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https://www.readbyqxmd.com/read/28623801/dna-analysis-of-root-canal-filled-teeth
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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...
May 7, 2017: Genomics
https://www.readbyqxmd.com/read/28466124/rapidly-mutating-y-str-analyses-of-compromised-forensic-samples
#7
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
#8
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...
April 20, 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
#9
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
#10
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
#11
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
#12
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
#13
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...
February 27, 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
#14
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
https://www.readbyqxmd.com/read/28242557/sensitive-dip-str-markers-for-the-analysis-of-unbalanced-mixtures-from-touch-dna-samples
#15
Fabio Oldoni, Vincent Castella, Frederic Grosjean, Diana Hall
Casework samples collected for forensic DNA analysis can produce genomic mixtures in which the DNA of the alleged offender is masked by high quantities of DNA coming from the victim. DIP-STRs are novel genetic markers specifically developed to enable the target analysis of a DNA of interest in the presence of exceeding quantities of a second DNA (up to 1000-fold). The genotyping system, which is based on allele-specific amplifications of haplotypes formed by a deletion/insertion polymorphism (DIP) and a short tandem repeat (STR), combines the capacity of targeting the DNA of an individual with a strong identification power...
February 14, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28210813/a-comprehensive-y-str-portrait-of-yousafzai-s-population
#16
Sadia Tabassum, Muhammad Ilyas, Inam Ullah, Muhammad Israr, Habib Ahmad
In the current study, 17 Y-Chromosomal short tandem repeats (Y-STRs) included in theAmpFlSTR Y-Filer amplification kit (Applied Biosystems, Foster City, USA) were investigated in 146 unrelated Yousafzai males residing in the Khyber Pakhtunkhwa Province of Pakistan. A total of 94 (89.52%) unique haplotypes were observed. Discrimination capacity was 71.92%. Haplotype diversity ranged from 0.354 (DYS456) to 0.663 (DYS458). Both Rst pairwise analysis and multidimensional scaling plot showed that the genetic structure of the Yousafzais is significantly different from neighbouring populations...
February 16, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28138773/revisiting-the-male-genetic-landscape-of-china-a-multi-center-study-of-almost-38-000-y-str-haplotypes
#17
Michael Nothnagel, Guangyao Fan, Fei Guo, Yongfeng He, Yiping Hou, Shengping Hu, Jiang Huang, Xianhua Jiang, Wook Kim, Kicheol Kim, Chengtao Li, Hui Li, Liming Li, Shilin Li, Zhao Li, Weibo Liang, Chao Liu, Di Lu, Haibo Luo, Shengjie Nie, Meisen Shi, Hongyu Sun, Jianpin Tang, Lei Wang, Chuan-Chao Wang, Dan Wang, Shao-Qing Wen, Hongyan Wu, Weiwei Wu, Jiaxin Xing, Jiangwei Yan, Shi Yan, Hongbing Yao, Yi Ye, Libing Yun, Zhaoshu Zeng, Lagabaiyila Zha, Suhua Zhang, Xiufen Zheng, Sascha Willuweit, Lutz Roewer
China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes...
May 2017: Human Genetics
https://www.readbyqxmd.com/read/28138757/genetic-variations-of-15-autosomal-and-17-y-str-markers-in-sindhi-population-of-pakistan
#18
Rukhsana Perveen, Ahmad Ali Shahid, Muhammad Shafique, Muhammad Shahzad, Tayyab Husnain
This study comprises genetic characterization of 15 autosomal and 17 Y-chromosomal STR loci in 103 unrelated male inhabitants of the Sindhi population to establish its lineage and parameters of forensic interest. The examined autosomal STRs revealed high combined power of discrimination, combined power of exclusion, and the combined matching probability as 0.99999999999999999042580, 0.9999977141, and 9.5742 × 10(-18), respectively. A total of 89 unique haplotypes were obtained, of which 84 were observed once with a haplotype diversity value of 0...
January 30, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28127629/genetic-polymorphisms-of-24-y-str-loci-in-hani-ethnic-minority-from-yunnan-province-southwest-china
#19
Liping Hu, Tao Gu, Xiaodong Fan, Xiaokun Yuan, Min Rao, Jing Bo Pang, Aiting Nie, Lei Du, Xiufeng Zhang, Shengjie Nie
In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 250 unrelated Hani male individuals from Lvchun county, Honghe Hani and Yi Autonomous Prefecture, Yunnan Province, Southwest China. The gene diversity of the 24 Y-STR loci in the studied Hani group ranged from 0.2683 (DYS437) to 0.8837 (DYS447). According to haplotypic analysis of the 24 Y-STR loci, 204 different haplotypes were obtained, 174 of which were unique. The haplotype diversity and discrimination capacity in Hani group were 0...
January 27, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28126691/performance-and-concordance-of-the-forenseq%C3%A2-system-for-autosomal-and-y-chromosome-short-tandem-repeat-sequencing-of-reference-type-specimens
#20
Rebecca S Just, Lilliana I Moreno, Jill B Smerick, Jodi A Irwin
Though the utility of next-generation sequencing (NGS) technologies for forensic short tandem repeat (STR) typing has been evident for several years, commercially available assays and software solutions developed specifically to meet forensic needs have only recently become available. One of these, the ForenSeq™ DNA Signature Prep Kit (Illumina, Inc.) sequences 27 autosomal STR (aSTR) and 24 Y chromosome STR (Y-STR) loci (concurrent with additional nuclear markers) per multiplexed sample, with automated secondary and tertiary analyses of the data accomplished via the associated ForenSeq™ Universal Analysis Software (UAS)...
January 9, 2017: Forensic Science International. Genetics
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