A population-specific reference panel empowers genetic studies of Anabaptist populations
dc.contributor.author | Hou, Liping | |
dc.contributor.author | Kember, Rachel L. | |
dc.contributor.author | Roach, Jared C. | |
dc.contributor.author | O'Connell, Jeffrey R. | |
dc.contributor.author | Craig, David W. | |
dc.contributor.author | Bucan, Maja | |
dc.contributor.author | Scott, William K. | |
dc.contributor.author | Pericak-Vance, Margaret | |
dc.contributor.author | Haines, Jonathan L. | |
dc.contributor.author | Crawford, Michael H. | |
dc.contributor.author | Shuldiner, Alan R. | |
dc.contributor.author | McMahon, Francis J. | |
dc.date.accessioned | 2018-10-31T20:03:40Z | |
dc.date.available | 2018-10-31T20:03:40Z | |
dc.date.issued | 2017-07-20 | |
dc.identifier.citation | Hou, L., (2017), A population-specific reference panel empowers genetic studies of Anabaptist populations, Scientific. Reports, 7, 6079, https://doi.org/10.1038/s41598-017-05445-3 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/27123 | |
dc.description.abstract | Genotype imputation is a powerful strategy for achieving the large sample sizes required for identification of variants underlying complex phenotypes, but imputation of rare variants remains problematic. Genetically isolated populations offer one solution, however population-specific reference panels are needed to assure optimal imputation accuracy and allele frequency estimation. Here we report the Anabaptist Genome Reference Panel (AGRP), the first whole-genome catalogue of variants and phased haplotypes in people of Amish and Mennonite ancestry. Based on high-depth whole-genome sequence (WGS) from 265 individuals, the AGRP contains >12 M high-confidence single nucleotide variants and short indels, of which ~12.5% are novel. These Anabaptist-specific variants were more deleterious than variants with comparable frequencies observed in the 1000 Genomes panel. About 43,000 variants showed enriched allele frequencies in AGRP, consistent with drift. When combined with the 1000 Genomes Project reference panel, the AGRP substantially improved imputation, especially for rarer variants. The AGRP is freely available to researchers through an imputation server. | en_US |
dc.publisher | Nature Research | en_US |
dc.rights | Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. | en_US |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_US |
dc.title | A population-specific reference panel empowers genetic studies of Anabaptist populations | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Crawford, Michael H. | |
kusw.kudepartment | Anthropology | en_US |
dc.identifier.doi | https://doi.org/10.1038/s41598-017-05445-3 | en_US |
kusw.oaversion | Scholarly/refereed, publisher version | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.rights.accessrights | openAccess | en_US |
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Except where otherwise noted, this item's license is described as: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.