Recombination networks as genetic markers in a human variation study of the Old World
13 páginas.-- Javed, Asif et al.
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2012-04
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| Online Access: | http://hdl.handle.net/10261/43322 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100002261 http://dx.doi.org/10.13039/100006363 |
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dig-ibe-es-10261-433222018-09-27T07:57:48Z Recombination networks as genetic markers in a human variation study of the Old World Javed, Asif Melé, Marta Pybus, Marc Comas, David Bertranpetit, Jaume Calafell, Francesc Instituto Nacional de Bioinformática (España) Ministerio de Ciencia e Innovación (España) Generalitat de Catalunya Russian Foundation for Basic Research National Geographic Society 13 páginas.-- Javed, Asif et al. We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia. This research is part of the Genographic Project, funded by National Geographic and IBM. Additional funding was provided by the Spanish Ministry of Science and Innovation projects BFU2007-63657, BFU2007-63171, and BFU2010-19443; MM was supported by grant AP2006-03268, Generalitat de Catalunya; OB was supported by Russian Foundation for Basic Research (grants 10-06-00451, 10-04-01603) and by the Presidium RAS Programme “Molecular and Cell Biology”. Peer reviewed 2011-12-14T11:39:18Z 2011-12-14T11:39:18Z 2012-04 artículo http://purl.org/coar/resource_type/c_6501 Human Genetics 131(4): 601-613 (2011) 0340-6717 http://hdl.handle.net/10261/43322 10.1007/s00439-011-1104-8 1432-1203 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100002261 http://dx.doi.org/10.13039/100006363 en http://dx.doi.org/10.1007/s00439-011-1104-8 Sí none Springer |
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13 páginas.-- Javed, Asif et al. |
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Instituto Nacional de Bioinformática (España) |
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Instituto Nacional de Bioinformática (España) Javed, Asif Melé, Marta Pybus, Marc Comas, David Bertranpetit, Jaume Calafell, Francesc |
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artículo |
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Javed, Asif Melé, Marta Pybus, Marc Comas, David Bertranpetit, Jaume Calafell, Francesc |
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Javed, Asif Melé, Marta Pybus, Marc Comas, David Bertranpetit, Jaume Calafell, Francesc Recombination networks as genetic markers in a human variation study of the Old World |
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Javed, Asif |
| title |
Recombination networks as genetic markers in a human variation study of the Old World |
| title_short |
Recombination networks as genetic markers in a human variation study of the Old World |
| title_full |
Recombination networks as genetic markers in a human variation study of the Old World |
| title_fullStr |
Recombination networks as genetic markers in a human variation study of the Old World |
| title_full_unstemmed |
Recombination networks as genetic markers in a human variation study of the Old World |
| title_sort |
recombination networks as genetic markers in a human variation study of the old world |
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Springer |
| publishDate |
2012-04 |
| url |
http://hdl.handle.net/10261/43322 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100002261 http://dx.doi.org/10.13039/100006363 |
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