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12. The Dutch Y-chromosomal landscape

Author

Altena, E, Smeding, R, van der Gaag, KJ, Larmuseau, MHD, Decorte, R, Lao Grueso, Oscar, Kayser, Manfred, Kraaijenbrink, T, de Knijff, P, Altena, E, Smeding, R, van der Gaag, KJ, Larmuseau, MHD, Decorte, R, Lao Grueso, Oscar, Kayser, Manfred, Kraaijenbrink, T, and de Knijff, P

Published
2020

19. The Dutch Y-chromosomal landscape

Author

Altena, E. (Eveline), Smeding, R. (Risha), Gaag, K. (Kristiaan) van der, Larmuseau, M.H.D. (Maarten), Decorte, R. (Ronny), Lao Grueso, O. (Oscar), Kayser, M.H. (Manfred), Kraaijenbrink, T. (Thirsa), Knijff, P. (Peter) de, Altena, E. (Eveline), Smeding, R. (Risha), Gaag, K. (Kristiaan) van der, Larmuseau, M.H.D. (Maarten), Decorte, R. (Ronny), Lao Grueso, O. (Oscar), Kayser, M.H. (Manfred), Kraaijenbrink, T. (Thirsa), and Knijff, P. (Peter) de

Abstract

Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic–geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.

Published
2019
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24. 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

26. Genetic Genealogy Comes of Age: Perspectives on the Use of Deep-Rooted Pedigrees in Human Population Genetics

Author

Larmuseau, MHD, Van Geystelen, A, Oven, Mannis, Decorte, R, and Genetic Identification

Abstract

In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies. Am J Phys Anthropol 150:505-511, 2013. (C) 2013 Wiley Periodicals, Inc.

Published
2013

27. Deep Into the Roots of the Libyan Tuareg: A Genetic Survey of Their Paternal Heritage

Author

Ottoni, C, Larmuseau, M, Vanderheyden, M, MARTINEZ-LABARGA, Mc, Primativo, G, Biondi, G, Decorte, R, and Rickards, O

Subjects
Genetic Markers, Male, Population, DNA Mutational Analysis, Libya, Biology, STR, Settore BIO/08, Polymerase Chain Reaction, Haplogroup, Nuclear Family, Fathers, Tuareg, Y-chromosome, biallelic markers, Genetic variation, Cluster Analysis, Humans, education, Holocene, Phylogeny, Transients and Migrants, education.field_of_study, Chromosomes, Human, Y, Haplotype, Racial Groups, Genetic Variation, Archaeology, Haplotypes, Anthropology, Data Interpretation, Statistical, Str loci, Ethnology, Gene pool, Anatomy, Founder effect, Microsatellite Repeats
Abstract

Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.

Published
2011

28. Signature of selection on the rhodopsin gene in the marine radiation of American seven-spined gobies (Gobiidae, Gobiosomatini)

Author

Larmuseau, M.H.D., Vanhove, M.P.M., Huyse, T., Volckaert, F.A.M., and Decorte, R.

Subjects
Photoreceptors, Phylogenetics, Rhodopsin, Genes, Gobiidae [Gobies], Amino acids, Spectral analysis, Photic environment, Radiation balance
Abstract

In comparison with terrestrial and freshwater ecosystems, information about speciation modes and the role of selection in marine environments is scarce. Recent studies have indicated that spectral adaptation could play an important role in the diversification of marine species flocks. Natural selection influences specific amino acids (AAs) that are involved in the spectral tuning mechanism of visual pigment genes. To study the wider occurrence and the characteristics of spectral adaptation in marine radiations, a reinterpretation of the rhodopsin (RH1) data of American seven-spined gobies (genus Elacatinus; Gobiidae; Teleostei) was carried out. Reanalysis revealed that some AAs, which are well known in the literature as spectral tuning sites, are variable in Elacatinus. Those crucial AA substitutions originated polyphyletically, indicating convergent evolution within the genus Elacatinus. Moreover, statistical tests based on the dN/dS ratio detected selection in several phylogenetic lineages and at specific AAs. Many of these AAs were previously shown to be under selection in other marine radiations. Therefore, the current phylogenetic approach provided an extended list of AAs that are probably involved in spectral tuning, and which should be validated by mutagenic experiments.

Published
2011

30. 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
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31. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

Author

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, Balitzki, B, Tschumi, S, Ballard, D, Court, D, 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, Jonkisz, A, Frank, We, Furac, I, Gehrig, C, Castella, V, Grskovic, B, Haas, C, Wobst, J, Hadzic, G, Drobnic, K, Immel, Ud, Lessig, R, Jakovski, Z, Ilievska, T, Klann, Ae, García, Cc, De Knijff, P, 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, L, Moreira, H, Neto, R, Nogueira, Tl, Morling, N, Onofri, V, Tagliabracci, A, Pamjav, H, Pelotti, S, Abreu Glowacka, M, Cárdenas, J, Rey Gonzalez, D, Salas, A, Brisighelli, Francesca, Capelli, C. Et Al, Brisighelli, Francesca (ORCID:0000-0001-5469-4413), 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, Balitzki, B, Tschumi, S, Ballard, D, Court, D, 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, Jonkisz, A, Frank, We, Furac, I, Gehrig, C, Castella, V, Grskovic, B, Haas, C, Wobst, J, Hadzic, G, Drobnic, K, Immel, Ud, Lessig, R, Jakovski, Z, Ilievska, T, Klann, Ae, García, Cc, De Knijff, P, 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, L, Moreira, H, Neto, R, Nogueira, Tl, Morling, N, Onofri, V, Tagliabracci, A, Pamjav, H, Pelotti, S, Abreu Glowacka, M, Cárdenas, J, Rey Gonzalez, D, Salas, A, Brisighelli, Francesca, Capelli, C. Et Al, and Brisighelli, Francesca (ORCID:0000-0001-5469-4413)

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.

Published
2014

33. Y-chromosomal diversity within Europe is clinal and influenced primarily by geography rather than language

Author

Rosser, Z. H., Zerjal, T., Hurles, M. E., Adojaan, M., Alavantic, D., Amorim, A., Amos, W., Armenteros, M., Arroyo, E., Barbujani, Guido, Beckman, L., BERTRANPETIT J., Bosch E., Bradley, D. G., Brede, G., Cooper, G., Corte Real, H. B. S. M., de Knijff, P., Decorte, R., Dubrova, Y. E., Evgrafov, O., Gilissen, A, Glisic, S., Golge, M, Hill, E. W., Jeziorowska, A, Kalaydjieva, L, Kayser, M, Kivisild, T, Kravchenko, S., Krumina, A, Kucinskas, V, Lavinha, J, Livshits, L. A., Malaspina, P, Syrrou, M, Mcelreavey, K, Meitinger, Ta, Mikelsaar, Av, Mitchell, Rj, Nafa, K, Nicholson, J, Nørby, S, Pandya, A, Parik, J, Patsalis, Pc, Pereira, L, Peterlin, B, Pielberg, G, Prata, Mj, Previderè, C, Roewer, L, Rootsi, S, Rubinsztein, Dc, Saillard, J, Santos, Fr, Stefanescu, G, Sykes, Bc, Tolun, A, Villems, R, Tyler Smith, C, and Jobling, Ma

Published
2000

34. Mutability of Y-chromosomal microsatellites: Rates, characteristics, molecular bases, and rorensic implications

Author

Ballantyne, K. (Kaye), Goedbloed, M.A. (Miriam), Fang, R.N. (Rixun), Schaap, O. (Onno), Lao Grueso, O. (Oscar), Wollstein, A. (Andreas), Choi, Y. (Ying), Duijn, K. (Kate) van, Vermeulen, M. (Mark), Brauer, S. (Silke), Decorte, R. (Ronny), Poetsch, M. (Micaela), Wurmb-Schwark, N. (Nicole) von, Knijff, P. (Peter) de, Labuda, D. (Damian), Vézina, H. (Hélne), Knoblauch, H. (Hans), Lessig, R. (Rüdiger), Roewer, L. (Lutz), Ploski, R. (Rafal), Dobosz, T. (Tadeusz), Henke, J. (Jürgen), Furtado, M.R. (Manohar), Kayser, M.H. (Manfred), Ballantyne, K. (Kaye), Goedbloed, M.A. (Miriam), Fang, R.N. (Rixun), Schaap, O. (Onno), Lao Grueso, O. (Oscar), Wollstein, A. (Andreas), Choi, Y. (Ying), Duijn, K. (Kate) van, Vermeulen, M. (Mark), Brauer, S. (Silke), Decorte, R. (Ronny), Poetsch, M. (Micaela), Wurmb-Schwark, N. (Nicole) von, Knijff, P. (Peter) de, Labuda, D. (Damian), Vézina, H. (Hélne), Knoblauch, H. (Hans), Lessig, R. (Rüdiger), Roewer, L. (Lutz), Ploski, R. (Rafal), Dobosz, T. (Tadeusz), Henke, J. (Jürgen), Furtado, M.R. (Manohar), and Kayser, M.H. (Manfred)

Abstract

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10-4(95% credible interval [CI], 1.38 × 10-5- 2.02 × 10-3) to 7.44 × 10-2(95% CI, 6.51 × 10-2- 9.09 × 10-2) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the father's age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.

Published
2010
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37. Mutations in human complement regulator, membrane cofactor protein (CD46), predispose to development of familial hemolytic uremic syndrome

Author

UCL - Cliniques universitaires Saint-Luc, UCL, Richards, A, Pirson, Yves, Kemp, EJ, Liszewski, MK, Goodship, JA, Lampe, AK, Decorte, R, Muslumanoglu, MH, Kavukcu, S, Filler, G, Wen, LS, Atkinson, JP, Goodship, THJ, UCL - Cliniques universitaires Saint-Luc, UCL, Richards, A, Pirson, Yves, Kemp, EJ, Liszewski, MK, Goodship, JA, Lampe, AK, Decorte, R, Muslumanoglu, MH, Kavukcu, S, Filler, G, Wen, LS, Atkinson, JP, and Goodship, THJ

Abstract

Membrane cofactor protein (MCP; CD46) is a widely expressed transmembrane complement regulator. Like factor H it inhibits complement activation by regulating Ob deposition on targets. Factor H mutations occur in 10-20% of patients with hemolytic uremic syndrome (HUS). We hypothesized that MCP mutations could predispose to HUS, and we sequenced MCP coding exons in affected individuals from 30 families. MCP mutations were detected in affected individuals of three families: a deletion of two amino acids (D237/S238) in family 1 (heterozygous) and a substitution, S206P, in families 2 (heterozygous) and 3 (homozygous). We evaluated protein expression and function in peripheral blood mononuclear cells from these individuals. An individual with the D237/S238 deletion had reduced MCP levels and approximate to50% C3b binding compared with normal controls. Individuals with the S206P change expressed normal quantities of protein, but demonstrated approximate to50% reduction in C3b binding in heterozygotes and complete lack of C3b binding in homozygotes. MCP expression and function was evaluated in transfectants reproducing these mutations. The deletion mutant was retained intracellularly. S206P protein was expressed on the cell surface but had a reduced ability to prevent complement activation, consistent with its reduced C3b binding and cofactor activity. This study presents further evidence that complement dysregulation predisposes to development of thrombotic microangiopathy and that screening patients for such defects could provide informed treatment strategies.

Published
2003

38. Familial hemolytic uremic syndrome and mutations in membrane cofactor protein (MCP; CD46) of the complement system.

Author

UCL - Cliniques universitaires Saint-Luc, UCL, Richards, A, Pirson, Yves, Kemp, EJ, Liszewski, K, Goodship, JA, Lampe, AK, Decorte, R, Muslumanoglu, H, Kavukcu, S, Filler, G, Wen, LS, Atkinson, JP, Goodship, THJ, 36th Annual Meeting of the American-Society-of-Nephrology, UCL - Cliniques universitaires Saint-Luc, UCL, Richards, A, Pirson, Yves, Kemp, EJ, Liszewski, K, Goodship, JA, Lampe, AK, Decorte, R, Muslumanoglu, H, Kavukcu, S, Filler, G, Wen, LS, Atkinson, JP, Goodship, THJ, and 36th Annual Meeting of the American-Society-of-Nephrology

Published
2003

39. Identification of internal variation in the pseudoautosomal VNTR DXYS17, with nonrandom distribution of the alleles on the X and the Y chromosomes

Author

Decorte, R., Wu, R., Marynen, P., and Cassiman, J. J.

Subjects
Genetic Markers, Male, X Chromosome, Base Sequence, Genotype, Research Support, Non-U.S. Gov't, European Continental Ancestry Group, Molecular Sequence Data, Restriction Mapping, DNA, Satellite, Polymerase Chain Reaction, White People, Blotting, Southern, Sex Factors, Belgium, Y Chromosome, Humans, Comparative Study, Female, Alleles, Research Article, DNA Primers
Abstract

The PCR technique was used to analyze the DXYS17 locus in the pseudoautosomal region of the X and the Y chromosomes. Analysis on an automated DNA sequencer allowed for sensitive and highly accurate typing of 16 different alleles with a size between 480 and 1,100 bp. Two DXYS17 alleles migrated with the same size on agarose or denaturing polyacrylamide gels but with different mobilities on nondenaturing polyacrylamide gels. Sequence analysis showed that, while an identical number of repeats were present in both alleles, differences in the composition of the units were observed. The origin of these differences was found in the 28- and 33-bp units, which only had a specific repeat pattern at the 5' and 3' ends of the region. The genotype distribution for DXYS17 in a Caucasian population did not deviate from the values expected under Hardy-Weinberg equilibrium. However, the frequency of one allele and one genotype was significantly different between males and females. Segregation analysis showed that this difference was the result of a nonrandom distribution of certain alleles on the sex chromosomes in males. ispartof: American Journal of Human Genetics vol:54 issue:3 pages:506-15 ispartof: location:United States status: published

Published
1994

40. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language.

Author

Rosser, Z H, Zerjal, T, Hurles, M E, Adojaan, M, Alavantic, D, Amorim, A, Amos, W, Armenteros, M, Arroyo, E, Barbujani, G, Beckman, G, Beckman, L, Bertranpetit, J, Bosch, E, Bradley, D G, Brede, G, Cooper, G, Côrte-Real, H B, de Knijff, P, Decorte, R, Dubrova, Y E, Evgrafov, O, Gilissen, A, Glisic, S, Gölge, M, Hill, E W, Jeziorowska, A, Kalaydjieva, L, Kayser, M, Kivisild, T, Kravchenko, S A, Krumina, A, Kucinskas, V, Lavinha, J, Livshits, L A, Malaspina, P, Maria, S, McElreavey, K, Meitinger, T A, Mikelsaar, A V, Mitchell, R J, Nafa, K, Nicholson, J, Nørby, S, Pandya, A, Parik, J, Patsalis, P C, Pereira, L, Peterlin, B, Pielberg, G, Prata, M J, Previderé, C, Roewer, L, Rootsi, S, Rubinsztein, D C, Saillard, J, Santos, F R, Stefanescu, G, Sykes, B C, Tolun, A, Villems, R, Tyler-Smith, C, Jobling, M A, Rosser, Z H, Zerjal, T, Hurles, M E, Adojaan, M, Alavantic, D, Amorim, A, Amos, W, Armenteros, M, Arroyo, E, Barbujani, G, Beckman, G, Beckman, L, Bertranpetit, J, Bosch, E, Bradley, D G, Brede, G, Cooper, G, Côrte-Real, H B, de Knijff, P, Decorte, R, Dubrova, Y E, Evgrafov, O, Gilissen, A, Glisic, S, Gölge, M, Hill, E W, Jeziorowska, A, Kalaydjieva, L, Kayser, M, Kivisild, T, Kravchenko, S A, Krumina, A, Kucinskas, V, Lavinha, J, Livshits, L A, Malaspina, P, Maria, S, McElreavey, K, Meitinger, T A, Mikelsaar, A V, Mitchell, R J, Nafa, K, Nicholson, J, Nørby, S, Pandya, A, Parik, J, Patsalis, P C, Pereira, L, Peterlin, B, Pielberg, G, Prata, M J, Previderé, C, Roewer, L, Rootsi, S, Rubinsztein, D C, Saillard, J, Santos, F R, Stefanescu, G, Sykes, B C, Tolun, A, Villems, R, Tyler-Smith, C, and Jobling, M A

Abstract

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.

Published
2000
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41. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language

Author

Rosser, ZH, Zerjal, T, Hurles, ME, Adojaan, M, Alavantić, Dragan, Amorim, A, Amos, W, Armenteros, M, Arroyo, E, Barbujani, G, Beckman, G, Beckman, L, Bertranpetit, J, Bosch, E, Bradley, DG, Brede, G, Cooper, G, Corte-Real, HBSM, de Knijff, P, Decorte, R, Dubrova, YE, Evgrafov, O, Gilissen, A, Glišić, Sanja (I), Golge, M, Hill, EW, Jeziorowska, A, Kalaydjieva, L, Kayser, M, Kivisild, T, Kravchenko, SA, Krumina, A, Kucinskas, V, Lavinha, J, Livshits, LA, Malaspina, P, Maria, S, McElreavey, K, Meitinger, TA, Mikelsaar, AV, Mitchell, RJ, Nafa, K, Nicholson, J, Norby, S, Pandya, A, Parik, J, Patsalis, PC, Pereira, L, Peterlin, B, Pielberg, G, Prata, ML, Previdere, C, Roewer, L, Rootsi, S, Rubinsztein, DC, Saillard, J, Santos, FR, Stefanescu, G, Sykes, BC, Tolun, A, Villems, R, Tyler-Smith, C, Jobling, MA, Rosser, ZH, Zerjal, T, Hurles, ME, Adojaan, M, Alavantić, Dragan, Amorim, A, Amos, W, Armenteros, M, Arroyo, E, Barbujani, G, Beckman, G, Beckman, L, Bertranpetit, J, Bosch, E, Bradley, DG, Brede, G, Cooper, G, Corte-Real, HBSM, de Knijff, P, Decorte, R, Dubrova, YE, Evgrafov, O, Gilissen, A, Glišić, Sanja (I), Golge, M, Hill, EW, Jeziorowska, A, Kalaydjieva, L, Kayser, M, Kivisild, T, Kravchenko, SA, Krumina, A, Kucinskas, V, Lavinha, J, Livshits, LA, Malaspina, P, Maria, S, McElreavey, K, Meitinger, TA, Mikelsaar, AV, Mitchell, RJ, Nafa, K, Nicholson, J, Norby, S, Pandya, A, Parik, J, Patsalis, PC, Pereira, L, Peterlin, B, Pielberg, G, Prata, ML, Previdere, C, Roewer, L, Rootsi, S, Rubinsztein, DC, Saillard, J, Santos, FR, Stefanescu, G, Sykes, BC, Tolun, A, Villems, R, Tyler-Smith, C, and Jobling, MA

Abstract

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant dines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.

Published
2000

48. Genetic genealogy comes of age Genetic genealogy comes of age: Perspectives on the use of deep-rooted pedigrees in human population genetics.

Author

Larmuseau, M.H.D., Geystelen, A., Oven, M., and Decorte, R.

Subjects
GENETIC genealogy, GENOMICS, POPULATION, GENETICS, ETHNIC groups, HAPLOIDY
Abstract

ABSTRACT In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies. Am J Phys Anthropol 150:505-511, 2013. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Published
2013
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