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

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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Mutation rates at Y chromosome short tandem repeats in Texas populations

Forensic Science International Genetics ◽

10.1016/j.fsigen.2009.01.007 ◽

2009 ◽

Vol 3 (3) ◽

pp. 179-184 ◽

Cited By ~ 47

Author(s):

Jianye Ge ◽

Bruce Budowle ◽

Xavier G. Aranda ◽

John V. Planz ◽

Arthur J. Eisenberg ◽

...

Keyword(s):

Y Chromosome ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Mutation Rates ◽

Short Tandem

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GENETIC POLYMORPHISM OF 23 Y-CHROMOSOME SHORT TANDEM REPEAT LOCI IN THE KINH POPULATION OF VIETNAM

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/16/2/13431 ◽

2018 ◽

Vol 16 (2) ◽

pp. 223-229

Author(s):

Ha Huu Hao ◽

Nguyen Duc Nhu ◽

Chu Hoang Ha ◽

Le Van Son ◽

Le Tuan Anh ◽

...

Keyword(s):

Y Chromosome ◽

Tandem Repeats ◽

Gene Diversity ◽

Haplotype Diversity ◽

Genetic Distances ◽

Reference Database ◽

Sample Population ◽

Forensic Application ◽

Str Loci ◽

Short Tandem

Y-chromosome microsatellites or short tandem repeats (STRs) have been proved to be ideal markers to delineate the differences between individuals in human population. Nowadays, Y-STR testing using the PowerPlex® Y23 amplification kit is considered as an extremely sensitive analysis method and has the potential to be used to perform forensic caseworks, and to explore the complexity in population substructures. However, little is known about the forensic Y-chromosome databases in the Vietnam population. In this study, 23 Y-STR loci (DYS576, DYS389I, DYS389 II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS393, DYS458 DYS456, DYS643, YGATAH4, and DYS385a/b) were investigated in 120 non-related males of the Kinh population in Northern Vietnam using PowerPlex® Y23 system kit (Promega). Our results showed that allele frequencies of 23 loci in the sample population, with the calculated average gene diversity (GD) for each locus, ranged from 0.24 (DYS438) to 0.92 (DYS385a/b). In addition, a total of 120 different haplotypes were found, all of them were unique. Therefore, we found that the haplotype diversity was 1 with a discrimination capacity of 100%, which serves as an essential prerequisite for using Y-chromosomal STR with PowerPlex® Y23 System kit in forensic application in Vietnam. We also compared genetic distances between Kinh population and 10 other neighboring populations from Y-chromosome haplotype reference database (YHRD). The Kinh population is significantly different from other populations. In conclusion, it was indicated that the 23 Y-STR loci were highly genetically polymorphic in the Kinh population in Vietnam and might be of great value in forensic application.

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Maximum likelihood estimation of locus-specific mutation rates in Y-chromosome short tandem repeats

Bioinformatics ◽

10.1093/bioinformatics/btq367 ◽

2010 ◽

Vol 26 (18) ◽

pp. i440-i445 ◽

Cited By ~ 7

Author(s):

O. Ravid-Amir ◽

S. Rosset

Keyword(s):

Maximum Likelihood ◽

Maximum Likelihood Estimation ◽

Y Chromosome ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Likelihood Estimation ◽

Mutation Rates ◽

Specific Mutation ◽

Short Tandem

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Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

Journal of Molecular Evolution ◽

10.1007/pl00006229 ◽

1997 ◽

Vol 45 (3) ◽

pp. 265-270 ◽

Cited By ~ 49

Author(s):

Anna Pérez-Lezaun ◽

Francesc Calafell ◽

Mark Seielstad ◽

Eva Mateu ◽

David Comas ◽

...

Keyword(s):

Population Genetics ◽

Y Chromosome ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Short Tandem

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Sex-Specific Migration Patterns in Central Asian Populations, Revealed by Analysis of Y-Chromosome Short Tandem Repeats and mtDNA

The American Journal of Human Genetics ◽

10.1086/302451 ◽

1999 ◽

Vol 65 (1) ◽

pp. 208-219 ◽

Cited By ~ 85

Author(s):

Anna Pérez-Lezaun ◽

Francesc Calafell ◽

David Comas ◽

Eva Mateu ◽

Elena Bosch ◽

...

Keyword(s):

Y Chromosome ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Migration Patterns ◽

Asian Populations ◽

Central Asian ◽

Short Tandem

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The Landscape of Human STR Variation

10.1101/004671 ◽

2014 ◽

Cited By ~ 1

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.

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Contribution of ABO-Rhesus/Electrophoresis of hemoglobin methods and Short Tandem Repeats analysis in the determination of paternity in Burkina Faso, West Africa

10.21203/rs.3.rs-41454/v1 ◽

2020 ◽

Author(s):

Missa Millogo ◽

Serge Theophile Soubeiga ◽

Bapio Valerie Jean Telesphore Bazie ◽

Theodora Mahoukede Zohoncon ◽

Albert Theophane Yonli ◽

...

Keyword(s):

Tandem Repeat ◽

Short Tandem Repeat ◽

High Performance ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Repeat Analysis ◽

Paternity Index ◽

Genetic Analyzer ◽

Short Tandem

Abstract Background: the establishment of filiation by the current ABO, HLA, MNS, Kells and serum tests, pose a real reliability problem. It is then necessary to combine these methods with or to use high-performance methods such as microsatellite genetic analysis or short tandem repeats. This study aimed to compare the short tandem repeat technique with ABO/Rhesus system in combination with electrophoresis of hemoglobin. Methods: Fourteen (14) contested paternity trios were investigated. Blood samples were collected to determine blood groups using the Beth-Vincent method and the type of hemoglobin by electrophoresis. Blood spots on FTA paper were used for the analysis of 16 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, Amel) by capillary electrophoresis on the ABI 31310 Genetic Analyzer. The generated sequences were analyzed with GeneMapper® software version 3.2.1. The data were analyzed to determine the paternity index and the probability of paternity. Results: Of the fourteen (14) trios studied, ten (10) cases were probable inclusion, three (03) cases were exclusion and one (01) case was an undetermined paternity outcome with the ABO-Rhesus/ electrophoresis of hemoglobin system. While the analysis of genetic polymorphisms in DNA gave five (05) inclusions versus nine (09) exclusions of paternity. Of the 10 probable inclusion cases given by the ABO-Rhesus/Electrophoresis of hemoglobin system, only 05 cases (50%) were confirmed for inclusion by Short tandem repeat analysis. Conclusion: The analysis of short tandem repeat with sixteen genetic markers is more reliable in determining paternity than ABO-Rhesus/hemoglobin electrophoresis techniques.

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

Genes ◽

10.3390/genes11040381 ◽

2020 ◽

Vol 11 (4) ◽

pp. 381 ◽

Cited By ~ 2

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.

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Analysis of Mutation Rate of 17 Y-Chromosome Short Tandem Repeats Loci Using Tanzanian Father-Son Paired Samples

Genetics Research International ◽

10.1155/2018/8090469 ◽

2018 ◽

Vol 2018 ◽

pp. 1-5

Author(s):

Fidelis Charles Bugoye ◽

Elias Mulima ◽

Gerald Misinzo

Keyword(s):

Y Chromosome ◽

Mutation Rate ◽

Standard Error ◽

Tandem Repeats ◽

Dna Typing ◽

Paternity Testing ◽

Mutation Rates ◽

Buccal Swab ◽

Age Difference ◽

Rate Analysis

Hundred unrelated father-son buccal swab sample pairs collected from consented Tanzanian population were examined to establish mutation rates using 17 Y-STRs loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTRYfiler kit used in forensics and paternity testing. Prior to 17 Y-STRs analysis, father-son pair biological relationships were confirmed using 15 autosomal STRs markers and found to be paternally related. A total of four single repeat mutational events were observed between father and sons. Two mutations resulted in the gain of a repeat and the other two resulted in a loss of a repeat in the son. All observed mutations occurred at tetranucleotide loci DYS389II, DYS385a, and DYS385b. The locus specific mutation rate varied between 0 and 1.176 x10−3 and the average mutation rate of 17Y-STRs loci in the present study was 2.353x10−3 (6.41x10−4 - 6.013x10−3) at 95% CI. Furthermore the mean fathers’ age with at least one mutation at son’s birth was 32 years with standard error of 2.387 while the average age of all fathers without mutation in a sampled population at son’s birth was 26.781 years with standard error of 0.609. The results shows that fathers’ age at son’s birth may have an effect on Y-STRs mutation rate analysis, though this age difference was statistically not significant using unpaired samples t-test (p = 0.05). As a consequence of observed mutation rates in this study, the precise and reliable understanding of mutation rate at Y-chromosome STR loci is necessary for a correct evaluation and interpretation of DNA typing results in forensics and paternity testing involving males. The criterion for exclusion in paternity testing should be defined, so that an exclusion from paternity has to be based on exclusion constellations at a minimum of two 17 Y-STRs loci.

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