This application addresses the NHLBI-RFA-OD-09-004 for Large-scale DNA Sequencing and Molecular Profiling of Well-phenotyped NHLBI Cohorts. We propose to establish a sequencing center to perform the production-level resequencing of exomes from 10,000 genomic DNA samples derived from well-phenotyped NHLBI cohorts. Second generation methods for targeted capture and DNA sequencing have matured rapidly. Exome sequencing currently has advantages over whole genome sequencing for studies aimed at understanding the contribution of rare variants to heart, lung and blood diseases. These advantages include much lower costs per sample and an increased likelihood of identifying variants of large effect that are amenable to functional interpretation. In our preliminary studies, we developed methods for targeted capture and second generation sequencing of protein-coding sequences at a genome-wide scale, i.e. the exome. We are consistently able to identify coding variants at 96% of targeted bases for 5% of the sequencing effort required for a whole genome. The result is high quality exomes, with a concordance to genotype calls of >99.75% and a false discovery rate for novel variants of <1%. We also show the power of exome sequencing for the direct identification of the causative gene for a monogenic disease. This proof-of-concept serves as a starting point for extending exome sequencing to study extreme and/or complex phenotypes of relevance to the NHLBI mission. Improvements that increase throughput or decrease costs while maintaining high data quality will be integrated into the exome production pipeline. Our recent innovations include a novel algorithm that nearly doubles the usable amount of sequence data that can be extracted from second generation sequencing image sets. The production focus of our team will be complemented by experts in high-throughput sequencing and genotyping, technology development (experimental and algorithmic), the statistical analysis of rare variation, population genetics, and copy number variation. Samples will be received from NHLBI cohorts and undergo extensive quality control prior to exome sequencing. Following sequencing, we will deliver a fully annotated set of coding variants for each individual. For the final deliverable, we will develop a custom genotyping chip for up to 50,000 high-impact, nonsynonymous variants to be assayed on a larger set of cohort samples (up to 50,000). We anticipate working closely with cohort investigators and the NHLBI to maximize the scientific value of these data and of this program.

Public Health Relevance

Project Narrative: Well-phenotyped cohorts provide a key resource for studying the contribution of genetic variation to traits related to heart, lung or blood diseases. Applying targeted capture and massively parallel sequencing of all protein coding regions in the human genome (the exome) to well-phenotyped cohorts will help to delineate the contributions of both rare and common protein-altering variants to common diseases for the first time.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
High Impact Research and Research Infrastructure Cooperative Agreement Programs (UC2)
Project #
Application #
Study Section
Special Emphasis Panel (ZHG1-HGR-P (O1))
Program Officer
Applebaum-Bowden, Deborah
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Washington
Schools of Medicine
United States
Zip Code
Gorvin, Caroline M; Babinsky, Valerie N; Malinauskas, Tomas et al. (2018) A calcium-sensing receptor mutation causing hypocalcemia disrupts a transmembrane salt bridge to activate ?-arrestin-biased signaling. Sci Signal 11:
Blum, Werner F; Klammt, Jürgen; Amselem, Serge et al. (2018) Screening a large pediatric cohort with GH deficiency for mutations in genes regulating pituitary development and GH secretion: Frequencies, phenotypes and growth outcomes. EBioMedicine 36:390-400
Katayama, Shintaro; Ranga, Vipin; Jouhilahti, Eeva-Mari et al. (2018) Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis. Sci Rep 8:17421
Sherrill, Joseph D; Kc, Kiran; Wang, Xinjian et al. (2018) Whole-exome sequencing uncovers oxidoreductases DHTKD1 and OGDHL as linkers between mitochondrial dysfunction and eosinophilic esophagitis. JCI Insight 3:
Epi4K Consortium; EuroEPINOMICS-RES Consortium; Epilepsy Phenome Genome Project (2017) Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data. Eur J Hum Genet 25:894-899
Bruel, Ange-Line; Franco, Brunella; Duffourd, Yannis et al. (2017) Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes. J Med Genet 54:371-380
Petrovski, Slavé; Todd, Jamie L; Durheim, Michael T et al. (2017) An Exome Sequencing Study to Assess the Role of Rare Genetic Variation in Pulmonary Fibrosis. Am J Respir Crit Care Med 196:82-93
Lim, Elaine T; Uddin, Mohammed; De Rubeis, Silvia et al. (2017) Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder. Nat Neurosci 20:1217-1224
Lamar, Tyra; Vanoye, Carlos G; Calhoun, Jeffrey et al. (2017) SCN3A deficiency associated with increased seizure susceptibility. Neurobiol Dis 102:38-48
Zhou, Zhan; Zou, Yangyun; Liu, Gangbiao et al. (2017) Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis. Oncotarget 8:58835-58846

Showing the most recent 10 out of 117 publications