Dataset Information

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

ABSTRACT: In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.

SUBMITTER: Purps J

PROVIDER: S-EPMC4127773 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

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A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Purps Josephine J Siegert Sabine S Willuweit Sascha S Nagy Marion M Alves Cíntia C Salazar Renato R Angustia Sheila M T SM Santos Lorna H LH Anslinger Katja K Bayer Birgit B Ayub Qasim Q Wei Wei W Xue Yali Y Tyler-Smith Chris C Bafalluy Miriam Baeta MB Martínez-Jarreta Begoña B Martínez-Jarreta Begoña B Egyed Balazs B Balitzki Beate B Tschumi Sibylle S Ballard David D Court Denise Syndercombe DS Barrantes Xinia X Bäßler Gerhard G Wiest Tina T Berger Burkhard B Niederstätter Harald H Parson Walther W Davis Carey C Budowle Bruce B Burri Helen H Borer Urs U Koller Christoph C Carvalho Elizeu F EF Domingues Patricia M PM Chamoun Wafaa Takash WT Coble Michael D MD Hill Carolyn R CR Corach Daniel D Caputo Mariela M D'Amato Maria E ME Davison Sean S Decorte Ronny R Larmuseau Maarten H D MH Ottoni Claudio C Rickards Olga O Lu Di D Jiang Chengtao C Dobosz Tadeusz T Jonkisz Anna A Frank William E WE Furac Ivana I Gehrig Christian C Castella Vincent V Grskovic Branka B Haas Cordula C Wobst Jana J Hadzic Gavrilo G Drobnic Katja K Honda Katsuya K Hou Yiping Y Zhou Di D Li Yan Y Hu Shengping S Chen Shenglan S Immel Uta-Dorothee UD Lessig Rüdiger R Jakovski Zlatko Z Ilievska Tanja T Klann Anja E AE García Cristina Cano CC de Knijff Peter P Kraaijenbrink Thirsa T Kondili Aikaterini A Miniati Penelope P Vouropoulou Maria M Kovacevic Lejla L Marjanovic Damir D Lindner Iris I Mansour Issam I Al-Azem Mouayyad M Andari Ansar El AE Marino Miguel M Furfuro Sandra S Locarno Laura L Martín Pablo P Luque Gracia M GM Alonso Antonio A Miranda Luís Souto LS Moreira Helena H Mizuno Natsuko N Iwashima Yasuki Y Neto Rodrigo S Moura RS Nogueira Tatiana L S TL Silva Rosane R Nastainczyk-Wulf Marina M Edelmann Jeanett J Kohl Michael M Nie Shengjie S Wang Xianping X Cheng Baowen B Núñez Carolina C Pancorbo Marian Martínez de MM Olofsson Jill K JK Morling Niels N Onofri Valerio V Tagliabracci Adriano A Pamjav Horolma H Volgyi Antonia A Barany Gusztav G Pawlowski Ryszard R Maciejewska Agnieszka A Pelotti Susi S Pepinski Witold W Abreu-Glowacka Monica M Phillips Christopher C Cárdenas Jorge J Rey-Gonzalez Danel D Salas Antonio A Brisighelli Francesca F Capelli Cristian C Toscanini Ulises U Piccinini Andrea A Piglionica Marilidia M Baldassarra Stefania L SL Ploski Rafal R Konarzewska Magdalena M Jastrzebska Emila E Robino Carlo C Sajantila Antti A Palo Jukka U JU Guevara Evelyn E Salvador Jazelyn J Ungria Maria Corazon De MC Rodriguez Jae Joseph Russell JJ Schmidt Ulrike U Schlauderer Nicola N Saukko Pekka P Schneider Peter M PM Sirker Miriam M Shin Kyoung-Jin KJ Oh Yu Na YN Skitsa Iulia I Ampati Alexandra A Smith Tobi-Gail TG Calvit Lina Solis de LS Stenzl Vlastimil V Capal Thomas T Tillmar Andreas A Nilsson Helena H Turrina Stefania S De Leo Domenico D Verzeletti Andrea A Cortellini Venusia V Wetton Jon H JH Gwynne Gareth M GM Jobling Mark A MA Whittle Martin R MR Sumita Denilce R DR Wolańska-Nowak Paulina P Yong Rita Y Y RY Krawczak Michael M Nothnagel Michael M Roewer Lutz L

Forensic science international. Genetics 20140428

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers wer ...[more]

PMID: 24854874

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Project description:BackgroundHaplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis, especially when short tandem repeats (STR) fail to resolve uncertainty in relationship analysis. STR located on the X chromosome show stronger linkage disequilibrium compared with autosomal STR. So, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific.Methodology and findingsTwenty-six X-STR loci including six clusters of linked markers DXS6807-DXS8378-DXS9902(Xp22), DXS7132-DXS10079-DXS10074-DXS10075-DXS981 (Xq12), DXS6801-DXS6809-DXS6789-DXS6799(Xq21), DXS7424-DXS101-DXS7133(Xq22), DXS6804-GATA172D05(Xq23), DXS8377-DXS7423 (Xq28) and the loci DXS6800, DXS6803, DXS9898, GATA165B12, DXS6854, HPRTB and GATA31E08 were typed in four nationality (Han, Uigur, Kazakh and Mongol) samples from China (n?=?1522, 876 males and 646 females). Allele and haplotype frequency as well as linkage disequilibrium data for kinship calculation were observed. The allele frequency distribution among different populations was compared. A total of 5-20 alleles for each locus were observed and altogether 289 alleles for all the selected loci were found. Allele frequency distribution for most X-STR loci is different in different populations. A total of 876 male samples were investigated by haplotype analysis and for linkage disequilibrium. A total of 89, 703, 335, 147, 39 and 63 haplotypes were observed. Haplotype diversity was 0.9584, 0.9994, 0.9935, 0.9736, 0.9427 and 0.9571 for cluster I, II, III, IV, V and VI, respectively. Eighty-two percent of the haplotype of cluster IIwas found only once. And 94% of the haplotype of cluster III show a frequency of <1%.ConclusionsThese results indicate that allele frequency distribution for most X-STR loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation. So it is necessary to obtain allele frequency and haplotypes data of the linked loci for forensic application.

Dataset Information

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Publications

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

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