Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

Frederick E. Dewey¹, Rong Chen², Sergio P. Cordero³, Kelly E. Ormond⁴^,⁵, Colleen Caleshu¹, Konrad J. Karczewski³^,⁴, Michelle Whirl-Carrillo⁴, Matthew T. Wheeler¹, Joel T. Dudley²^,³, Jake K. Byrnes⁴, Omar E. Cornejo⁴, Joshua W. Knowles¹, Mark Woon⁴, Katrin Sangkuhl⁴, Li Gong⁴, Caroline F. Thorn⁴, Joan M. Hebert⁴, Emidio Capriotti⁴, Sean P. David⁴, Aleksandra Pavlovic¹, Anne West⁶, Joseph V. Thakuria⁷, Madeleine P. Ball⁸, Alexander W. Zaranek⁸, Heidi L. Rehm⁹, George M. Church⁸, John S. West¹⁰, Carlos D. Bustamante⁴, Michael Snyder⁴, Russ B. Altman⁴^,¹¹, Teri E. Klein⁴, Atul J. Butte², Euan A. Ashley¹^*

1 Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California, United States of America, 2 Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America, 3 Biomedical Informatics Graduate Training Program, Stanford University School of Medicine, Stanford, California, United States of America, 4 Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America, 5 Center for Biomedical Ethics, Stanford University, Stanford, California, United States of America, 6 Wellesley College, Wellesley, Massachusetts, United States of America, 7 Division of Genetics, Massachusetts General Hospital, Boston, Massachusetts, United States of America, 8 Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America, 9 Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America, 10 Personalis, Palo Alto, California, United States of America, 11 Department of Bioengineering, Stanford University, Stanford, California, United States of America

Abstract

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.

Author Summary

An individual's genetic profile plays an important role in determining risk for disease and response to medical therapy. The development of technologies that facilitate rapid whole-genome sequencing will provide unprecedented power in the estimation of disease risk. Here we develop methods to characterize genetic determinants of disease risk and response to medical therapy in a nuclear family of four, leveraging population genetic profiles from recent large scale sequencing projects. We identify the way in which genetic information flows through the family to identify sequencing errors and inheritance patterns of genes contributing to disease risk. In doing so we identify genetic risk factors associated with an inherited predisposition to blood clot formation and response to blood thinning medications. We find that this aligns precisely with the most significant disease to occur to date in the family, namely pulmonary embolism, a blood clot in the lung. These ethnicity-specific, family-based approaches to interpretation of individual genetic profiles are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.

Citation: Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, et al. (2011) Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence. PLoS Genet 7(9): e1002280. doi:10.1371/journal.pgen.1002280

Editor: Gregory P. Copenhaver, The University of North Carolina at Chapel Hill, United States of America

Received: April 21, 2011; Accepted: July 26, 2011; Published: September 15, 2011

Copyright: © 2011 Dewey 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.

Funding: FED was supported by NIH/NHLBI training grant T32 HL094274-01A2 and the Stanford University School of Medicine Dean’s Postdoctoral Fellowship. MTW was supported by NIH National Research Service Award fellowship F32 HL097462. JKB, OEC, and CDB were supported by NHGRI grant U01HG005715. CFT, JMH, KS, LG, MW-C, MW, and RBA were supported by grants from the NIH/NIGMS U01 GM61374. KEO was supported by NIH/NHGRI 5 P50 HG003389-05. AJB was supported by the Lucile Packard Foundation for Children’s Health, Hewlett Packard Foundation, and NIH/NIGMS R01 GM079719. JTD and KJK were supported by NIH/NLM T15 LM007033. EAA was supported by NIH/NHLBI KO8 HL083914, NIH New Investigator DP2 Award OD004613, and a grant from the Breetwor Family Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: JVT and AWZ are founders, consultants, and equity holders in Clinical Future; GMC has advisory roles in and research sponsorships from several companies involved in genome sequencing technology and personal genomics (see http://arep.med.harvard.edu/gmc/tech.html); MS is on the scientific advisory board of DNA Nexus and holds stock in Personalis; RBA has received consultancy fees from Novartis and 23andMe and holds stock in Personalis; AJB is a scientific advisory board member and founder for NuMedii and Genstruct, a scientific advisory board member for Johnson and Johnson, has received consultancy fees from Lilly, NuMedii, Johnson and Johnson, Genstruct, Tercica, and Prevendia and honoraria from Lilly and Siemens, and holds stock in NuMedii, Genstruct, and Personalis. EAA holds stock in Personalis.
* E-mail: euan@stanford.edu

full-text:
PLoS Genetics: Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence