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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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Marker-wise frequency of variant alleles. PPY23-specific markers are given in bold. Light gray: copy number variants; gray: intermediate alleles; dark gray:  allele.
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fig0020: Marker-wise frequency of variant alleles. PPY23-specific markers are given in bold. Light gray: copy number variants; gray: intermediate alleles; dark gray: allele.

Mentions: Variant alleles not representing simple repetitions of the respective STR motif occurred at all loci (Table S3). This included alleles, likely due to a deletion or primer site mutation, intermediate alleles comprising fractional repeats, and copy-number variants such as duplications and triplications of the whole locus. All variant alleles were confirmed by retyping or sequencing at the laboratory that had performed the original STR typing. The proportion of variant alleles differed greatly among markers (Fig. 4), with DYS458 showing the highest (n = 385) and DYS391 and DYS549 showing the lowest number (n = 1). Four of the six PPY23-specific markers (DYS481, DYS570, DYS576 and DYS643) had comparatively high numbers of variant alleles. Only two single non-fractional off-ladder alleles (allele 6 at GATAH4, allele 15 at DYS481) were observed in this study. On the other hand, only five of the 19 intermediate alleles observed for the six PPY23-specific markers (18.2, 18.3, 19.3 and 20.3 at DYS570, 11.1 at DYS643) were included in the bin set of the allelic ladder (Table S3).


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)

Marker-wise frequency of variant alleles. PPY23-specific markers are given in bold. Light gray: copy number variants; gray: intermediate alleles; dark gray:  allele.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

fig0020: Marker-wise frequency of variant alleles. PPY23-specific markers are given in bold. Light gray: copy number variants; gray: intermediate alleles; dark gray: allele.
Mentions: Variant alleles not representing simple repetitions of the respective STR motif occurred at all loci (Table S3). This included alleles, likely due to a deletion or primer site mutation, intermediate alleles comprising fractional repeats, and copy-number variants such as duplications and triplications of the whole locus. All variant alleles were confirmed by retyping or sequencing at the laboratory that had performed the original STR typing. The proportion of variant alleles differed greatly among markers (Fig. 4), with DYS458 showing the highest (n = 385) and DYS391 and DYS549 showing the lowest number (n = 1). Four of the six PPY23-specific markers (DYS481, DYS570, DYS576 and DYS643) had comparatively high numbers of variant alleles. Only two single non-fractional off-ladder alleles (allele 6 at GATAH4, allele 15 at DYS481) were observed in this study. On the other hand, only five of the 19 intermediate alleles observed for the six PPY23-specific markers (18.2, 18.3, 19.3 and 20.3 at DYS570, 11.1 at DYS643) were included in the bin set of the allelic ladder (Table S3).

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