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1. Towards complete male individualization with rapidly mutating Y-chromosomal STRs

Author

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, Butler, J, Capal, T, Caratti, S, Carracedo, A, Cartault, F, Carvalho, EF, Cheng, B, Coble, MD, Comas, D, Corach, D, D'Amato, ME, Davison, S, de Carvalho, EF, de Knijff, Peter, de Ungria, M, Decorte, Ronny, Dobosz, T, Dupuy, BM, Elmrghni, S, Gliwinski, M, Gomes, SC, Grol, L, Haas, C, Hanson, E, Henke, J, Hill, CR, Holmlund, G, Honda, K, Immel, U, Inoue, S, Jobling, MA, Kaddura, M, Kim, JS, Kim, SH, Kim, W, King, TE, Klausriegler, E, Kling, D, Kovacevic, LL, Kovatsi, L, Krajewski, P, Kravchenko, S, Larmuseau, Maarten, Lee, EY, Lee, SH, Lessig, R, Livshits, LA, Marjanovic, D, Minarik, M, Mizuno, N, Moreira, H, Morling, N, Mukherjee, M, Nagaraju, J, Neuhuber, F, Nie, S, Nilasitsataporn, P, Nishi, T, Oh, HH, Olofsson, J, Onofri, V, Palo, JU, Pamjav, H, Parson, W, Payet, C, Petlach, M, Phillips, C, Ploski, R, Prasad, SPR, Primorac, D, Purnnomo, GA, Purps, J, Rangel, H, Rebala, K, Rerkamnuaychoke, B, Rey, D, Robino, C, Rodríguez, F, Roewer, L, Rosa, A, Sajantila, A, Sala, A, Salvador, J, Sanz, P, Schmitt, C, Sharma, AK, Silva, DA, Shin, KJ, Sijen, T, Sirker, M, Siváková, D, Skaro, V, Solano-Matamoros, C, Souto, L, Stenzl, V, Sudoyo, H, Syndercombe-Court, D, Tagliabracci, A, Taylor, D, Tillmar, A, Tsybovsky, IS, Tyler-Smith, C, van der Gaag, K, Vanek, D, Völgyi, A, Ward, D, Willemse, P, Winkler, C, Yap, EPH, Yong, RYY, Zupanic Pajnic, I, and Kayser, M

Subjects
haplotypes, paternal lineage, RM YSTRs, Y-STRs, forensic, Y-chromosome
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 RMY-STRs in identifying and separating unrelated and related males and provides a reference database. ispartof: Human Mutation vol:35 issue:8 pages:1021-1032 status: published

Published
2014

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

Author

Ballantyne, K.N., Ralf, A., Aboukhalid, R., Achakzai, N.M., Anjos, M.J., Ayub, Q., Balazic, J., Ballantyne, J., Ballard, D.J., Berger, B., Bobillo, C., Bouabdellah, M., Burri, H., Capal, T., Caratti, S., Cardenas, J., Cartault, F., Carvalho, E.F., Carvalho, M., Cheng, B.W., Coble, M.D., Comas, D., Corach, D., D'Amato, M.E., Davison, S., Knijff, P. de, Ungria, M.C.A. de, Decorte, R., Dobosz, T., Dupuy, B.M., Elmrghni, S., Gliwinski, M., Gomes, S.C., Grol, L., Haas, C., Hanson, E., Henke, J., Henke, L., Herrera-Rodriguez, F., Hill, C.R., Holmlund, G., Honda, K., Immel, U.D., Inokuchi, S., Jobling, M.A., Kaddura, M., Kim, J.S., Kim, S.H., Kim, W., King, T.E., Klausriegler, E., Kling, D., Kovacevic, L., Kovatsi, L., Krajewski, P., Kravchenko, S., Larmuseau, M.H.D., Lee, E.Y., Lessig, R., Livshits, L.A., Marjanovic, D., Minarik, M., Mizuno, N., Moreira, H., Morling, N., Mukherjee, M., Munier, P., Nagaraju, J., Neuhuber, F., Nie, S.J., Nilasitsataporn, P., Nishi, T., Oh, H.H., Olofsson, J., Onofri, V., Palo, J.U., Pamjav, H., Parson, W., Petlach, M., Phillips, C., Ploski, R., Prasad, S.P.R., Primorac, D., Purnomo, G.A., Purps, J., Rangel-Villalobos, H., Rebala, K., Rerkamnuaychoke, B., Gonzalez, D.R., Robino, C., Roewer, L., Rosa, A., Sajantila, A., Sala, A., Salvador, J.M., Sanz, P., Schmitt, C., Sharma, A.K., Silva, D.A., Shin, K.J., Sijen, T., Sirker, M., Sivakova, D., Skaro, V., Solano-Matamoros, C., Souto, L., Stenzl, V., Sudoyo, H., Syndercombe-Court, D., Tagliabracci, A., Taylor, D., Tillmar, A., Tsybovsky, I.S., Tyler-Smith, C., Gaag, K.J. van der, Vanek, D., Volgyi, A., Ward, D., Willemse, P., Yap, E.P.H., Yong, R.Y.Y., Pajnic, I.Z., Kayser, M., Hjelt Institute (-2014), Forensic Medicine, PaleOmics Laboratory, and Genetic Identification

Subjects
Male, Rural Population, haplotypes, Y-chromosome, Y-STRs, RM Y-STRs, paternal lineage, forensic, Asia, Forensic Science, Urban Population, Cell- och molekylärbiologi, education, Paternity, Gene Frequency, Humans, Alleles, Chromosomes, Human, Y, 1184 Genetics, developmental biology, physiology, Genetic Variation, DNA Fingerprinting, RM Y-STRs, Y-STRs, Y-chromosome, forensic, haplotypes, paternal lineage, Pedigree, Europe, Genetics, Population, Africa, 3111 Biomedicine, Americas, Cell and Molecular Biology, Microsatellite Repeats, Rättsmedicin
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 RMY-STRs in identifying and separating unrelated and related males and provides a reference database. Published 2014 Wiley Periodicals, Inc.**

Published
2014

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

Author

Ballantyne, K. (Kaye), Ralf, A. (Arwin), Aboukhalid, R. (Rachid), Achakzai, N.M. (Niaz), Anjos, T. (Tania), Ayub, Q. (Qasim), Balažic, J. (Jože), Ballantyne, J. (Jack), Ballard, D.J. (David), Berger, B. (Burkhard), Bobillo, C. (Cecilia), Bouabdellah, M. (Mehdi), Burri, H. (Helen), Capal, T. (Tomas), Caratti, S. (Stefano), Cárdenas, J. (Jorge), Cartault, F. (François), Carvalho, E.F. (Elizeu), Carvalho, M. (Margarete) de, Cheng, B. (Baowen), Coble, M.D. (Michael), Comas, D. (David), Corach, D. (Daniel), D'Amato, M. (Mauro), Davison, S. (Sean), Knijff, P. (Peter) de, Ungria, M.C.A. (Maria Corazon) de, Decorte, R. (Ronny), Dobosz, T. (Tadeusz), Dupuy, B.M. (Berit), Elmrghni, S. (Samir), Gliwiński, M. (Mateusz), Gomes, S.C. (Sara), Grol, L. (Laurens), Haas, C. (Cordula), Hanson, E. (Erin), Henke, J. (Jürgen), Henke, L. (Lotte), Herrera-Rodríguez, F. (Fabiola), Hill, C.R. (Carolyn), Holmlund, G. (Gunilla), Honda, K. (Katsuya), Immel, U.-D. (Uta-Dorothee), Inokuchi, S. (Shota), Jobling, R., Kaddura, M. (Mahmoud), Kim, J.S. (Jong), Kim, S.H. (Soon), Kim, W. (Wook), King, T.E. (Turi), Klausriegler, E. (Eva), Kling, D. (Daniel), Kovačević, L. (Lejla), Kovatsi, L. (Leda), Krajewski, P. (Paweł), Kravchenko, S. (Sergey), Larmuseau, M.H.D. (Maarten), Lee, E.Y. (Eun Young), Lessig, R. (Rüdiger), Livshits, L.A. (Ludmila), Marjanović, D. (Damir), Minarik, M. (Marek), Mizuno, N. (Natsuko), Moreira, H. (Helena), Morling, N. (Niels), Mukherjee, M. (Meeta), Munier, P. (Patrick), Nagaraju, J. (Javaregowda), Neuhuber, F. (Franz), Nie, S. (Shengjie), Nilasitsataporn, P. (Premlaphat), Nishi, T. (Takeki), Oh, H.H. (Hye), Olofsson, S. (Sylvia), Onofri, V. (Valerio), Palo, J. (Jukka), Pamjav, H. (Horolma), Parson, W. (Walther), Petlach, M. (Michal), Phillips, C. (Christopher), Ploski, R. (Rafal), Prasad, S.P.R. (Samayamantri P.), Primorac, D. (Dragan), Purnomo, G.A. (Gludhug), Purps, J. (Josephine), Rangel-Villalobos, H. (Hector), Reogonekbała, K. (Krzysztof), Rerkamnuaychoke, B. (Budsaba), Gonzalez, D.R. (Danel Rey), Robino, C. (Carlo), Roewer, L. (Lutz), Rosa, A. (Anna) de, Sajantila, A. (Antti), Sala, A. (Andrea), Salvador, J.M. (Jazelyn), Sanz, P. (Paula), Schmitt, C. (Christian), Sharma, A.K. (Anisha K.), Silva, D.A. (Dayse), Shin, K.-J. (Kyoung-Jin), Sijen, T. (Titia), Sirker, M. (Miriam), Siváková, D. (Daniela), Škaro, V. (Vedrana), Solano-Matamoros, C. (Carlos), Souto, L. (L.), Stenzl, V. (Vlastimil), Sudoyo, H. (Herawati), Syndercombe-Court, D. (Denise), Tagliabracci, A. (Adriano), Taylor, D. (Duncan), Tillmar, A. (Andreas), Tsybovsky, I.S. (Iosif), Tyler-Smith, C. (Chris), Gaag, K. (Kristiaan) van der, Vanek, D. (Daniel), Völgyi, A. (Antónia), Ward, D. (Denise), Willemse, P. (Patricia), Yap, E.P.H. (Eric), Yong, Z-Y. (Ze-Yie), Pajnič, I.Z. (Irena Zupanič), Kayser, M.H. (Manfred), Ballantyne, K. (Kaye), Ralf, A. (Arwin), Aboukhalid, R. (Rachid), Achakzai, N.M. (Niaz), Anjos, T. (Tania), Ayub, Q. (Qasim), Balažic, J. (Jože), Ballantyne, J. (Jack), Ballard, D.J. (David), Berger, B. (Burkhard), Bobillo, C. (Cecilia), Bouabdellah, M. (Mehdi), Burri, H. (Helen), Capal, T. (Tomas), Caratti, S. (Stefano), Cárdenas, J. (Jorge), Cartault, F. (François), Carvalho, E.F. (Elizeu), Carvalho, M. (Margarete) de, Cheng, B. (Baowen), Coble, M.D. (Michael), Comas, D. (David), Corach, D. (Daniel), D'Amato, M. (Mauro), Davison, S. (Sean), Knijff, P. (Peter) de, Ungria, M.C.A. (Maria Corazon) de, Decorte, R. (Ronny), Dobosz, T. (Tadeusz), Dupuy, B.M. (Berit), Elmrghni, S. (Samir), Gliwiński, M. (Mateusz), Gomes, S.C. (Sara), Grol, L. (Laurens), Haas, C. (Cordula), Hanson, E. (Erin), Henke, J. (Jürgen), Henke, L. (Lotte), Herrera-Rodríguez, F. (Fabiola), Hill, C.R. (Carolyn), Holmlund, G. (Gunilla), Honda, K. (Katsuya), Immel, U.-D. (Uta-Dorothee), Inokuchi, S. (Shota), Jobling, R., Kaddura, M. (Mahmoud), Kim, J.S. (Jong), Kim, S.H. (Soon), Kim, W. (Wook), King, T.E. (Turi), Klausriegler, E. (Eva), Kling, D. (Daniel), Kovačević, L. (Lejla), Kovatsi, L. (Leda), Krajewski, P. (Paweł), Kravchenko, S. (Sergey), Larmuseau, M.H.D. (Maarten), Lee, E.Y. (Eun Young), Lessig, R. (Rüdiger), Livshits, L.A. (Ludmila), Marjanović, D. (Damir), Minarik, M. (Marek), Mizuno, N. (Natsuko), Moreira, H. (Helena), Morling, N. (Niels), Mukherjee, M. (Meeta), Munier, P. (Patrick), Nagaraju, J. (Javaregowda), Neuhuber, F. (Franz), Nie, S. (Shengjie), Nilasitsataporn, P. (Premlaphat), Nishi, T. (Takeki), Oh, H.H. (Hye), Olofsson, S. (Sylvia), Onofri, V. (Valerio), Palo, J. (Jukka), Pamjav, H. (Horolma), Parson, W. (Walther), Petlach, M. (Michal), Phillips, C. (Christopher), Ploski, R. (Rafal), Prasad, S.P.R. (Samayamantri P.), Primorac, D. (Dragan), Purnomo, G.A. (Gludhug), Purps, J. (Josephine), Rangel-Villalobos, H. (Hector), Reogonekbała, K. (Krzysztof), Rerkamnuaychoke, B. (Budsaba), Gonzalez, D.R. (Danel Rey), Robino, C. (Carlo), Roewer, L. (Lutz), Rosa, A. (Anna) de, Sajantila, A. (Antti), Sala, A. (Andrea), Salvador, J.M. (Jazelyn), Sanz, P. (Paula), Schmitt, C. (Christian), Sharma, A.K. (Anisha K.), Silva, D.A. (Dayse), Shin, K.-J. (Kyoung-Jin), Sijen, T. (Titia), Sirker, M. (Miriam), Siváková, D. (Daniela), Škaro, V. (Vedrana), Solano-Matamoros, C. (Carlos), Souto, L. (L.), Stenzl, V. (Vlastimil), Sudoyo, H. (Herawati), Syndercombe-Court, D. (Denise), Tagliabracci, A. (Adriano), Taylor, D. (Duncan), Tillmar, A. (Andreas), Tsybovsky, I.S. (Iosif), Tyler-Smith, C. (Chris), Gaag, K. (Kristiaan) van der, Vanek, D. (Daniel), Völgyi, A. (Antónia), Ward, D. (Denise), Willemse, P. (Patricia), Yap, E.P.H. (Eric), Yong, Z-Y. (Ze-Yie), Pajnič, I.Z. (Irena Zupanič), and Kayser, M.H. (Manfred)

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

Published
2014
Full Text
View/download PDF

4. Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.

Author

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 MC, 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 UD, 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 MH, 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 SP, 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 KJ, Sijen T, Sirker M, Siváková D, Skaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EP, Yong RY, Pajnič IZ, and Kayser M

Subjects
Africa, Alleles, Americas, Asia, DNA Fingerprinting statistics & numerical data, Europe, Gene Frequency, Genetic Variation, Humans, Male, Paternity, Pedigree, Rural Population, Urban Population, Chromosomes, Human, Y chemistry, DNA Fingerprinting methods, Genetics, Population, Haplotypes, Microsatellite Repeats
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., (© 2014 The Authors. **Human Mutation published by Wiley Periodicals, Inc.)

Published
2014
Full Text
View/download PDF

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