95 results on '"Decorte R"'
Search Results
2. The Dutch Y-chromosomal landscape
- Author
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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
3. A single course of remission reinduction chemotherapy for acute myelogenous leukemia relapsing after allogeneic bone marrow transplantation is complicated by graft-versus-host disease and followed by sustained complete remission
- Author
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Vandenberghe, P, Verhoef, GEG, Emonds, MP, Demuynck, H, Zachée, P, De Wolf-Peeters, C, Decorte, R, Cassiman, JJ, and Boogaerts, MA
- Published
- 1997
- Full Text
- View/download PDF
4. Imatinib mesylate induces durable complete remission of advanced CML persisting after allogeneic bone marrow transplantation
- Author
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Vandenberghe, P, Boeckx, N, Ronsyn, E, Decorte, R, Verhoef, G, and Hagemeijer, A
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- 2003
- Full Text
- View/download PDF
5. The Dutch Y-chromosomal landscape
- Author
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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.
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- 2019
- Full Text
- View/download PDF
6. 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
- 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
7. Deep Into the Roots of the Libyan Tuareg: A Genetic Survey of Their Paternal Heritage
- Author
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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
8. Signature of selection on the rhodopsin gene in the marine radiation of American seven-spined gobies (Gobiidae, Gobiosomatini)
- Author
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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
9. High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment
- Author
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Larmuseau, M H D, primary, Boon, N, additional, Vanderheyden, N, additional, Van Geystelen, A, additional, Larmuseau, H F M, additional, Matthys, K, additional, De Clercq, W, additional, and Decorte, R, additional
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- 2015
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10. 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
11. 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, 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
12. Mutability of Y-chromosomal microsatellites: Rates, characteristics, molecular bases, and rorensic implications
- Author
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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
- Full Text
- View/download PDF
13. Localisation of a new gene for non-specific mental retardation to Xq22-q26
- Author
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Gu, X.X., Decorte, R., Marynen, P., Fryns, J.P., Cassiman, J.J., and Raeymaekers, Peter
- Published
- 1996
14. In the name of the migrant father—Analysis of surname origins identifies genetic admixture events undetectable from genealogical records
- Author
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Larmuseau, M H D, primary, Vanoverbeke, J, additional, Gielis, G, additional, Vanderheyden, N, additional, Larmuseau, H F M, additional, and Decorte, R, additional
- Published
- 2012
- Full Text
- View/download PDF
15. Mutations in human complement regulator, membrane cofactor protein (CD46), predispose to development of familial hemolytic uremic syndrome
- Author
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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
16. Familial hemolytic uremic syndrome and mutations in membrane cofactor protein (MCP; CD46) of the complement system.
- Author
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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
17. Identification of internal variation in the pseudoautosomal VNTR DXYS17, with nonrandom distribution of the alleles on the X and the Y chromosomes
- Author
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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
18. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language.
- Author
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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
- Full Text
- View/download PDF
19. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language
- Author
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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
20. Possible association of CD3 and CD4 polymorphisms with insulin-dependent diabetes mellitus (IDDM)
- Author
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GHABANBASANI, M ZAMANI, primary, BUYSE, I, additional, LEGIUS, E, additional, DECORTE, R, additional, MARYNEN, P, additional, BOUILLON, R, additional, and CASSIMAN, J-J, additional
- Published
- 1994
- Full Text
- View/download PDF
21. Genetic heterogeneity in Rieger eye malformation.
- Author
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Legius, E, primary, de Die-Smulders, C E, additional, Verbraak, F, additional, Habex, H, additional, Decorte, R, additional, Marynen, P, additional, Fryns, J P, additional, and Cassiman, J J, additional
- Published
- 1994
- Full Text
- View/download PDF
22. Forensic medicine and the polymerase chain reaction technique.
- Author
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Decorte, R, primary and Cassiman, J J, additional
- Published
- 1993
- Full Text
- View/download PDF
23. Possible association of CD3 and CD4 polymorphisms with insulin-dependent diabetes mellitus (IDDM).
- Author
-
Ghanbanbasni, M. Zamani, Buyse, I., Legius, E., Decorte, R., Marynen, P., Bouillon, R., and Cassiman, J. -J.
- Subjects
DIABETES ,CARBOHYDRATE intolerance ,CARBOHYDRATE metabolism disorders ,GENETIC polymorphisms ,GENETIC research ,HEREDITY - Abstract
Population and family studies show that predisposition to type I diabetes (IDDM) is multi- factorial, and that polymorphisms in the MHC region contribute substantially to the susceptibility to IDDM. In the present study the association of polymorphisms in the CD4 and the δ subunit of CD3 with IDDM were examined in a Belgian population. We observed that the frequency of the CD4*A4/A4 genotype and of the CD3*91 allele were significantly increased (P = 0.0077) and decreased (P = 3.8 × 10
-5 ), respectively, in IDDM compared with controls. These results therefore suggest that CD4, CD3 or neighbouring genes might contribute to IDDM susceptibility. These results are, however, preliminary and cannot be considered as established until re-tested in a new population. [ABSTRACT FROM AUTHOR]- Published
- 1994
24. Y-chromosomal STR haplotypes in three major population groups in Bulgaria
- Author
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Zaharova, B., Andonova, S., Gilissen, A., Cassiman, J. J., Decorte, R., and Kremensky, I.
- Published
- 2001
- Full Text
- View/download PDF
25. Quadruplex fluorescent STR typing system (HUMVWA, HUMTH01, D21S11 and HPRT) with sequence-defined allelic laddersIdentification of a new allele at D21S11
- Author
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Xiao, F.-X., Gilissen, A., Cassiman, J.-J., and Decorte, R.
- Published
- 1998
- Full Text
- View/download PDF
26. Evaluation of a decontamination protocol for hair shafts before mtDNA sequencing
- Author
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Jehaes, E., Gilissen, A., Cassiman, J.-J., and Decorte, R.
- Published
- 1998
- Full Text
- View/download PDF
27. AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications
- Author
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Van Geystelen Anneleen, Decorte Ronny, and Larmuseau Maarten HD
- Subjects
Haploid marker ,Phylogeny ,Next-generation sequencing ,SNP calling ,Y-SNP mutations ,Y chromosome haplogroups ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree. Results We present an automated approach, ‘AMY-tree’, which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs. Conclusions Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.
- Published
- 2013
- Full Text
- View/download PDF
28. A Historical-Genetic Reconstruction of Human Extra-Pair Paternity
- Author
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Pieter van den Berg, Michiel Vandenbosch, Leen Gruyters, Tom Wenseleers, Kelly Nivelle, Francesc Calafell, Alessio Boattini, Ronny Decorte, Maarten Larmuseau, Sofie Claerhout, Generalitat de Catalunya, European Commission, Ministerio de Economía y Competitividad (España), Larmuseau M.H.D., van den Berg P., Claerhout S., Calafell F., Boattini A., Gruyters L., Vandenbosch M., Nivelle K., Decorte R., and Wenseleers T.
- Subjects
0301 basic medicine ,Sexual behavior ,Male ,Luxembourg ,Genetic genealogy ,Low Countries ,Sexual Behavior ,Family history ,Paternity ,Biology ,Citizen science ,Affect (psychology) ,Y chromosome ,General Biochemistry, Genetics and Molecular Biology ,Sexual conflict ,03 medical and health sciences ,0302 clinical medicine ,extra-pair paternity ,Belgium ,citizen science ,genetic genealogy ,Humans ,Human behavioral ecology ,Socioeconomic status ,Netherlands ,family history ,Social environment ,Low Countrie ,human behavioral ecology ,030104 developmental biology ,Genetic marker ,Extra-pair paternity ,Female ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery ,Demography - Abstract
Paternity testing using genetic markers has shown that extra-pair paternity (EPP) is common in many pair-bonded species [1, 2]. Evolutionary theory and empirical data show that extra-pair copulations can increase the fitness of males as well as females [3, 4]. This can carry a significant fitness cost for the social father, who then invests in rearing offspring that biologically are not his own [5]. In human populations, the incidence and correlates of extra-pair paternity remain highly contentious [2, 6, 7]. Here, we use a population-level genetic genealogy approach [6, 8] to reconstruct spatiotemporal patterns in human EPP rates. Using patrilineal genealogies from the Low Countries spanning a period of over 500 years and Y chromosome genotyping of living descendants, our analysis reveals that historical EPP rates, while low overall, were strongly impacted by socioeconomic and demographic factors. Specifically, we observe that estimated EPP rates among married couples varied by more than an order of magnitude, from 0.4% to 5.9%, and peaked among families with a low socioeconomic background living in densely populated cities of the late 19 century. Our results support theoretical predictions that social context can strongly affect the outcomes of sexual conflict in human populations by modulating the incentives and opportunities for engaging in extra-pair relationships [9–11]. These findings show how contemporary genetic data combined with in-depth genealogies open up a new window on the sexual behavior of our ancestors. Larmuseau et al. combine genetic data with family trees to reconstruct historical patterns of human extra-pair paternity (EPP). They show that EPP rates in Western society were low overall (∼1%) but varied in function of social context, peaking at ∼6% among families with low socioeconomic status in densely populated cities of the 19 century., Funding was provided by KU Leuven (BOF-C1 grant C12/15/013) and the Fund for Scientific Research – Flanders (Research grant number 1503216N and postdoc grants of M.H.D.L. and P.v.d.B.). F.C. was supported by Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2017 SGR00702, and “Unidad de Excelencia María de Maeztu,” funded by the MINECO (ref: MDM-2014-0370).
- Published
- 2019
29. Fully Automatic Camera for Personalized Highlight Generation in Sporting Events.
- Author
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Decorte R, De Bock J, Taelman J, Slembrouck M, and Verstockt S
- Subjects
- Humans, Male, Female, Video Recording, Athletes, Bicycling
- Abstract
Personally curated content in short-form video formats provides added value for participants and spectators but is often disregarded in lower-level events because it is too labor-intensive to create or is not recorded at all. Our smart sensor-driven tripod focuses on supplying a unified sensor and video solution to capture personalized highlights for participants in various sporting events with low computational and hardware costs. The relevant parts of the video for each participant are automatically determined by using the timestamps of his/her received sensor data. This is achieved through a customizable clipping mechanism that processes and optimizes both video and sensor data. The clipping mechanism is driven by sensing nearby signals of Adaptive Network Topology (ANT+) capable devices worn by the athletes that provide both locality information and identification. The device was deployed and tested in an amateur-level cycling race in which it provided clips with a detection rate of 92.9%. The associated sensor data were used to automatically extract peloton passages and report riders' positions on the course, as well as which participants were grouped together. Insights derived from sensor signals can be processed and published in real time, and an upload optimization scheme is proposed that can provide video clips for each rider a maximum of 5 min after the passage if video upload is enabled.
- Published
- 2024
- Full Text
- View/download PDF
30. CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics.
- Author
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Claerhout S, Verstraete P, Warnez L, Vanpaemel S, Larmuseau M, and Decorte R
- Subjects
- Evolution, Molecular, Genetic Markers, Humans, Chromosomes, Human, Y, Genetics, Population, Microsatellite Repeats, Polymorphism, Single Nucleotide
- Abstract
Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the 'CSYseq', which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2021
- Full Text
- View/download PDF
31. Cell survival and DNA damage repair are promoted in the human blood thanatotranscriptome shortly after death.
- Author
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Antiga LG, Sibbens L, Abakkouy Y, Decorte R, Van Den Bogaert W, Van de Voorde W, and Bekaert B
- Subjects
- Aged, Aged, 80 and over, DNA Damage, Female, Forensic Medicine methods, Gene Expression, Gene Ontology, Humans, Male, Middle Aged, Models, Genetic, RNA, Messenger biosynthesis, RNA, Messenger genetics, Time Factors, Cell Survival genetics, DNA Repair genetics, Postmortem Changes, RNA, Messenger blood, Transcriptome
- Abstract
RNA analysis of post-mortem tissues, or thanatotranscriptomics, has become a topic of interest in forensic science due to the essential information it can provide in forensic investigations. Several studies have previously investigated the effect of death on gene transcription, but it has never been conducted with samples of the same individual. For the first time, a longitudinal mRNA expression analysis study was performed with post-mortem human blood samples from individuals with a known time of death. The results reveal that, after death, two clearly differentiated groups of up- and down-regulated genes can be detected. Pathway analysis suggests active processes that promote cell survival and DNA damage repair, rather than passive degradation, are the source of early post-mortem changes of gene expression in blood. In addition, a generalized linear model with an elastic net restriction predicted post-mortem interval with a root mean square error of 4.75 h. In conclusion, we demonstrate that post-mortem gene expression data can be used as biomarkers to estimate the post-mortem interval though further validation using independent sample sets is required before use in forensic casework., (© 2021. The Author(s).)
- Published
- 2021
- Full Text
- View/download PDF
32. At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics.
- Author
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Ahannach S, Spacova I, Decorte R, Jehaes E, and Lebeer S
- Abstract
Microbial forensics represents a promising tool to strengthen traditional forensic investigative methods and fill related knowledge gaps. Large-scale microbiome studies indicate that microbial fingerprinting can assist forensics in areas such as trace evidence, source tracking, geolocation, and circumstances of death. Nevertheless, the majority of forensic microbiome studies focus on soil and internal organ samples, whereas the microbiome of skin, mouth, and especially vaginal samples that are routinely collected in sexual assault and femicide cases remain underexplored. This review discusses the current and emerging insights into vaginal, skin, and salivary microbiome-modulating factors during life (e.g., lifestyle and health status) and after death (e.g., environmental influences and post-mortem interval) based on next-generation sequencing. We specifically highlight the key aspects of female reproductive tract, skin, and mouth microbiome samples relevant in forensics. To fill the current knowledge gaps, future research should focus on the degree to which the post-mortem succession rate and profiles of vaginal, skin, and saliva microbiota are sensitive to abiotic and biotic factors, presence or absence of oxygen and other gases, and the nutrient richness of the environment. Application of this microbiome-related knowledge could provide valuable complementary data to strengthen forensic cases, for example, to shed light on the circumstances surrounding death with (post-mortem) microbial fingerprinting. Overall, this review synthesizes the present knowledge and aims to provide a framework to adequately comprehend the hurdles and potential application of vaginal, skin, and salivary post-mortem microbiomes in forensic investigations., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Ahannach, Spacova, Decorte, Jehaes and Lebeer.)
- Published
- 2021
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33. The Dutch Y-chromosomal landscape.
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Altena E, Smeding R, van der Gaag KJ, Larmuseau MHD, Decorte R, Lao O, Kayser M, Kraaijenbrink T, and de Knijff P
- Subjects
- Haplotypes, Humans, Male, Netherlands, Chromosomes, Human, Y genetics, Polymorphism, Single Nucleotide, Population genetics
- 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
- 2020
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34. Correction to: The Dutch Y-chromosomal landscape.
- Author
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Altena E, Smeding R, van der Gaag KJ, Larmuseau MHD, Decorte R, Lao O, Kayser M, Kraaijenbrink T, and de Knijff P
- Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
- Published
- 2020
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- View/download PDF
35. A Historical-Genetic Reconstruction of Human Extra-Pair Paternity.
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Larmuseau MHD, van den Berg P, Claerhout S, Calafell F, Boattini A, Gruyters L, Vandenbosch M, Nivelle K, Decorte R, and Wenseleers T
- Subjects
- Belgium, Female, Humans, Luxembourg, Male, Netherlands, Sexual Behavior, Paternity
- Abstract
Paternity testing using genetic markers has shown that extra-pair paternity (EPP) is common in many pair-bonded species [1, 2]. Evolutionary theory and empirical data show that extra-pair copulations can increase the fitness of males as well as females [3, 4]. This can carry a significant fitness cost for the social father, who then invests in rearing offspring that biologically are not his own [5]. In human populations, the incidence and correlates of extra-pair paternity remain highly contentious [2, 6, 7]. Here, we use a population-level genetic genealogy approach [6, 8] to reconstruct spatiotemporal patterns in human EPP rates. Using patrilineal genealogies from the Low Countries spanning a period of over 500 years and Y chromosome genotyping of living descendants, our analysis reveals that historical EPP rates, while low overall, were strongly impacted by socioeconomic and demographic factors. Specifically, we observe that estimated EPP rates among married couples varied by more than an order of magnitude, from 0.4% to 5.9%, and peaked among families with a low socioeconomic background living in densely populated cities of the late 19
th century. Our results support theoretical predictions that social context can strongly affect the outcomes of sexual conflict in human populations by modulating the incentives and opportunities for engaging in extra-pair relationships [9-11]. These findings show how contemporary genetic data combined with in-depth genealogies open up a new window on the sexual behavior of our ancestors., (Copyright © 2019 Elsevier Ltd. All rights reserved.)- Published
- 2019
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36. A game of hide and seq: Identification of parallel Y-STR evolution in deep-rooting pedigrees.
- Author
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Claerhout S, Van der Haegen M, Vangeel L, Larmuseau MHD, and Decorte R
- Subjects
- Adult, Alleles, DNA Fingerprinting, Genotype, High-Throughput Nucleotide Sequencing, Humans, INDEL Mutation genetics, Male, Meiosis genetics, Middle Aged, Pedigree, Chromosomes, Human, Y genetics, Evolution, Molecular, Haplotypes genetics, Microsatellite Repeats genetics
- Abstract
Short tandem repeats on the Y-chromosome (Y-STRs) are common DNA polymorphisms useful for genetic genealogy, population and evolutionary genetics, human genetics, pathology and forensic sciences. It is important to identify all Y-STR variants and to have knowledge of Y-STR mutation rates in order to correctly estimate the time to the most recent common ancestor (tMRCA) between paternally related individuals. When capillary electrophoresis (CE) is performed to analyze genealogical pairs, Y-STR sequence variations remain hidden when the number of repeats is identical. These hidden variations could be due to parallel Y-STR changes or modifications (PM) that occur independently in different lineages leading to alleles with identical number of repeats. In this study, we detect for the first time twelve PM by analyzing 133 males (960 meiosis) in extended deep-rooting family pedigrees on 42 Y-STRs. These PM were observed in nine Y-STR loci with mutation rates of at least 5.94 × 10
-3 per generation. Sequencing analysis made it possible to distinguish insertions/deletions in different repeat regions revealing the presence of two unique changes in three PM on rapidly mutating and complex Y-STRs DYS724-ab and DYS518. Sequencing unraveled more information concerning the identity of alleles, and increased allelic discrimination possibilities which is of great importance in population genetics and forensic analysis. Limiting the analysis to CE could lead to wrong ancestral allele assumptions, to false negative interpretations and to tMRCA underestimations. These observations highlight the importance and added value of sequencing analysis and suggest a shift in genotyping methods from CE to next generation sequencing.- Published
- 2019
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37. An interdisciplinary study around the reliquary of the late cardinal Jacques de Vitry.
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Decorte R, Polet C, Boudin M, Tilquin F, Matroule JY, Dieu M, Charles C, Carlier A, Lebecque F, and Deparis O
- Subjects
- Animals, Humans, Male, Anthropology, Cultural, Belgium, Chromosomes, Human, Y genetics, Genetic Testing, History, Medieval, Interdisciplinary Studies, Radiometric Dating, Autopsy methods, Clergy history, Proteomics methods, Religion and Science, Theology history
- Abstract
The reliquary of Jacques de Vitry, a prominent clergyman and theologian in the early 13th century, has experienced several transfers over the last centuries, which seriously question the attribution of the remains to the late Cardinal. Uncertainty about the year of his birth poses an additional question regarding his age at death in 1240. The reliquary, located in the Saint Marie d'Oigines church, Belgium, was reopened in 2015 for an interdisciplinary study around his relics as well as the Treasure of Oignies, a remarkable cultural heritage notably built from Jacques de Vitry's donation. Anthropological, isotopic and genetic analyses were performed independently on the remains found in the reliquary. Results of the analyses provided evidence that the likelihood that these remains are those of Jacques de Vitry is very high: the remains belong to the same human male individual and the historical tradition about his age is confirmed. In addition, a separate relic (left tibia) was analysed and found to match with the remains of the reliquary (right tibia). The unique Jacques de Vitry's mitre, made of parchment, was sampled non-destructively and the extracted parchment collagen was analysed by a proteomic method in order to determine the animal species. The results showed that, surprisingly, not all parts of the mitre were made from the same species. All together, these findings are expected to fertilize knowledge carried by historical tradition around the relics of Jacques de Vitry and his related cultural heritage., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2019
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38. Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry.
- Author
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Primativo G, Ottoni C, Biondi G, Serafino S, Martínez-Labarga C, Larmuseau MH, Scardi M, Decorte R, and Rickards O
- Subjects
- Black or African American genetics, Benin, Black People genetics, Enslavement, Female, Genetic Variation, Haplotypes, Human Migration, Humans, Language, Male, United States, DNA, Mitochondrial genetics
- Abstract
The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area., (© 2017 John Wiley & Sons Ltd/University College London.)
- Published
- 2017
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39. Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey.
- Author
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Ottoni C, Rasteiro R, Willet R, Claeys J, Talloen P, Van de Vijver K, Chikhi L, Poblome J, and Decorte R
- Abstract
More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.
- Published
- 2016
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40. The Paternal Landscape along the Bight of Benin - Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers.
- Author
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Larmuseau MH, Vessi A, Jobling MA, Van Geystelen A, Primativo G, Biondi G, Martínez-Labarga C, Ottoni C, Decorte R, and Rickards O
- Subjects
- Benin, Genomics, Genotyping Techniques, Haplotypes, Humans, Male, Microsatellite Repeats genetics, Polymorphism, Single Nucleotide, Chromosomes, Human, Y genetics, Fathers, Genetic Markers genetics
- Abstract
Patterns of genetic variation in human populations across the African continent are still not well studied in comparison with Eurasia and America, despite the high genetic and cultural diversity among African populations. In population and forensic genetic studies a single sample is often used to represent a complete African region. In such a scenario, inappropriate sampling strategies and/or the use of local, isolated populations may bias interpretations and pose questions of representativeness at a macrogeographic-scale. The non-recombining region of the Y-chromosome (NRY) has great potential to reveal the regional representation of a sample due to its powerful phylogeographic information content. An area poorly characterized for Y-chromosomal data is the West-African region along the Bight of Benin, despite its important history in the trans-Atlantic slave trade and its large number of ethnic groups, languages and lifestyles. In this study, Y-chromosomal haplotypes from four Beninese populations were determined and a global meta-analysis with available Y-SNP and Y-STR data from populations along the Bight of Benin and surrounding areas was performed. A thorough methodology was developed allowing comparison of population samples using Y-chromosomal lineage data based on different Y-SNP panels and phylogenies. Geographic proximity turned out to be the best predictor of genetic affinity between populations along the Bight of Benin. Nevertheless, based on Y-chromosomal data from the literature two population samples differed strongly from others from the same or neighbouring areas and are not regionally representative within large-scale studies. Furthermore, the analysis of the HapMap sample YRI of a Yoruban population from South-western Nigeria based on Y-SNPs and Y-STR data showed for the first time its regional representativeness, a result which is important for standard population and forensic genetic applications using the YRI sample. Therefore, the uniquely and powerful geographical information carried by the Y-chromosome makes it an important locus to test the representativeness of a certain sample even in the genomic era, especially in poorly investigated areas like Africa.
- Published
- 2015
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- View/download PDF
41. Improved age determination of blood and teeth samples using a selected set of DNA methylation markers.
- Author
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Bekaert B, Kamalandua A, Zapico SC, Van de Voorde W, and Decorte R
- Subjects
- Acetyltransferases genetics, Adolescent, Adult, Age Determination by Teeth, Aged, Aged, 80 and over, Aging blood, Amidohydrolases genetics, Child, Child, Preschool, Cyclic Nucleotide Phosphodiesterases, Type 4 genetics, Edar-Associated Death Domain Protein genetics, Fatty Acid Elongases, Female, Humans, Infant, Infant, Newborn, Male, Middle Aged, Aging genetics, CpG Islands genetics, DNA Methylation genetics
- Abstract
Age estimation from DNA methylation markers has seen an exponential growth of interest, not in the least from forensic scientists. The current published assays, however, can still be improved by lowering the number of markers in the assay and by providing more accurate models to predict chronological age. From the published literature we selected 4 age-associated genes (ASPA, PDE4C, ELOVL2, and EDARADD) and determined CpG methylation levels from 206 blood samples of both deceased and living individuals (age range: 0-91 years). This data was subsequently used to compare prediction accuracy with both linear and non-linear regression models. A quadratic regression model in which the methylation levels of ELOVL2 were squared showed the highest accuracy with a Mean Absolute Deviation (MAD) between chronological age and predicted age of 3.75 years and an adjusted R(2) of 0.95. No difference in accuracy was observed for samples obtained either from living and deceased individuals or between the 2 genders. In addition, 29 teeth from different individuals (age range: 19-70 years) were analyzed using the same set of markers resulting in a MAD of 4.86 years and an adjusted R(2) of 0.74. Cross validation of the results obtained from blood samples demonstrated the robustness and reproducibility of the assay. In conclusion, the set of 4 CpG DNA methylation markers is capable of producing highly accurate age predictions for blood samples from deceased and living individuals.
- Published
- 2015
- Full Text
- View/download PDF
42. Pseudoautosomal region 1 length polymorphism in the human population.
- Author
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Mensah MA, Hestand MS, Larmuseau MH, Isrie M, Vanderheyden N, Declercq M, Souche EL, Van Houdt J, Stoeva R, Van Esch H, Devriendt K, Voet T, Decorte R, Robinson PN, and Vermeesch JR
- Subjects
- Animals, Chromosomes genetics, Haplotypes, Hominidae genetics, Homologous Recombination genetics, Humans, Polymorphism, Genetic, Repetitive Sequences, Nucleic Acid genetics, Translocation, Genetic, Chromosomes, Human, X genetics, Chromosomes, Human, Y genetics, Evolution, Molecular
- Abstract
The human sex chromosomes differ in sequence, except for the pseudoautosomal regions (PAR) at the terminus of the short and the long arms, denoted as PAR1 and PAR2. The boundary between PAR1 and the unique X and Y sequences was established during the divergence of the great apes. During a copy number variation screen, we noted a paternally inherited chromosome X duplication in 15 independent families. Subsequent genomic analysis demonstrated that an insertional translocation of X chromosomal sequence into the Y chromosome generates an extended PAR [corrected].The insertion is generated by non-allelic homologous recombination between a 548 bp LTR6B repeat within the Y chromosome PAR1 and a second LTR6B repeat located 105 kb from the PAR boundary on the X chromosome. The identification of the reciprocal deletion on the X chromosome in one family and the occurrence of the variant in different chromosome Y haplogroups demonstrate this is a recurrent genomic rearrangement in the human population. This finding represents a novel mechanism shaping sex chromosomal evolution.
- Published
- 2014
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43. Genetic genealogy reveals true Y haplogroup of House of Bourbon contradicting recent identification of the presumed remains of two French Kings.
- Author
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Larmuseau MH, Delorme P, Germain P, Vanderheyden N, Gilissen A, Van Geystelen A, Cassiman JJ, and Decorte R
- Subjects
- DNA, Mitochondrial, Genealogy and Heraldry, Humans, Male, Phylogeny, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, DNA Fingerprinting, Forensic Anthropology, Haplotypes
- Abstract
Genetic analysis strongly increases the opportunity to identify skeletal remains or other biological samples from historical figures. However, validation of this identification is essential and should be done by DNA typing of living relatives. Based on the similarity of a limited set of Y-STRs, a blood sample and a head were recently identified as those belonging respectively to King Louis XVI and his paternal ancestor King Henry IV. Here, we collected DNA samples from three living males of the House of Bourbon to validate the since then controversial identification of these remains. The three living relatives revealed the Bourbon's Y-chromosomal variant on a high phylogenetic resolution for several members of the lineage between Henry IV and Louis XVI. This 'true' Bourbon's variant is different from the published Y-STR profiles of the blood as well as of the head. The earlier identifications of these samples can therefore not be validated. Moreover, matrilineal genealogical data revealed that the published mtDNA sequence of the head was also different from the one of a series of relatives. This therefore leads to the conclusion that the analyzed samples were not from the French kings. Our study once again demonstrated that in order to realize an accurate genetic identification of historical remains DNA typing of living persons, who are paternally or maternally related with the presumed donor of the samples, is required.
- Published
- 2014
- Full Text
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44. Recent radiation within Y-chromosomal haplogroup R-M269 resulted in high Y-STR haplotype resemblance.
- Author
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Larmuseau MH, Vanderheyden N, Van Geystelen A, van Oven M, de Knijff P, and Decorte R
- Subjects
- Belgium, Genetic Variation, Genetics, Population, Haplotypes, Humans, Male, Netherlands, Phylogeny, Polymorphism, Single Nucleotide, White People classification, Chromosomes, Human, Y genetics, Microsatellite Repeats, White People genetics
- Abstract
Y-chromosomal short tandem repeats (Y-STRs) are often used in addition to Y-chromosomal single-nucleotide polymorphisms (Y-SNP) to detect subtle patterns in a population genetic structure. There are, however, indications for Y-STR haplotype resemblance across different subhaplogroups within haplogroup R1b1b2 (R-M269) which may lead to erosion in the observation of the population genetic pattern. Hence the question arises whether Y-STR haplotypes are still informative beyond high-resolution Y-SNP genotyping for population genetic studies. To address this question, we genotyped the Y chromosomes of more than 1000 males originating from the West-European regions of Flanders (Belgium), North-Brabant and Limburg (the Netherlands) at the highest resolution of the current Y-SNP tree together with 38 commonly used Y-STRs. We observed high resemblance of Y-STR haplotypes between males belonging to different subhaplogroups of haplogroup R-M269. Several subhaplogroups within R-M269 could not be distinguished from each other based on differences in Y-STR haplotype variation. The most likely hypothesis to explain this similarity of Y-STR haplotypes within the population of R-M269 members is a recent radiation where various subhaplogroups originated within a relatively short time period. We conclude that high-resolution Y-SNP typing rather than Y-STR typing might be more useful to study population genetic patterns in (Western) Europe., (© 2014 John Wiley & Sons Ltd/University College London.)
- Published
- 2014
- Full Text
- View/download PDF
45. Evaluation of Staff's Job Satisfaction in the Spinal Cord Unit in Italy.
- Author
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Cominetti L, Lorenza G, Decorte R, Felisi N, Matta E, Actis MV, Carone R, Gregorino S, and Valerio D
- Abstract
In July 2007 a Spinal Cord Unit was set up in Turin (Italy) within the newly integrated structure of the Orthopaedic Traumatologic Centre, warranting a multidisciplinary and professional approach according to International Guidelines. This approach will be possible through experimentation of a personalized care model. To analyze job satisfaction of health care professionals operating within the Spinal Cord Unit, preliminary to organizational change. Data collection was carried out by using questionnaires, interviews, shadowing. Results from quantitative analysis on the self-filled questionnaires were integrated with results from qualitative analysis. All the health care professionals operating in the field were involved. Positive aspects were the perception of carrying out a useful job, the feeling of personal fulfilment and the wish to engage new energies and resources. Problematic aspects included role conflict among staff categories and communication with managers. The positive aspects can be exploited to create professional practices facilitating role and expertise integration, information spreading and staff identification within the organization rather than team work. Data of job satisfaction and self efficacy of health care workers can be considered basic requirement before implementing an organizational change. The main challenges is multiprofessional collaboration.
- Published
- 2013
- Full Text
- View/download PDF
46. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.
- Author
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Ottoni C, Flink LG, Evin A, Geörg C, De Cupere B, Van Neer W, Bartosiewicz L, Linderholm A, Barnett R, Peters J, Decorte R, Waelkens M, Vanderheyden N, Ricaut FX, Cakirlar C, Cevik O, Hoelzel AR, Mashkour M, Karimlu AF, Seno SS, Daujat J, Brock F, Pinhasi R, Hongo H, Perez-Enciso M, Rasmussen M, Frantz L, Megens HJ, Crooijmans R, Groenen M, Arbuckle B, Benecke N, Vidarsdottir US, Burger J, Cucchi T, Dobney K, and Larson G
- Subjects
- Animal Distribution, Animals, Animals, Domestic genetics, Asia, Europe, Humans, Phylogeography, Sequence Analysis, DNA, Swine genetics, DNA, Mitochondrial genetics, Molar anatomy & histology, Sus scrofa genetics
- Abstract
Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.
- Published
- 2013
- Full Text
- View/download PDF
47. Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics.
- Author
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Larmuseau MH, Ottoni C, Raeymaekers JA, Vanderheyden N, Larmuseau HF, and Decorte R
- Subjects
- Genealogy and Heraldry, Genetic Variation, Genetics, Population, Genotype, Humans, Male, Chromosomes, Human, Y genetics, White People genetics
- Abstract
The pattern of population genetic variation and allele frequencies within a species are unstable and are changing over time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome (Y-chr) genotyping to disentangle signals of historical population genetic structures because of the exponential increase in genetic genealogical data. To test this approach, we studied the temporal pattern of the 'autochthonous' micro-geographical genetic structure in the region of Brabant in Belgium and the Netherlands (Northwest Europe). Genealogical data of 881 individuals from Northwest Europe were collected, from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chr genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chr distribution was detected through a north-south gradient in the frequencies distribution of sub-haplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-U152). The gradient on R-U106 faded in time and even became totally invisible during the Industrial Revolution in the first half of the nineteenth century. Therefore, genealogical data for at least 200 years are required to study small-scale 'autochthonous' population structure in Western Europe.
- Published
- 2012
- Full Text
- View/download PDF
48. Mitochondrial analysis of a Byzantine population reveals the differential impact of multiple historical events in South Anatolia.
- Author
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Ottoni C, Ricaut FX, Vanderheyden N, Brucato N, Waelkens M, and Decorte R
- Subjects
- DNA, Mitochondrial genetics, Humans, Molecular Sequence Data, Turkey, Genes, Mitochondrial, Genetics, Population
- Abstract
The archaeological site of Sagalassos is located in Southwest Turkey, in the western part of the Taurus mountain range. Human occupation of its territory is attested from the late 12th millennium BP up to the 13th century AD. By analysing the mtDNA variation in 85 skeletons from Sagalassos dated to the 11th-13th century AD, this study attempts to reconstruct the genetic signature potentially left in this region of Anatolia by the many civilizations, which succeeded one another over the centuries until the mid-Byzantine period (13th century BC). Authentic ancient DNA data were determined from the control region and some SNPs in the coding region of the mtDNA in 53 individuals. Comparative analyses with up to 157 modern populations allowed us to reconstruct the origin of the mid-Byzantine people still dwelling in dispersed hamlets in Sagalassos, and to detect the maternal contribution of their potential ancestors. By integrating the genetic data with historical and archaeological information, we were able to attest in Sagalassos a significant maternal genetic signature of Balkan/Greek populations, as well as ancient Persians and populations from the Italian peninsula. Some contribution from the Levant has been also detected, whereas no contribution from Central Asian population could be ascertained.
- Published
- 2011
- Full Text
- View/download PDF
49. Towards personalized care for persons with spinal cord injury: a study on patients' perceptions.
- Author
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Garrino L, Curto N, Decorte R, Felisi N, Matta E, Gregorino S, Actis MV, Marchisio C, and Carone R
- Subjects
- Adult, Aged, Disability Evaluation, Female, Humans, Interviews as Topic, Male, Middle Aged, Patient Care Planning, Physical Therapy Modalities, Precision Medicine, Qualitative Research, Young Adult, Adaptation, Psychological, Critical Pathways, Patient Satisfaction, Rehabilitation Nursing methods, Spinal Cord Injuries nursing, Spinal Cord Injuries psychology, Spinal Cord Injuries rehabilitation
- Abstract
Objective/background: A newly designed Spinal Cord Unit (SCU) was set up at the Orthopedic Traumatology Center (OTC), Turin, Italy, in July 2007. With the relocation of the SCU came the need to reorganize and improve the delivery of its services. The study reported here is a preliminary part of a project entitled 'Experimentation and evaluation of personalized healthcare for patients with spinal cord injury', which is a component of an overarching program of targeted research into healthcare funded by the Piedmont Region in 2006. The aim of this study was to assess the perception of care by patients with spinal cord injury (SCI) by collecting important data in order to determine whether an integrated and personalized care pathway could be effective both in hospital and in a rehabilitation setting., Design: Qualitative research study. The interview format was based on a narrative approach., Methods: Qualitative in-depth semi-structured interviews were conducted with 21 patients with SCI. Qualitative content analysis was used to identify categories and themes arising from the data., Results: Six main categories emerged from the perspectives of patients: expectations of rehabilitation care, impact and welcome, relationship with nurses and their involvement in treatment, relationship with physical therapists and participation in rehabilitation programs, relationship with physicians and their availability and attendance, and imparting of information on injury and rehabilitation outcomes. Care was the aspect new patients admitted to the SCU found most important. When closer relationships with staff formed, the healthcare professionals became an essential support. Patients with SCI commonly stated that receiving explicit information was necessary for accepting their condition., Conclusions: Analysis of the patients' perceptions revealed a wealth of details on their experience in the SCU and the need for flexible planning of care time in particular. Incorporating the patients' perceptions into a new care model could increase professionals' awareness of patients' needs and provide a useful basis for constructing a personalized care plan.
- Published
- 2011
- Full Text
- View/download PDF
50. Genetic identification in the 21st century--Current status and future developments.
- Author
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Decorte R
- Subjects
- Chromosomes, Human, X, Chromosomes, Human, Y, DNA Fingerprinting, Humans, Mass Casualty Incidents, Polymorphism, Single Nucleotide, Tandem Repeat Sequences, Forensic Genetics trends
- Abstract
In 2010, it is the 25th anniversary of the first paper describing the genetic identification of human individuals by DNA fingerprint analysis. Since then DNA analysis has become a major tool to relate biological evidence to the persons involved in a crime or to determine the biological relationship among individuals. The currently used methodology is the result of major technological changes that were partly driven by criticism on previous methodologies, and partly driven by demand especially due to mass disasters such as the '9/11 attack' on the World Trade Center in New York. This review will give an overview of the current methodology in genetic identification and new developments that will have a future impact on forensic identification., (Copyright 2010 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
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