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https://www.readbyqxmd.com/read/28903432/genetic-variation-and-forensic-characteristic-analysis-of-25-strs-of-a-novel-fluorescence-co-amplification-system-in-chinese-southern-shaanxi-han-population
#1
Yao-Shun Liu, Jian-Gang Chen, Ting Mei, Yu-Xin Guo, Hao-Tian Meng, Jian-Fei Li, Yuan-Yuan Wei, Xiao-Ye Jin, Bo-Feng Zhu, Li-Ping Zhang
We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28900279/next-generation-sequencing-plus-ngs-with-y-chromosomal-markers-for-forensic-pedigree-searches
#2
Xiaoqin Qian, Jiayi Hou, Zheng Wang, Yi Ye, Min Lang, Tianzhen Gao, Jing Liu, Yiping Hou
There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs)...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28806630/case-report-coincidental-inclusion-in-a-17-locus-y-str-mixture-wrongful-conviction-and-exoneration
#3
Greg Hampikian, Gianluca Peri, Shih-Shiang Lo, Mong-Hwa Chin, Kuo-Lan Liu
We report the case of a suspect (Suspect-3) who was convicted (and later exonerated) of participating in the multiple-attacker rape of two women. The forensic evidence against him was his inclusion in a 17-marker Y-STR mixture isolated from semen on one victim's clothing. The DNA inclusion produced a match statistic with a combined probability of inclusion of 1 in 741, and a Likelihood Ratio of 3296. While the defense team was told that Suspect-3 was included in the semen DNA mixture, they were not told that all of the Y-STR alleles could also be explained by just the other two accused attackers' haplotypes...
August 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28797659/a-preliminary-evaluation-study-of-new-generation-multiplex-str-kits-comprising-of-the-codis-core-loci-and-the-european-standard-set-loci
#4
Jolena Ying Ying Tan, Yuen Peng Tan, Shilen Ng, Annabel Suan Tay, Yong Han Phua, Wei Jie Tan, Terenze Yao Rui Ong, Li Min Chua, Christopher Kiu Choong Syn
The GlobalFiler™ (Life Technologies), Investigator(®) 24plex QS (Qiagen), and PowerPlex(®) Fusion 6C (Promega) kits are the latest generation 6-dye fluorescent chemistry STR-PCR amplification kits. These kits allow for the simultaneous amplification of the CODIS core loci and the European Standard Set loci, as well as a few Y-STR loci in addition to the standard sex-determining marker Amelogenin. The present study was designed to be a preliminary evaluation of the three STR-PCR kits in terms of sensitivity, profile recovery from degraded DNA samples, tolerance to PCR inhibitors, and detection of minor components in DNA mixtures...
July 25, 2017: Journal of Forensic and Legal Medicine
https://www.readbyqxmd.com/read/28746047/genetic-variation-and-forensic-characteristic-analysis-of-25-strs-of-a-novel-fluorescence-co-amplification-system-in-chinese-southern-shaanxi-han-population
#5
Yao-Shun Liu, Jian-Gang Chen, Ting Mei, Yu-Xin Guo, Hao-Tian Meng, Jian-Fei Li, Yuan-Yuan Wei, Xiao-Ye Jin, Bo-Feng Zhu, Li-Ping Zhang
We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28704439/inner-and-inter-population-structure-construction-of-chinese-jiangsu-han-population-based-on-y23-str-system
#6
Huipin Wang, Huajie Ba, Chun Yang, Jianqiu Zhang, Yunchun Tai
In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations...
2017: PloS One
https://www.readbyqxmd.com/read/28623801/dna-analysis-of-root-canal-filled-teeth
#7
Hikaru Izawa, Hirofumi Tsutsumi, Sayaka Maruyama, Toshinobu Komuro
Teeth are markedly useful as samples for DNA analysis; however, intact teeth are not always available. This study examined the possibility of identifying autosomal and Y-chromosome short tandem repeat (STR) types in samples from 34 teeth (15 intact and 19 root canal filled) that had been preserved for 10-33years after dental extraction. The aim was to explore the feasibility of individual identification by DNA analysis of samples obtained from highly decomposed and skeletonized corpses. Only one out of 24 autosomal STR loci was not identified in two of the 15 intact teeth, whereas all 23 loci of the Y chromosome STR were detected...
May 10, 2017: Legal Medicine
https://www.readbyqxmd.com/read/28622394/y-chromosomal-analysis-of-greek-cypriots-reveals-a-primarily-common-pre-ottoman-paternal-ancestry-with-turkish-cypriots
#8
Alexandros Heraclides, Evy Bashiardes, Eva Fernández-Domínguez, Stefania Bertoncini, Marios Chimonas, Vasilis Christofi, Jonathan King, Bruce Budowle, Panayiotis Manoli, Marios A Cariolou
Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages...
2017: PloS One
https://www.readbyqxmd.com/read/28566770/phylogeny-of-y-chromosome-haplogroup-c3b-f1756-an-important-paternal-lineage-in-altaic-speaking-populations
#9
Lan-Hai Wei, Yun-Zhi Huang, Shi Yan, Shao-Qing Wen, Ling-Xiang Wang, Pan-Xin Du, Da-Li Yao, Shi-Lin Li, Ya-Jun Yang, Li Jin, Hui Li
In previous studies, a specific paternal lineage with a null value for the Y-chromosome short tandem repeat (Y-STR) marker DYS448 was identified as common among Mongolic- and Turkic-speaking populations. This paternal lineage (temporarily named C3*-DYS448del) was determined to be M217+, M93-, P39-, M48-, M407-, and P53.1-, and its origin and phylogeny remain ambiguous. Here, we analyzed Y-chromosome sequences of 10 male that are related this paternal lineage and redefined it as C3b1a1a1a-F1756 (C3b-F1756). We generated a highly revised phylogenetic tree of haplogroup C3b-F1756, including 21 sub-clades and 360 non-private Y-chromosome polymorphisms...
June 1, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28555242/y-chromosomal-deletion-pattern-in-koreans-inhabiting-jeju-island
#10
Ji Hyun Lee, Hong Xuan Jin, Sohee Cho, Han Na Kim, Hee Jin Seo, Kyoung-Jin Shin, Dong Hoon Shin, Soong Deok Lee
Mutations occur in Y chromosome genes similar to autosomal genes. However, unlike autosomal genes, Y chromosome genes do not undergo recombination, which produce distinctive characteristics and distribution patterns in different geographic regions. Therefore, detailed analysis of mutations of Y chromosome genes might provide information for personal identification or analysis of phylogenetic history. In Y-STR (short tandem repeat) analysis tests on 668 habitants of Jeju Island, the largest island in the Korean peninsula located apart from the mainland, a deletion at DYS448 was found in 10 samples...
May 30, 2017: Anthropologischer Anzeiger; Bericht über die Biologisch-anthropologische Literatur
https://www.readbyqxmd.com/read/28523410/genomic-portrait-of-population-of-jharkhand-india-drawn-with-15-autosomal-strs-and-17-y-strs
#11
Jahangir Imam, Romana Reyaz, Rama Shankar Singh, Arun Kumar Bapuly, Pankaj Shrivastava
We analysed 15 autosomal STRs in 200 unrelated individuals (102 males and 98 females) and 17 Y-STRs in 102 unrelated males living in Jharkhand, India, to establish parameters of forensic interest. The examined autosomal STRs revealed high combined power of exclusion (CPE) and combined power of discrimination (CPD) as equal to 0.9999 and greater than 0.99999, respectively. The combined probability of match (CPm) and combined paternity index (CPI) for all 15 autosomal STR loci were found to be 5.15 × 10(-18) and 6...
May 18, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28487173/patrilineal-background-of-the-she-minority-population-from-chaoshan-fenghuang-mountain-an-isolated-mountain-region-in-china
#12
Shuhui Liu, Guangcan Chen, Haihua Huang, Wenting Lin, Dan Guo, Shukun Zhao, Dongping Tian, Min Su
The She ethnic minority population is distributed in southern China. The origin of the She population has been controversial. The purpose of this work was to investigate the genomic diversity of She. The Chaoshan She population living in the Chaoshan Fenghuang mountain is a relatively isolated population. We detected 14 Y chromosome biallelic markers (Y-SNPs) and 6 Y chromosome short tandem repeat (Y-STR) loci in Chaoshan She people. Y-SNP analysis showed the Chaoshan She was closely related to the Chaoshan Hakka, Chaoshanese, Tujia and Gaoshan national minority...
July 2017: Genomics
https://www.readbyqxmd.com/read/28466124/rapidly-mutating-y-str-analyses-of-compromised-forensic-samples
#13
Rashed Alghafri, Irena Zupanič Pajnič, Tomaž Zupanc, Jože Balažic, Pankaj Shrivastava
Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were identified to improve differentiation of unrelated males and also to enable separating closely and distantly related males in human identity testing in forensic and other applications. RM-Yplex assay was developed as a single multiplex that is capable of simultaneously amplifying all currently known RM Y-STRs, and reproducibility and sensitivity testing were performed on reference samples. Additional analyses are necessary to test its suitability for analysing compromised forensic samples...
May 2, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28461042/forensic-characteristics-and-phylogenetic-analysis-of-hubei-han-population-in-central-china-using-17-y-str-loci
#14
Zheng Wang, Weian Du, Guanglin He, Jing Liu, Yiping Hou
Currently, the largest national database within the Y chromosome haplotype reference database (YHRD, https://yhrd.org, release 53) is China, which has approximately 38000 Y chromosomal 17-marker (Yfiler) haplotypes. These haplotype profiles derived from the vast majority of Chinese administrative divisions, but no haplotype data was available for Hubei province, which is located in the Central China region. Herein, 429 unrelated male Chinese Han individuals residing in Hubei province were recruited and genotyped with 17 Y-STR loci...
July 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28455625/toward-a-consensus-on-snp-and-str-mutation-rates-on-the-human-y-chromosome
#15
REVIEW
O Balanovsky
The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate...
May 2017: Human Genetics
https://www.readbyqxmd.com/read/28405751/developmental-validation-of-a-6-dye-str-kit-with-27-loci
#16
Shuanglin Li, Ling Chen, Yanfang Wang, Quyi Xu, Hong Liu, Yue Li, Chao Liu
The EX27 System is a 6-dye (i.e., FAM, HEX, TAMAR, ROX, VIG, and SIZ-500) kit that combines the 24 autosomal STR loci (i.e., D3S1358, D13S317, D7S820, D16S539, D1S1656, Penta E, TPOX, TH01, D2S1338, CSF1PO, Penta D, D10S1248, D19S433, vWA, D21S11, D18S51, D6S1043, D8S1179, D5S818, D12S391, FGA, D22S1045, D2S441, SE33) with a Y-STR locus (DYS391), an Indel site (YIndel) and Amelogenin, which is designed to amplify DNA from extracts as well as direct amplification from substrates. The new system contains most of the widely used autosomal STR loci around the world and is sensitive to the male component in mixtures and is more accurate in gender determination owing to the DYS391 and YIndel...
April 12, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28363008/analysis-of-the-19-y-str-and-16-x-str-loci-system-in-the-han-population-of-shandong-province-china
#17
H M Gao, C Wang, S Y Han, S H Sun, D J Xiao, Y S Wang, C T Li, M X Zhang
The sex-linked short tandem repeats (STR), Y-STR and X-STR, are important for autosomal STRs in forensic paternity testing. We evaluated the forensic parameters of 19 Y-STRs and 16 X-STRs in the Han population of Shandong province, China. A Goldeneye 20Y kit (DYS391, DYS389I, DYS390, DYS389II, DYS348, DYS456, Y-GATA-H4, DYS447, DYS19, DYS392, DYS393, DYS388, DYS439, DYS635, DYS448, DYS460, DYS458, DYS437, DYS385 a/b) was used to analyze the forensic parameters of 534 unrelated males. A Goldeneye17X system (DXS6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS10159, DXS6789, DXS6810, amelogenin) was used to analyze 97 unrelated males and 214 females...
March 30, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28315050/forensic-use-of-y-chromosome-dna-a-general-overview
#18
REVIEW
Manfred Kayser
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases...
May 2017: Human Genetics
https://www.readbyqxmd.com/read/28273507/flanking-region-variation-of-forenseq%C3%A2-dna-signature-prep-kit-str-and-snp-loci-in-yavapai-native-americans
#19
Frank R Wendt, Jonathan L King, Nicole M M Novroski, Jennifer D Churchill, Jillian Ng, Robert F Oldt, Kelly L McCulloh, Jessica A Weise, David Glenn Smith, Sreetharan Kanthaswamy, Bruce Budowle
Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif...
May 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28271363/yfiler-%C3%A2-plus-population-samples-and-dilution-series-stutters-analytic-thresholds-and-drop-out-probabilities
#20
Mikkel Meyer Andersen, Helle Smidt Mogensen, Poul Svante Eriksen, Niels Morling
The Yfiler (Ⓡ) Plus Amplification Kit amplifies 27 Y chromosomal small tandem repeat (STR) markers. The kit has five-fluorescent dye chemistry and the improved PCR buffer system of modern STR kits. We validated the kit for accredited investigations of crime scene samples by a thorough study of kit dynamics and performance. We determined dye-dependent analytical thresholds by receiver operating characteristics (ROC) and made a customised artefact filter that includes theoretical known artefacts by use of previously analysed population samples...
March 7, 2017: International Journal of Legal Medicine
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