Recombination networks as genetic markers in a human variation study of the Old World
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 constructi...
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2012
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| Online Access: | http://hdl.handle.net/10725/11118 https://doi.org/10.1007/s00439-011-1104-8 http://libraries.lau.edu.lb/research/laur/terms-of-use/articles.php https://link.springer.com/article/10.1007/s00439-011-1104-8 |
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| _version_ | 1864513488288743424 |
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| author | Javed, Asif |
| author2 | Mele, Marta Pybus, Marc Zalloua, Pierre Haber, Marc Comas, David Netea, Mihai G. Balanovsky, Oleg Balanovsky, Elena Jin, Li Yang, Yajun ArunKumar, GaneshPrasad Pitchappan, Ramasamy Bertranpetit, Jaume Calafell, Francesc |
| author2_role | author author author author author author author author author author author author author author |
| author_facet | Javed, Asif Mele, Marta Pybus, Marc Zalloua, Pierre Haber, Marc Comas, David Netea, Mihai G. Balanovsky, Oleg Balanovsky, Elena Jin, Li Yang, Yajun ArunKumar, GaneshPrasad Pitchappan, Ramasamy Bertranpetit, Jaume Calafell, Francesc |
| author_role | author |
| dc.creator.none.fl_str_mv | Javed, Asif Mele, Marta Pybus, Marc Zalloua, Pierre Haber, Marc Comas, David Netea, Mihai G. Balanovsky, Oleg Balanovsky, Elena Jin, Li Yang, Yajun ArunKumar, GaneshPrasad Pitchappan, Ramasamy Bertranpetit, Jaume Calafell, Francesc |
| dc.date.none.fl_str_mv | 2012 2019-07-22T08:02:46Z 2019-07-22T08:02:46Z 2019-07-22 |
| dc.identifier.none.fl_str_mv | 1432-1203 http://hdl.handle.net/10725/11118 https://doi.org/10.1007/s00439-011-1104-8 Javed, A., Melé, M., Pybus, M., Zalloua, P., Haber, M., Comas, D., ... & Yang, Y. (2012). Recombination networks as genetic markers in a human variation study of the Old World. Human genetics, 131(4), 601-613. http://libraries.lau.edu.lb/research/laur/terms-of-use/articles.php https://link.springer.com/article/10.1007/s00439-011-1104-8 |
| dc.language.none.fl_str_mv | en |
| dc.relation.none.fl_str_mv | Human Genetics |
| dc.rights.*.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.title.none.fl_str_mv | Recombination networks as genetic markers in a human variation study of the Old World |
| dc.type.none.fl_str_mv | Article info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
| description | 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. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | LAURepo_dc3e0a7dde9c9a084d227e565471fc74 |
| identifier_str_mv | 1432-1203 Javed, A., Melé, M., Pybus, M., Zalloua, P., Haber, M., Comas, D., ... & Yang, Y. (2012). Recombination networks as genetic markers in a human variation study of the Old World. Human genetics, 131(4), 601-613. |
| language_invalid_str_mv | en |
| network_acronym_str | LAURepo |
| network_name_str | Lebanese American University repository |
| oai_identifier_str | oai:laur.lau.edu.lb:10725/11118 |
| publishDate | 2012 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| spelling | Recombination networks as genetic markers in a human variation study of the Old WorldJaved, AsifMele, MartaPybus, MarcZalloua, PierreHaber, MarcComas, DavidNetea, Mihai G.Balanovsky, OlegBalanovsky, ElenaJin, LiYang, YajunArunKumar, GaneshPrasadPitchappan, RamasamyBertranpetit, JaumeCalafell, FrancescWe 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.PublishedN/A2019-07-22T08:02:46Z2019-07-22T08:02:46Z20122019-07-22Articleinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1432-1203http://hdl.handle.net/10725/11118https://doi.org/10.1007/s00439-011-1104-8Javed, A., Melé, M., Pybus, M., Zalloua, P., Haber, M., Comas, D., ... & Yang, Y. (2012). Recombination networks as genetic markers in a human variation study of the Old World. Human genetics, 131(4), 601-613.http://libraries.lau.edu.lb/research/laur/terms-of-use/articles.phphttps://link.springer.com/article/10.1007/s00439-011-1104-8enHuman Geneticsinfo:eu-repo/semantics/openAccessoai:laur.lau.edu.lb:10725/111182021-03-19T10:47:35Z |
| spellingShingle | Recombination networks as genetic markers in a human variation study of the Old World Javed, Asif |
| status_str | publishedVersion |
| title | 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_short | 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 |
| url | http://hdl.handle.net/10725/11118 https://doi.org/10.1007/s00439-011-1104-8 http://libraries.lau.edu.lb/research/laur/terms-of-use/articles.php https://link.springer.com/article/10.1007/s00439-011-1104-8 |