Towards male individualization with rapidly mutating Y-chromosomal STRs

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 Cheng; Michael 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 Rębała; 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 Skaro; 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

doi:10.1002/humu.22599

Towards male individualization with rapidly mutating Y-chromosomal STRs

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 Rębała, 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 Skaro, 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

Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Australia.

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Abstract

Relevant for various areas of human genetics, Y-chromosomal STRs (Y-STRs) are commonly used for testing close paternal relationships amongst 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: 0.99919-0.9999988). 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% non-unique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). AMOVA 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 fathers/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.

Original language	English
Pages (from-to)	1021-1032
Number of pages	12
Journal	Human Mutation
Volume	35
Issue number	8
DOIs	https://doi.org/10.1002/humu.22599
Publication status	Published - Aug 2014

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Ballantyne_et_al_2014_Human_MutationFinal published version, 992 KBLicence: CC BY

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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). Towards male individualization with rapidly mutating Y-chromosomal STRs. Human Mutation, 35(8), 1021-1032. https://doi.org/10.1002/humu.22599

@article{6ab29e820a4245edba75a22a7f1e6ac5,

title = "Towards male individualization with rapidly mutating Y-chromosomal STRs",

abstract = "Relevant for various areas of human genetics, Y-chromosomal STRs (Y-STRs) are commonly used for testing close paternal relationships amongst 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: 0.99919-0.9999988). 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% non-unique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). AMOVA 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 fathers/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.",

author = "Ballantyne, {Kaye N} and Arwin Ralf and Rachid Aboukhalid and Achakzai, {Niaz M} and Anjos, {Maria J} and Qasim Ayub and Jo{\v z}e Bala{\v z}ic and Jack Ballantyne and Ballard, {David J} and Burkhard Berger and Cecilia Bobillo and Mehdi Bouabdellah and Helen Burri and Tomas Capal and Stefano Caratti and Jorge C{\'a}rdenas and Fran{\c c}ois Cartault and Carvalho, {Elizeu F} and Monica Carvalho and Baowen Cheng and Coble, {Michael D} and David Comas and Daniel Corach and D'Amato, {Maria E} and Sean Davison and {de Knijff}, Peter and {De Ungria}, {Maria Corazon A} and Ronny Decorte and Tadeusz Dobosz and Dupuy, {Berit M} and Samir Elmrghni and Mateusz Gliwi{\'n}ski and Gomes, {Sara C} and Laurens Grol and Cordula Haas and Erin Hanson and J{\"u}rgen Henke and Lotte Henke and Fabiola Herrera-Rodr{\'i}guez and Hill, {Carolyn R} and Gunilla Holmlund and Katsuya Honda and Uta-Dorothee Immel and Shota Inokuchi and Jobling, {Mark A} and Mahmoud Kaddura and Kim, {Jong S} and Kim, {Soon H} and Wook Kim and King, {Turi E} and Eva Klausriegler and Daniel Kling and Lejla Kova{\v c}evi{\'c} and Leda Kovatsi and Pawe{\l} Krajewski and Sergey Kravchenko and Larmuseau, {Maarten H D} and Lee, {Eun Young} and Ruediger Lessig and Livshits, {Ludmila A} and Damir Marjanovi{\'c} and Marek Minarik and Natsuko Mizuno and Helena Moreira and Niels Morling and Meeta Mukherjee and Patrick Munier and Javaregowda Nagaraju and Franz Neuhuber and Shengjie Nie and Premlaphat Nilasitsataporn and Takeki Nishi and Oh, {Hye H} and Jill Olofsson and Valerio Onofri and Palo, {Jukka U} and Horolma Pamjav and Walther Parson and Michal Petlach and Christopher Phillips and Rafal Ploski and Prasad, {Samayamantri P R} and Dragan Primorac and Purnomo, {Gludhug A} and Josephine Purps and Hector Rangel-Villalobos and Krzysztof R{\c e}ba{\l}a and Budsaba Rerkamnuaychoke and Gonzalez, {Danel Rey} and Carlo Robino and Lutz Roewer and Alexandra Rosa and Antti Sajantila and Andrea Sala and Salvador, {Jazelyn M} and Paula Sanz and Cornelia Schmitt and Sharma, {Anil K} and Silva, {Dayse A} and Kyoung-Jin Shin and Titia Sijen and Miriam Sirker and Daniela Siv{\'a}kov{\'a} and Vedrana Skaro and Carlos Solano-Matamoros and Luis Souto and Vlastimil Stenzl and Herawati Sudoyo and Court, {Denise Syndercombe} and Adriano Tagliabracci and Duncan Taylor and Andreas Tillmar and Tsybovsky, {Iosif S} and Chris Tyler-Smith and {van der Gaag}, {Kristiaan J} and Daniel Vanek and Ant{\'o}nia V{\"o}lgyi and Denise Ward and Patricia Willemse and Yap, {Eric P H} and Yong, {Rita Y Y} and Pajni{\v c}, {Irena Zupani{\v c}} and Manfred Kayser",

year = "2014",

month = aug,

doi = "10.1002/humu.22599",

language = "English",

volume = "35",

pages = "1021--1032",

journal = "Human Mutation",

issn = "1059-7794",

publisher = "Wiley",

number = "8",

}

Ballantyne, KN, Ralf, A, Aboukhalid, R, Achakzai, NM, Anjos, MJ, Ayub, Q, Balažic, J, Ballantyne, J, Ballard, DJ, Berger, B, Bobillo, C, Bouabdellah, M, Burri, H, Capal, T, Caratti, S, Cárdenas, J, Cartault, F, Carvalho, EF, Carvalho, M, Cheng, B, Coble, MD, Comas, D, Corach, D, D'Amato, ME, Davison, S, de Knijff, P, De Ungria, MCA, Decorte, R, Dobosz, T, Dupuy, BM, Elmrghni, S, Gliwiński, M, Gomes, SC, Grol, L, Haas, C, Hanson, E, Henke, J, Henke, L, Herrera-Rodríguez, F, Hill, CR, Holmlund, G, Honda, K, Immel, U-D, Inokuchi, S, Jobling, MA, Kaddura, M, Kim, JS, Kim, SH, Kim, W, King, TE, Klausriegler, E, Kling, D, Kovačević, L, Kovatsi, L, Krajewski, P, Kravchenko, S, Larmuseau, MHD, Lee, EY, Lessig, R, Livshits, LA, Marjanović, D, Minarik, M, Mizuno, N, Moreira, H, Morling, N, Mukherjee, M, Munier, P, Nagaraju, J, Neuhuber, F, Nie, S, Nilasitsataporn, P, Nishi, T, Oh, HH, Olofsson, J, Onofri, V, Palo, JU, Pamjav, H, Parson, W, Petlach, M, Phillips, C, Ploski, R, Prasad, SPR, Primorac, D, Purnomo, GA, Purps, J, Rangel-Villalobos, H, Rębała, K, Rerkamnuaychoke, B, Gonzalez, DR, Robino, C, Roewer, L, Rosa, A, Sajantila, A, Sala, A, Salvador, JM, Sanz, P, Schmitt, C, Sharma, AK, Silva, DA, Shin, K-J, Sijen, T, Sirker, M, Siváková, D, Skaro, V, Solano-Matamoros, C, Souto, L, Stenzl, V, Sudoyo, H, Court, DS, Tagliabracci, A, Taylor, D, Tillmar, A, Tsybovsky, IS, Tyler-Smith, C, van der Gaag, KJ, Vanek, D, Völgyi, A, Ward, D, Willemse, P, Yap, EPH, Yong, RYY, Pajnič, IZ & Kayser, M 2014, 'Towards male individualization with rapidly mutating Y-chromosomal STRs', Human Mutation, vol. 35, no. 8, pp. 1021-1032. https://doi.org/10.1002/humu.22599

TY - JOUR

T1 - Towards male individualization with rapidly mutating Y-chromosomal STRs

AU - Ballantyne, Kaye N

AU - Ralf, Arwin

AU - Aboukhalid, Rachid

AU - Achakzai, Niaz M

AU - Anjos, Maria J

AU - Ayub, Qasim

AU - Balažic, Jože

AU - Ballantyne, Jack

AU - Ballard, David J

AU - Berger, Burkhard

AU - Bobillo, Cecilia

AU - Bouabdellah, Mehdi

AU - Burri, Helen

AU - Capal, Tomas

AU - Caratti, Stefano

AU - Cárdenas, Jorge

AU - Cartault, François

AU - Carvalho, Elizeu F

AU - Carvalho, Monica

AU - Cheng, Baowen

AU - Coble, Michael D

AU - Comas, David

AU - Corach, Daniel

AU - D'Amato, Maria E

AU - Davison, Sean

AU - de Knijff, Peter

AU - De Ungria, Maria Corazon A

AU - Decorte, Ronny

AU - Dobosz, Tadeusz

AU - Dupuy, Berit M

AU - Elmrghni, Samir

AU - Gliwiński, Mateusz

AU - Gomes, Sara C

AU - Grol, Laurens

AU - Haas, Cordula

AU - Hanson, Erin

AU - Henke, Jürgen

AU - Henke, Lotte

AU - Herrera-Rodríguez, Fabiola

AU - Hill, Carolyn R

AU - Holmlund, Gunilla

AU - Honda, Katsuya

AU - Immel, Uta-Dorothee

AU - Inokuchi, Shota

AU - Jobling, Mark A

AU - Kaddura, Mahmoud

AU - Kim, Jong S

AU - Kim, Soon H

AU - Kim, Wook

AU - King, Turi E

AU - Klausriegler, Eva

AU - Kling, Daniel

AU - Kovačević, Lejla

AU - Kovatsi, Leda

AU - Krajewski, Paweł

AU - Kravchenko, Sergey

AU - Larmuseau, Maarten H D

AU - Lee, Eun Young

AU - Lessig, Ruediger

AU - Livshits, Ludmila A

AU - Marjanović, Damir

AU - Minarik, Marek

AU - Mizuno, Natsuko

AU - Moreira, Helena

AU - Morling, Niels

AU - Mukherjee, Meeta

AU - Munier, Patrick

AU - Nagaraju, Javaregowda

AU - Neuhuber, Franz

AU - Nie, Shengjie

AU - Nilasitsataporn, Premlaphat

AU - Nishi, Takeki

AU - Oh, Hye H

AU - Olofsson, Jill

AU - Onofri, Valerio

AU - Palo, Jukka U

AU - Pamjav, Horolma

AU - Parson, Walther

AU - Petlach, Michal

AU - Phillips, Christopher

AU - Ploski, Rafal

AU - Prasad, Samayamantri P R

AU - Primorac, Dragan

AU - Purnomo, Gludhug A

AU - Purps, Josephine

AU - Rangel-Villalobos, Hector

AU - Rębała, Krzysztof

AU - Rerkamnuaychoke, Budsaba

AU - Gonzalez, Danel Rey

AU - Robino, Carlo

AU - Roewer, Lutz

AU - Rosa, Alexandra

AU - Sajantila, Antti

AU - Sala, Andrea

AU - Salvador, Jazelyn M

AU - Sanz, Paula

AU - Schmitt, Cornelia

AU - Sharma, Anil K

AU - Silva, Dayse A

AU - Shin, Kyoung-Jin

AU - Sijen, Titia

AU - Sirker, Miriam

AU - Siváková, Daniela

AU - Skaro, Vedrana

AU - Solano-Matamoros, Carlos

AU - Souto, Luis

AU - Stenzl, Vlastimil

AU - Sudoyo, Herawati

AU - Court, Denise Syndercombe

AU - Tagliabracci, Adriano

AU - Taylor, Duncan

AU - Tillmar, Andreas

AU - Tsybovsky, Iosif S

AU - Tyler-Smith, Chris

AU - van der Gaag, Kristiaan J

AU - Vanek, Daniel

AU - Völgyi, Antónia

AU - Ward, Denise

AU - Willemse, Patricia

AU - Yap, Eric P H

AU - Yong, Rita Y Y

AU - Pajnič, Irena Zupanič

AU - Kayser, Manfred

PY - 2014/8

Y1 - 2014/8

N2 - Relevant for various areas of human genetics, Y-chromosomal STRs (Y-STRs) are commonly used for testing close paternal relationships amongst 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: 0.99919-0.9999988). 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% non-unique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). AMOVA 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 fathers/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.

AB - Relevant for various areas of human genetics, Y-chromosomal STRs (Y-STRs) are commonly used for testing close paternal relationships amongst 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: 0.99919-0.9999988). 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% non-unique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). AMOVA 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 fathers/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.

U2 - 10.1002/humu.22599

DO - 10.1002/humu.22599

M3 - Article

C2 - 24917567

SN - 1059-7794

VL - 35

SP - 1021

EP - 1032

JO - Human Mutation

JF - Human Mutation

IS - 8

ER -

Towards male individualization with rapidly mutating Y-chromosomal STRs

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