Show simple item record Dewey, Frederick E. Chen, Rong Cordero, Sergio P. Ormond, Kelly E. Caleshu, Colleen Karczewski, Konrad J. Whirl-Carrillo, Michelle Wheeler, Matthew T. Dudley, Joel T. Byrnes, Jake T. Cornejo, Omar E. Knowles, Joshua W. Woon, Mark Sangkuhl, Katrin Gong, Li Thorn, Caroline F. Hebert, Joan M. Capriotti, Emidio David, Sean P. Pavlovic, Aleksandra West, Anne Thakuria, Joseph V. Ball, Madeline P. Zaranek, Alexander W. Rehm, Heidi L. Church, George M. West, John S. Bustamante, Carlos D. Snyder, Michael Altman, Russ B. Klein, Teri E. Butte, Atul J. Ashley, Euan A. 2011-09-19T17:57:20Z 2011-09-19T17:57:20Z 2011-09-15
dc.identifier doi:10.5061/dryad.34q0d
dc.identifier.citation Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JT, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA (2011) Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genetics 7(9): e1002280.
dc.description Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (<1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.
dc.relation.ispartofseries 7;9;2011
dc.relation.haspart doi:10.5061/dryad.34q0d/2
dc.relation.haspart doi:10.5061/dryad.34q0d/3
dc.relation.haspart doi:10.5061/dryad.34q0d/4
dc.relation.isreferencedby doi:10.1371/journal.pgen.1002280
dc.relation.isreferencedby PMID:21935354
dc.title Data from: Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
dc.type Article *
dc.contributor.correspondingAuthor Dewey, Frederick E.
prism.publicationName PLoS Genetics

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