuan yang dilaporkan hilang oleh keluarganya. Polisi kemudian meminta pemeriksaan identifikasi melalui metode analisis DNA untuk membandingkan DNA mayat dengan DNA individu-individu yang mengaku sebagai keluarga korban. Pada saat autopsi forensik, diambil sampel tulang padat iga kanan dan kiri sepanjang 10 cm dari mayat. Sebagai pembanding diambil apusan mukosa pipi dan 2 cc darah tepi dari individu-individu yang diduga ayah dan adik kandung dari mayat yang ditemukan. Proses ekstraksi, kuantifikasi, PCR, dan proses analisis akan dilakukan di Pusat Laboratorium Forensik Kepolisian Republik Indonesia. Kata kunci: identitas mayat, identifikasi DNA, PCR, STR.     Abstract: Ms X’s corpse was brought to Prof.R.D Kandou general hospital by police officers. Ms X was found in Malalayang without any identity attached to her body. Her body had begun to decompose, and the police had difficulties in finding Ms X’s relatives. In order to uncover the case behind Ms X’s death, the police had to first discover the true identity of Ms X. Medical data was acquired during an autopsy, and from a list that the police made, a match was found in a report of missing persons when two data were compared. The Police requested a paternity DNA examination in order to have a positive identification of Ms X. During the forensic autopsy of Ms X, 10 cm of left and right costal compact bones were obtained. Buccal swabs were made and 2 cc of peripheral blood were taken, each from the suspected father and a suspected sister of Ms X. Extraction, quantification, PCR, and the analysis was made at Pusat Laboratorium Forensik Kepolisian Republik Indonesia the main Police Forensic Laboratory of Indonesia. PCR involves 13 to 15 of nuclear STR loci, and the analyzing process of the samples involves comparing the 13 to 15 nuclear STR loci of the 3 people. If a match is found with 99% accuracy, then identification is verified. The Paternity Index indicates the greatest possibility that the suspected father is the real father of Ms X, compared to other males in the Asian / Indonesian Population.1 Keywords: corpse identity,  DNA identification, PCR, STR.

Double- and single-strand conformation polymorphism analysis of point mutations and short tandem repeats

1994 ◽  
Vol 15 (1) ◽  
pp. 566-571 ◽  
Author(s):  
Francisco Barros ◽  
Ignacio Muñoz-Barús ◽  
Maria V. Lareu ◽  
Maria S. Rodriguez-Calvo ◽  
Angel Carracedo
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Point Mutations ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Polymorphism Analysis ◽  
Conformation Polymorphism Analysis ◽  
Conformation Polymorphism ◽  
Short Tandem

Estimation of the Y-chromosomal short tandem repeat (Y-STR) mutation rates in Turkey

2018 ◽  
Vol 43 (2) ◽  
pp. 142-150
Author(s):  
Elif Mertoglu ◽  
Gonul Filoglu ◽  
Tolga Zorlu ◽  
Ozlem Bulbul
Keyword(s):  
Y Chromosome ◽  
Tandem Repeats ◽  
Turkish Population ◽  
Mutation Rates ◽  
Forensic Sciences ◽  
Str Loci ◽  
Kinship Relations ◽  
Unchanged Form ◽  
Short Tandem

Abstract Background: The Non-recombining region of the Y-chromosome (NRY) is transferred from father to son in an unchanged form without recombination in meiosis. Since Short tandem repeats on Y-chromosome (Y-STRs) in this region do not have any recombination, these regions are identical in all male individuals who are related to the father except for mutations. Therefore, these regions gain importance in identification for the forensic sciences or determination of paternity. In determination of paternity, if mismatches are observed between father and child, population-specific mutation rates should be used to determine whether it is a mutation or a true exclusion. Therefore in this study, we aim to determine the mutation rates of 17 Y-STR loci in Turkey. Material and methods: 17 Y-STR loci were typed by using AmpFlSTR® Yfiler™ Kit in 90 volunteer father-son pairs. Mutation rates were calculated and compared with other populations. Results: The mutations were found between three father-son pairs at DYS439 and DYS458 loci. In addition, a duplication in DYS389 II loci* 30, 31 was observed. The average mutation rate was determined as 1.96×10−3 for Turkish population. Conclusion: This investigation will contribute to minimize the possibility of false exclusion of the father-son and kinship relations.

scholarly journals A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Zhongzi Wu ◽  
Huanfa Gong ◽  
Mingpeng Zhang ◽  
Xinkai Tong ◽  
Huashui Ai ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Nucleotide Polymorphisms ◽  
Loss Of Function ◽  
Sequencing Data ◽  
Wild Boars ◽  
A Genome ◽  
Average Annual Temperature ◽  
Short Tandem

Abstract Background Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs. Results This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such as AHR, LAS1L and PDK1. Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window. Conclusions This study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation.

scholarly journals Genome-wide profiling of heritable and de novo STR variations

2016 ◽  
Author(s):  
Thomas Willems ◽  
Dina Zielinski ◽  
Assaf Gordon ◽  
Melissa Gymrek ◽  
Yaniv Erlich
Keyword(s):  
Tandem Repeats ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Genetic Diseases ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Genome Wide ◽  
A Genome ◽  
Short Tandem

AbstractShort tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, STRs have proven problematic to genotype from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping, haplotyping, and phasing STRs from whole genome sequencing data and report a genome-wide analysis and validation of de novo STR mutations.

Male Individualization Based on Y-Chromosomal Short Tandem Repeats: A Comparative Information Theoretical Analysis of 16 Y-STR Loci in Central Anatolia and Iraqi Populations

2015 ◽  
Vol 15 (4) ◽  
pp. 157-171
Author(s):  
Aysun Baransel Isir ◽  
Abdulmuttalip Ozkorkmaz ◽  
Cesur Baransel ◽  
Ebru Gokalp Ozkorkmaz ◽  
Sacide Pehlivan
Keyword(s):  
Theoretical Analysis ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Central Anatolia ◽  
Str Loci ◽  
Comparative Information ◽  
Short Tandem

scholarly journals Efficiency of Tetrameric Short Tandem Repeats in Prestice Black-Pied Pig for Traceability and Parentity Testing

2016 ◽  
Vol 64 (2) ◽  
pp. 557-565
Author(s):  
Irena Vrtková ◽  
Štěpán Vrtek ◽  
Lenka Falková
Keyword(s):  
Information Content ◽  
Polymorphism Information Content ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Genetic Resource ◽  
Marker Panel ◽  
Str Loci ◽  
Related Individuals ◽  
Crossbred Pigs ◽  
Short Tandem

The main goal of the research was to evaluate suitability of 11 tetrameric STRs (Short Tandem Repeats) marker panel for the Prestice Black-Pied pig (PC) breed as the only genetic resource in the Czech Republic.The analysis was carried out in 522 breeding and slaughter PC individuals. We observed 94 alleles overall across whole 11 STR panel. The observed heterozygosityHOwas 0.677, the polymorphism information content (PIC) was in average 0.664 per locus. The probability of identity of two independent samples (PI) using all 11 STR loci was 4.037·10−11and the probability of identity related individuals (PISibs) was 8.315·10−5. The power of exclusion for loci combinations when both parents are known (P1), when only one of the parent is known (P2) and for two putative parents (P3) were 0.9996, 0.9899 and 0.9999. The efficiency of the 11 tetrameric STRs (Animaltype Pig kit) is higher in PC in comparison to commercial breeds and slaughter crossbred pigs. In genetic resource PC, the 11 STRs panel is usable for forensic purpose such parentity testing and traceability.

scholarly journals Sibling Indices as Comparisons in Personal Identification Process through Short Tandem Repeats [STR] Loci CSF1PO, THOI, TPOX, vWA of Maduranese Ethnic in Surabaya

2021 ◽  
Vol 6 (2) ◽  
pp. 60318
Author(s):  
Ahmad Yudianto ◽  
Fery Setiawan ◽  
Simon Martin Manyanza Nzilibili
Keyword(s):  
Observational Study ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Personal Identification ◽  
Allele Sharing ◽  
Blood Samples ◽  
Identification Process ◽  
Str Loci ◽  
Calculation Results ◽  
Short Tandem

Sibling indices can be used as a comparison through alleles Short Tandem Repeats [STR] loci. This is an observational study among Maduranese with 4 STR loci (CSF1PO, THOI, TPOX, vWA) obtained from their blood samples. The percentage of alleles shared: 82.5% [33 times] with 2 allele sharing, 12.5% [5 times] with 1 allele sharing, and 5 % [2 times] with 0 sharing alleles. Sibling indices (SI) calculation results: 65% of sibling indices pairs have SI greater than 100 and 15% of them were between 10-100 (strong and very strong). Sibling indices interpretation is supported; therefore, the claimed sibling indices relationships were indeed true among Maduranese ethnic group in Surabaya.

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