scholarly journals The Polymorphism Analyses of Short Tandem Repeats as a Basis for Understanding the Genetic Characteristics of the Guanzhong Han Population

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Shuyan Mei ◽  
Yanfang Liu ◽  
Congying Zhao ◽  
Hui Xu ◽  
Shuanglin Li ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Principal Component ◽  
Individual Identification ◽  
Scaling Analysis ◽  
Dna Index ◽  
Genetic Characteristics ◽  
Han Population ◽  
Allelic Frequencies ◽  
Str Loci ◽  
Short Tandem

The short tandem repeat (STR) loci are polymorphic markers in the combined DNA index system (CODIS) and non-CODIS STR loci. Due to the highly polymorphic characteristic of STR loci, they are popular and widely used in forensic DNA typing laboratories. In this study, 22 STR loci (1 CODIS, 21 non-CODIS STR loci) and an Amelogenin locus were genotyped and analyzed in 590 unrelated individuals of the Guanzhong Han population. None of the 22 STR loci deviated from the Hardy–Weinberg equilibrium, and all the loci were in the linkage equilibrium state. We observed 247 alleles, and the corresponding allelic frequencies ranged from 0.0008 to 0.3695 in the Guanzhong Han population. The combined power of discrimination and the cumulative exclusion probability was 0.999 999 999 999 999 999 999 999 999 346 36 and 0.999 999 999 709 74, respectively. The results including Nei’s D A genetic distance, multidimensional scaling analysis, and principal component analysis showed that the Guanzhong Han population has closer genetic affinities with Northern Han, Chengdu Han, and Xinjiang Hui groups from China based on allelic frequencies of 15 overlapped STR loci from Guanzhong Han and 13 reference groups. The present results indicated that Microreader™ 23sp ID kit included highly polymorphic loci, and it could be well used for individual identification, paternity testing, and population genetics in the Guanzhong Han population.

scholarly journals Forensic efficiency estimate and phylogenetic analysis for Chinese Kyrgyz ethnic group revealed by a panel of 21 short tandem repeats

2018 ◽  
Vol 5 (6) ◽  
pp. 172089 ◽  
Author(s):  
Yuxin Guo ◽  
Chong Chen ◽  
Tong Xie ◽  
Wei Cui ◽  
Haotian Meng ◽  
...  
Keyword(s):  
Ethnic Group ◽  
Phylogenetic Trees ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Forensic Genetics ◽  
Genetic Relationships ◽  
Individual Identification ◽  
Forensic Sciences ◽  
Dna Index ◽  
Short Tandem

Short tandem repeats (STRs) with a high level of polymorphisms and convenient detection method play an indispensable role in human population and forensic genetics. Recently, we detected the 21 autosomal non-combined DNA index system (non-CODIS) STR loci in a Kyrgyz ethnic group, calculated their forensic parameters and analysed its genetic relationships with reference populations from China. In total, 168 alleles were observed at 21 non-CODIS STRs with corresponding allelic frequencies from 0.0016 to 0.4788. No significant deviations at these STRs were observed from the Hardy–Weinberg equilibrium. The values of cumulative power of discrimination and probability of exclusion for all the 21 non-CODIS STRs were 0.99999999999999999998835 and 0.9999994002, respectively. Furthermore, the analyses of phylogenetic trees, genetic distances and interpopulation differentiations demonstrated that the Kyrgyz group had relatively close genetic relationships with the Uygur and Kazak groups. These 21 non-CODIS STRs were characterized by high genetic diversities in the Kyrgyz group and could be applied as a robust tool for individual identification and kinship testing in forensic sciences.

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.

Characterization of human short tandem repeats (STRs) for individual identification using the Ion Torrent

2015 ◽  
Vol 9 (2) ◽  
pp. 164-172 ◽  
Author(s):  
Seri Lim ◽  
Jong Pil Youn ◽  
Sang Ok Moon ◽  
Youn Hyung Nam ◽  
Seung Bum Hong ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Individual Identification ◽  
Ion Torrent ◽  
Short Tandem

Mutation analysis of 21 autosomal short tandem repeats in Han population from Hunan, China

2019 ◽  
Vol 46 (3) ◽  
pp. 254-260
Author(s):  
Wei Xu ◽  
Yuequn Wang ◽  
Dandan Zhang ◽  
Daixin Wang ◽  
Liang Zhou ◽  
...  
Keyword(s):  
Mutation Analysis ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Han Population ◽  
Autosomal Short Tandem Repeats ◽  
Short Tandem

Distributions of Allelic Frequencies and Haplotypes of Two New Y-STR Loci in a Chinese Han Population

2003 ◽  
Vol 48 (4) ◽  
pp. 2003068
Author(s):  
X. D. Wang ◽  
H. L. Dai ◽  
Y. P. Hou ◽  
J. P. Tang ◽  
Q. F. Zhu ◽  
...  
Keyword(s):  
Chinese Han Population ◽  
Chinese Han ◽  
Han Population ◽  
Allelic Frequencies ◽  
Str Loci

Distributions of Allelic Frequencies and Haplotypes of Three New STR Loci in a Chinese Han Population

2004 ◽  
Vol 49 (6) ◽  
pp. 1-1
Author(s):  
Z. J. Jia ◽  
Y. B. Li ◽  
H. Li ◽  
X. P. Zhou ◽  
W. J. Zhang ◽  
...  
Keyword(s):  
Chinese Han Population ◽  
Chinese Han ◽  
Han Population ◽  
Allelic Frequencies ◽  
Str Loci

Mutation analysis of 19 autosomal short tandem repeats in Chinese Han population from Shanghai

2016 ◽  
Vol 130 (6) ◽  
pp. 1439-1444 ◽  
Author(s):  
Chengchen Shao ◽  
Mingxi Lin ◽  
Zhihan Zhou ◽  
Yueqin Zhou ◽  
Yiwen Shen ◽  
...  
Keyword(s):  
Mutation Analysis ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Chinese Han Population ◽  
Chinese Han ◽  
Han Population ◽  
Autosomal Short Tandem Repeats ◽  
Short Tandem

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.

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.

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