Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Kaye N. Ballantyne, Arwin Ralf, Rachid Aboukhalid, Niaz M. Achakzai, Maria J. Anjos, Qasim Ayub, Jože Balažic, Jack Ballantyne, David J. Ballard, Burkhard Berger, Cecilia Bobillo, Mehdi Bouabdellah, Helen Burri, Tomas Capal, Stefano Caratti, Jorge Cárdenas, François Cartault, Elizeu F. Carvalho, Monica Carvalho, Baowen ChengMichael D. Coble, David Comas, Daniel Corach, Maria E. D'Amato, Sean Davison, Peter de Knijff, Maria Corazon A. De Ungria, Ronny Decorte, Tadeusz Dobosz, Berit M. Dupuy, Samir Elmrghni, Mateusz Gliwiński, Sara C. Gomes, Laurens Grol, Cordula Haas, Erin Hanson, Jürgen Henke, Lotte Henke, Fabiola Herrera-Rodríguez, Carolyn R. Hill, Gunilla Holmlund, Katsuya Honda, Uta Dorothee Immel, Shota Inokuchi, Mark A. Jobling, Mahmoud Kaddura, Jong S. Kim, Soon H. Kim, Wook Kim, Turi E. King, Eva Klausriegler, Daniel Kling, Lejla Kovačević, Leda Kovatsi, Paweł Krajewski, Sergey Kravchenko, Maarten H.D. Larmuseau, Eun Young Lee, Ruediger Lessig, Ludmila A. Livshits, Damir Marjanović, Marek Minarik, Natsuko Mizuno, Helena Moreira, Niels Morling, Meeta Mukherjee, Patrick Munier, Javaregowda Nagaraju, Franz Neuhuber, Shengjie Nie, Premlaphat Nilasitsataporn, Takeki Nishi, Hye H. Oh, Jill Olofsson, Valerio Onofri, Jukka U. Palo, Horolma Pamjav, Walther Parson, Michal Petlach, Christopher Phillips, Rafal Ploski, Samayamantri P.R. Prasad, Dragan Primorac, Gludhug A. Purnomo, Josephine Purps, Hector Rangel-Villalobos, Krzysztof Reogonekbała, Budsaba Rerkamnuaychoke, Danel Rey Gonzalez, Carlo Robino, Lutz Roewer, Alexandra Rosa, Antti Sajantila, Andrea Sala, Jazelyn M. Salvador, Paula Sanz, Cornelia Schmitt, Anil K. Sharma, Dayse A. Silva, Kyoung Jin Shin, Titia Sijen, Miriam Sirker, Daniela Siváková, Vedrana Škaro, Carlos Solano-Matamoros, Luis Souto, Vlastimil Stenzl, Herawati Sudoyo, Denise Syndercombe-Court, Adriano Tagliabracci, Duncan Taylor, Andreas Tillmar, Iosif S. Tsybovsky, Chris Tyler-Smith, Kristiaan J. van der Gaag, Daniel Vanek, Antónia Völgyi, Denise Ward, Patricia Willemse, Eric P.H. Yap, Rita Y.Y. Yong, Irena Zupanič Pajnič, Manfred Kayser

Research output: Contribution to journalArticle

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Abstract

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database. The value of 13 rapidly-mutating (RM) Y-STRs for differentiating male individuals is investigated in 14,644 related and unrelated men sampled from 111 worldwide populations. Over 99% of the 12,272 unrelated men were completely individualized. Of the 2,378 father-son pairs, 27% were separated. Figure: blue lines represent Y-STR haplotypes shared between population pairs in a subset of 7,784 males from 65 populations. Almost all shared haplotypes defined by conventional 17 Yfiler Y-STRs (above) are resolved with the 13 RM Y-STRs (below).

Original languageEnglish
Pages (from-to)1021-1032
Number of pages12
JournalHuman Mutation
Volume35
Issue number8
DOIs
StatePublished - Aug 2014

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Keywords

  • Forensic
  • Haplotypes
  • Paternal lineage
  • RM Y-STRs
  • Y-STRs
  • Y-chromosome

Cite this

Ballantyne, K. N., Ralf, A., Aboukhalid, R., Achakzai, N. M., Anjos, M. J., Ayub, Q., Balažic, J., Ballantyne, J., Ballard, D. J., Berger, B., Bobillo, C., Bouabdellah, M., Burri, H., Capal, T., Caratti, S., Cárdenas, J., Cartault, F., Carvalho, E. F., Carvalho, M., ... Kayser, M. (2014). Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats. Human Mutation, 35(8), 1021-1032. https://doi.org/10.1002/humu.22599