11 results on '"Capal T"'
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2. Towards complete male individualization with rapidly mutating Y-chromosomal STRs
- Author
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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
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- 2014
3. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- Author
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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
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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
4. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise
- Author
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Santos, C, Fondevila, M, Ballard, D, Banemann, R, Bento, AM, Børsting, C, Branicki, W, BRISIGHELLI, FRANCESCA, Burrington, M, Capal, T, Chaitanya, L, Daniel, R, Decroyer, V, England, R, Gettings, KB, Gross, TE, Haas, C, Harteveld, J, Hoff-Olsen, P, Hoffmann, A, Kayser, M, Kohler, P, Linacre, A, Mayr-Eduardoff, M, McGovern, C, Morling, N, O'Donnell, G, Parson, W, Pascali, VL, Porto, MJ, Roseth, A, Schneider, PM, Sijen, T, Stenzl, V, Court, DS, Templeton, JE, Turanska, M, Vallone, PM, van Oorschot, RAH, Zatkalikova, L, Carracedo, Á, Phillips, C, Santos, C, Fondevila, M, Ballard, D, Banemann, R, Bento, AM, Børsting, C, Branicki, W, BRISIGHELLI, FRANCESCA, Burrington, M, Capal, T, Chaitanya, L, Daniel, R, Decroyer, V, England, R, Gettings, KB, Gross, TE, Haas, C, Harteveld, J, Hoff-Olsen, P, Hoffmann, A, Kayser, M, Kohler, P, Linacre, A, Mayr-Eduardoff, M, McGovern, C, Morling, N, O'Donnell, G, Parson, W, Pascali, VL, Porto, MJ, Roseth, A, Schneider, PM, Sijen, T, Stenzl, V, Court, DS, Templeton, JE, Turanska, M, Vallone, PM, van Oorschot, RAH, Zatkalikova, L, Carracedo, Á, and Phillips, C
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- 2015
5. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels:Results of a collaborative EDNAP exercise
- Author
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Santos, C, Fondevila, M, Ballard, D, Banemann, R, Bento, A M, Børsting, C, Branicki, W, Brisighelli, F, Burrington, M, Capal, T, Chaitanya, L, Daniel, R, Decroyer, V, England, R, Gettings, K B, Gross, T E, Haas, C, Harteveld, J, Hoff-Olsen, P, Hoffmann, A, Kayser, M, Kohler, P, Linacre, A, Mayr-Eduardoff, M, McGovern, C, Morling, N, O'Donnell, G, Parson, W, Pascali, V L, Porto, M J, Roseth, A, Schneider, P M, Sijen, T, Stenzl, V, Court, D Syndercombe, Templeton, J E, Turanska, M, Vallone, P M, Oorschot, R A H van, Zatkalikova, L, Carracedo, Á, Phillips, C, Santos, C, Fondevila, M, Ballard, D, Banemann, R, Bento, A M, Børsting, C, Branicki, W, Brisighelli, F, Burrington, M, Capal, T, Chaitanya, L, Daniel, R, Decroyer, V, England, R, Gettings, K B, Gross, T E, Haas, C, Harteveld, J, Hoff-Olsen, P, Hoffmann, A, Kayser, M, Kohler, P, Linacre, A, Mayr-Eduardoff, M, McGovern, C, Morling, N, O'Donnell, G, Parson, W, Pascali, V L, Porto, M J, Roseth, A, Schneider, P M, Sijen, T, Stenzl, V, Court, D Syndercombe, Templeton, J E, Turanska, M, Vallone, P M, Oorschot, R A H van, Zatkalikova, L, Carracedo, Á, and Phillips, C
- Abstract
There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain
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- 2015
6. Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour
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Chaitanya, L.C. (Lakshmi), Walsh, S. (Susan), Andersen, J.D. (Jeppe Dyrberg), Ansell, R. (Ricky), Ballantyne, K. (Kaye), Ballard, D.J. (David), Banemann, R. (Regine), Bauer, C.M. (Christiane Maria), Bento, A.M. (Ana Margarida), Brisighelli, F. (Francesca), Capal, T. (Tomas), Clarisse, L. (Lindy), Gross, T.E. (Theresa), Haas, C. (Cordula), Hoff-Olsen, P. (Per), Hollard, C. (Clémence), Keyser, C. (Christine), Kiesler, K.M. (Kevin), Kohler, P. (Priscila), Kupiec, T. (Tomasz), Linacre, A. (Adrian), Minawi, A. (Anglika), Morling, N. (Niels), Nilsson, H. (Helena), Norén, L. (Lina), Ottens, R. (Renée), Palo, J. (Jukka), Parson, W. (Walther), Pascali, V.L. (Vincenzo), Phillips, C. (Christopher), Porto, M.J. (Maria João), Sajantila, A. (Antti), Schneider, P.M. (Peter), Sijen, T. (Titia), Söchtig, J. (Jens), Syndercombe-Court, D. (Denise), Tillmar, A. (Andreas), Turanska, M. (Martina), Vallone, P.M. (Peter), Zatkalíková, L. (Lívia), Zidkova, A. (Anastassiya), Branicki, W. (Wojciech), Kayser, M.H. (Manfred), Chaitanya, L.C. (Lakshmi), Walsh, S. (Susan), Andersen, J.D. (Jeppe Dyrberg), Ansell, R. (Ricky), Ballantyne, K. (Kaye), Ballard, D.J. (David), Banemann, R. (Regine), Bauer, C.M. (Christiane Maria), Bento, A.M. (Ana Margarida), Brisighelli, F. (Francesca), Capal, T. (Tomas), Clarisse, L. (Lindy), Gross, T.E. (Theresa), Haas, C. (Cordula), Hoff-Olsen, P. (Per), Hollard, C. (Clémence), Keyser, C. (Christine), Kiesler, K.M. (Kevin), Kohler, P. (Priscila), Kupiec, T. (Tomasz), Linacre, A. (Adrian), Minawi, A. (Anglika), Morling, N. (Niels), Nilsson, H. (Helena), Norén, L. (Lina), Ottens, R. (Renée), Palo, J. (Jukka), Parson, W. (Walther), Pascali, V.L. (Vincenzo), Phillips, C. (Christopher), Porto, M.J. (Maria João), Sajantila, A. (Antti), Schneider, P.M. (Peter), Sijen, T. (Titia), Söchtig, J. (Jens), Syndercombe-Court, D. (Denise), Tillmar, A. (Andreas), Turanska, M. (Martina), Vallone, P.M. (Peter), Zatkalíková, L. (Lívia), Zidkova, A. (Anastassiya), Branicki, W. (Wojciech), and Kayser, M.H. (Manfred)
- Abstract
The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FT
- Published
- 2014
- Full Text
- View/download PDF
7. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- Author
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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
8. Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour
- Author
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Chaitanya, L, Walsh, S, Andersen, Jd, Ansell, R, Ballantyne, K, Ballard, D, Banemann, R, Bauer, Cm, Bento, Am, Brisighelli, Francesca, Capal, T, Clarisse, L, Gross, Te, Haas, C, Hoff Olsen, P, Hollard, C, Keyser, C, Kiesler, Km, Kohler, P, Kupiec, T, Linacre, A, Minawi, A, Morling, N, Nilsson, H, Norén, L, Ottens, R, Palo, Ju, Parson, W, Pascali, Vincenzo Lorenzo, Phillips, C, Porto, Mj, Sajantila, A, Schneider, Pm, Sijen, T, Söchtig, J, Syndercombe Court, D, Tillmar, A, Turanska, M, Vallone, Pm, Zatkalíková, L, Zidkova, A, Branicki, W, Kayser, M., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Pascali, Vincenzo Lorenzo (ORCID:0000-0001-6520-5224), Chaitanya, L, Walsh, S, Andersen, Jd, Ansell, R, Ballantyne, K, Ballard, D, Banemann, R, Bauer, Cm, Bento, Am, Brisighelli, Francesca, Capal, T, Clarisse, L, Gross, Te, Haas, C, Hoff Olsen, P, Hollard, C, Keyser, C, Kiesler, Km, Kohler, P, Kupiec, T, Linacre, A, Minawi, A, Morling, N, Nilsson, H, Norén, L, Ottens, R, Palo, Ju, Parson, W, Pascali, Vincenzo Lorenzo, Phillips, C, Porto, Mj, Sajantila, A, Schneider, Pm, Sijen, T, Söchtig, J, Syndercombe Court, D, Tillmar, A, Turanska, M, Vallone, Pm, Zatkalíková, L, Zidkova, A, Branicki, W, Kayser, M., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), and Pascali, Vincenzo Lorenzo (ORCID:0000-0001-6520-5224)
- Abstract
The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising la
- Published
- 2014
9. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.
- Author
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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, and Roewer L
- Subjects
- Alleles, Forensic Genetics, Humans, Chromosomes, Human, Y, Haplotypes, Microsatellite Repeats
- Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. 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., (Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
10. Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.
- Author
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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
11. Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour.
- Author
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Chaitanya L, Walsh S, Andersen JD, Ansell R, Ballantyne K, Ballard D, Banemann R, Bauer CM, Bento AM, Brisighelli F, Capal T, Clarisse L, Gross TE, Haas C, Hoff-Olsen P, Hollard C, Keyser C, Kiesler KM, Kohler P, Kupiec T, Linacre A, Minawi A, Morling N, Nilsson H, Norén L, Ottens R, Palo JU, Parson W, Pascali VL, Phillips C, Porto MJ, Sajantila A, Schneider PM, Sijen T, Söchtig J, Syndercombe-Court D, Tillmar A, Turanska M, Vallone PM, Zatkalíková L, Zidkova A, Branicki W, and Kayser M
- Subjects
- Humans, DNA genetics, Eye Color genetics
- Abstract
The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising laboratory and judged; 96% of the eye colour phenotypes were inferred correctly across 100 samples and 19 laboratories. The high success rates in genotyping and eye colour phenotyping clearly demonstrate the reproducibility and the robustness of the IrisPlex assay as well as the accuracy of the IrisPlex model to predict blue and brown eye colour from DNA. Additionally, this study demonstrates the ease with which the IrisPlex system is implementable and applicable across forensic laboratories around the world with varying pre-existing experiences., (Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
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