NHLBI Deep Whole Genome Sequencing

From Statgen Internal Wiki
Jump to navigationJump to search

Overview[edit]

The NIH National Heart, Lung and Blood Institute (NHLBI) has committed to deep (30x coverage) whole genome sequencing for all of the collected samples from 9 (now 11) of its ongoing disease-specific research projects (detailed below). The total will approach 20,000 individuals. The sequencing will start in February, 2015 and is projected to be finished by the end of December.

The sequencing is divided by project among four sequencing centers: Broad Institute, University of Washington, New York Genome Center and Illumina (commercial). Groups at University of Washington and University of Michigan will share the tasks of data handling and project coordination. UW is designated as the Data Coordinating Center (DCC) and will coordinate phenotype information and the monthly conference calls. U.Mich is designated as the Informatics Research Core (IRC) with responsibility for creating a unified variant call set. The sequence and genotype data will be deposited to dbGaP, initially in a special protected "Exchange Area" accessible only to project participants. it is expected that each contributing disease-specific study will write their own paper on findings from whole genome sequencing.

Within the U.Mich component of the project, we provide:


September 2016 Site Visit[edit]

TOPMed Site Visit 2016

Table of year 2 studies[edit]

Table of year 1 studies[edit]

PI Name(s) Institution Disease / Phenotype Study Title Sample Size Seq Center Populations
Kathleen C. Barnes Johns Hopkins University asthma genetics in high prevalence populations of African descent New approaches for empowering studies of asthma in populations of African descent 1,100 Illumina African descent Barbados families with > 40% of asthmatic members
John Blangero (contact); Joanne E. Curran; David C. Glahn UT Health Sciences Center San Antonio cardiometabolic risk factors Whole genome sequencing to identify causal genetic variants influencing CVD risk 1,142 Illumina Mexican American in SAFHS extended pedigrees
Esteban Gonzalez Burchard University of California, San Francisco racial and ethnic disparities in response to asthma treatment Pharmacogenomics of bronchodilator response in minority children with asthma 1,500 NYGC 500 AA, 500 Puerto Rican and 500 Mexican of extremely non-responding asthma patients
Patrick Thomas Ellinor (contact); Emelia J. Benjamin; Kathryn L. Lunetta Massachusetts General Hospital early atrial fibrillation Identification of common genetic variants for atrial fibrillation and PR interval 2,799 Broad Atrial fibrillation cases all European American (uses Framingham as controls)
Braxton D. Mitchell University of Maryland School of Medicine cardiometabolic risk factors Identification and functional characterization of a gene influencing LDL cholesterol on 5q 1,100 Broad Old Order Amish large extended pedigrees
Vasan Ramachandran (contact) Boston University longitudinal cardiometabolic risk factors Framingham Heart Study 4,089 Broad 3 generation European American pedigrees
Edwin K. Silverman Brigham and Women's Hospital genetic risk and protective variants for COPD in African American and European American populations Genetic epidemiology of COPD 2,000 UW 1,000 EA and 900 AA of extremely severe, early onset COPD patients vs extreme healthy smokers
Scott T. Weiss Brigham and Women's Hospital asthma genetics in high prevalence Hispanic population The genetic epidemiology of asthma in Costa Rica 1,198 UW Costa Rica is a special Hispanic population with asthma prevalence at 24%
Adolfo Correa
James Wilson (contact)
University of Mississippi cardiometabolic risk factors Jackson Heart Study 3,499 UW AA mixed family and population based
Stephen T. McGarvey International Health Institute, Brown University genes influencing obesity Samoan Family Study of Overweight and Diabetes 384 UW with planned imputation to other pedigree members
Susan Redline Brigham and Women's Hospital genes influencing sleep apnea Cleveland Family Study 1,000 UW 500 African American, 500 European American

(This information from Cathy Laurie as of Dec 2, 2014, with numbers subsequently updated. Two more studies added February 15, 2015.)

U.Mich personnel[edit]

Goncalo tentatively designated different people to contribute to the four major commitments:

  • Data Monitoring web site: Hyun Min Kang, Kevin Li
  • Variant Calling Pipeline: Hyun Min Kang, Mary Kate Wing, Chris Scheller, additional students
  • Population Genetic Analyses: Sebastian Zoellner, Keng-Han Lin
  • Cross Study Analyses: Shawn Lee, Xiang Zhou
  • Liaison with study investigators: Tom Blackwell, Ellen Schmidt