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

Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SM, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MH, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RS, Nogueira TL, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MM, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MC, Rodriguez JJ, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LS, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RY, Krawczak M, Nothnagel M, Roewer L - Forensic Sci Int Genet (2014)

Bottom Line: Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.

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Ranking of PPY23 markers by gene diversity (GD). For the calculation of GD, DYS385ab was treated as a single marker. DYS389II.I equals the difference between DYS389II and DYS389I. PPY23-specific markers are given in bold. (a) Rank within the whole data set; (b) rank within continental residency groups, i.e. Africa (orange; n = 445), Asia (red; n = 3458), Europe (magenta; n = 11,968), Latin America (blue; n = 1183) or North America (green; n = 2576). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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fig0015: Ranking of PPY23 markers by gene diversity (GD). For the calculation of GD, DYS385ab was treated as a single marker. DYS389II.I equals the difference between DYS389II and DYS389I. PPY23-specific markers are given in bold. (a) Rank within the whole data set; (b) rank within continental residency groups, i.e. Africa (orange; n = 445), Asia (red; n = 3458), Europe (magenta; n = 11,968), Latin America (blue; n = 1183) or North America (green; n = 2576). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Mentions: A high level of genetic diversity was observed in our study at all 23 Y-STRs of the PPY23 panel. Some 521 different alleles were observed in the 19,630 Y-chromosomes analyzed, with a median number of 16 alleles per marker and a range of 10 (DYS391) to 31 (DYS458; Table S3). Marker DYS385ab showed 146 different allele combinations (i.e. unordered haplotypes). A total of 133 alleles occurred at 17 of the 23 loci, 75 intermediate alleles (18 loci) and 69 copy-number variants (21 loci; 57 duplications excluding all duplicates at DYS385ab, 11 triplications, one quadruplication). Of the six markers that distinguish PPY23 from Yfiler, the DYS481 and DYS570 markers showed the largest numbers of different alleles (30 and 28, respectively; Fig. 2). Gene diversity (GD) values exceeded 0.5 for all 23 markers, 0.6 for 21 (91.3%) and even 0.7 for 10 (43.5%) markers (Fig. 3a; Table S4). While of the 17 markers in common with the Yfiler kit, markers DYS385ab (GD = 0.923) on the one hand, and DYS391 (0.521) and DYS393 (0.534) on the other marked the extremes of the GD distribution, four of the six PPY23-specific markers, namely DYS481, DYS570, DYS576 and DYS643, ranked near the top, with GD values exceeding 0.72. Notably, some loci ranked differently with respect to GD in different continental (Fig. 3b) or ancestry groups (Fig. S2), most prominently with regard to the African meta-population (Table S4). For example, the DYS390, DYS438 and DYS392 markers were found to be less variable in Africa than, for example, in Europe. Of the six PPY23-specific markers, all but DYS643 showed similar GD values on most continents. The DYS643 marker was found to be more variable in Africans, but less variable in Native Americans from Latin America, than in the other continental groups (Fig. S2).


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

Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SM, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MH, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RS, Nogueira TL, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MM, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MC, Rodriguez JJ, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LS, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RY, Krawczak M, Nothnagel M, Roewer L - Forensic Sci Int Genet (2014)

Ranking of PPY23 markers by gene diversity (GD). For the calculation of GD, DYS385ab was treated as a single marker. DYS389II.I equals the difference between DYS389II and DYS389I. PPY23-specific markers are given in bold. (a) Rank within the whole data set; (b) rank within continental residency groups, i.e. Africa (orange; n = 445), Asia (red; n = 3458), Europe (magenta; n = 11,968), Latin America (blue; n = 1183) or North America (green; n = 2576). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4127773&req=5

fig0015: Ranking of PPY23 markers by gene diversity (GD). For the calculation of GD, DYS385ab was treated as a single marker. DYS389II.I equals the difference between DYS389II and DYS389I. PPY23-specific markers are given in bold. (a) Rank within the whole data set; (b) rank within continental residency groups, i.e. Africa (orange; n = 445), Asia (red; n = 3458), Europe (magenta; n = 11,968), Latin America (blue; n = 1183) or North America (green; n = 2576). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Mentions: A high level of genetic diversity was observed in our study at all 23 Y-STRs of the PPY23 panel. Some 521 different alleles were observed in the 19,630 Y-chromosomes analyzed, with a median number of 16 alleles per marker and a range of 10 (DYS391) to 31 (DYS458; Table S3). Marker DYS385ab showed 146 different allele combinations (i.e. unordered haplotypes). A total of 133 alleles occurred at 17 of the 23 loci, 75 intermediate alleles (18 loci) and 69 copy-number variants (21 loci; 57 duplications excluding all duplicates at DYS385ab, 11 triplications, one quadruplication). Of the six markers that distinguish PPY23 from Yfiler, the DYS481 and DYS570 markers showed the largest numbers of different alleles (30 and 28, respectively; Fig. 2). Gene diversity (GD) values exceeded 0.5 for all 23 markers, 0.6 for 21 (91.3%) and even 0.7 for 10 (43.5%) markers (Fig. 3a; Table S4). While of the 17 markers in common with the Yfiler kit, markers DYS385ab (GD = 0.923) on the one hand, and DYS391 (0.521) and DYS393 (0.534) on the other marked the extremes of the GD distribution, four of the six PPY23-specific markers, namely DYS481, DYS570, DYS576 and DYS643, ranked near the top, with GD values exceeding 0.72. Notably, some loci ranked differently with respect to GD in different continental (Fig. 3b) or ancestry groups (Fig. S2), most prominently with regard to the African meta-population (Table S4). For example, the DYS390, DYS438 and DYS392 markers were found to be less variable in Africa than, for example, in Europe. Of the six PPY23-specific markers, all but DYS643 showed similar GD values on most continents. The DYS643 marker was found to be more variable in Africans, but less variable in Native Americans from Latin America, than in the other continental groups (Fig. S2).

Bottom Line: Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.

Show MeSH