The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing
dc.contributor.author | Magwene, Paul M. | |
dc.contributor.author | Willis, John H. | |
dc.contributor.author | Kelly, John K. | |
dc.date.accessioned | 2014-03-19T19:11:23Z | |
dc.date.available | 2014-03-19T19:11:23Z | |
dc.date.issued | 2011-11-03 | |
dc.identifier.citation | Magwene, P. M., Willis, J. H., & Kelly, J. K. (2011). The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing. PLoS Comput Biol, 7(11). http://dx.doi.org/10.1371/journal.pcbi.1002255 | |
dc.identifier.uri | http://hdl.handle.net/1808/13267 | |
dc.description.abstract | We describe a statistical framework for QTL mapping using bulk segregant analysis (BSA) based on high throughput, short-read sequencing. Our proposed approach is based on a smoothed version of the standard statistic, and takes into account variation in allele frequency estimates due to sampling of segregants to form bulks as well as variation introduced during the sequencing of bulks. Using simulation, we explore the impact of key experimental variables such as bulk size and sequencing coverage on the ability to detect QTLs. Counterintuitively, we find that relatively large bulks maximize the power to detect QTLs even though this implies weaker selection and less extreme allele frequency differences. Our simulation studies suggest that with large bulks and sufficient sequencing depth, the methods we propose can be used to detect even weak effect QTLs and we demonstrate the utility of this framework by application to a BSA experiment in the budding yeast Saccharomyces cerevisiae. | |
dc.description.sponsorship | This research was supported by NIH grant P50GM081883-04 (to PMM), NIH grant R01-GM073990 (to JKK and JHW), NSF grant DEB-10-19753 (to PMM) and NSF grant IOS-10-24966 (to JHW). | |
dc.publisher | Public Library of Science | |
dc.rights | © 2011 Magwene et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.subject | Alleles | |
dc.subject | Bandwidth (Singal processing) | |
dc.subject | DNA recombination | |
dc.subject | DNA sequencing | |
dc.subject | Genomic libraries | |
dc.subject | High throughput sequencing | |
dc.subject | Sequence alignment | |
dc.subject | Signal filtering | |
dc.title | The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing | |
dc.type | Article | |
kusw.kuauthor | Kelly, John K. | |
kusw.kudepartment | Department of Ecology and Evolutionary Biology | |
kusw.oanotes | PLOS project: This item has a Creative Commons license that allows it to be shared in KU ScholarWorks. | |
kusw.oastatus | fullparticipation | |
dc.identifier.doi | 10.1371/journal.pcbi.1002255 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item meets KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |
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Except where otherwise noted, this item's license is described as: © 2011 Magwene et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.