Abstract

The primary goal of this supplement request is to create a comprehensive, high quality map of genome variation from the complete set of whole genome sequencing (WGS) data produced by the CCDG program to date. The genome variation map will encompass small variants (SNVs and indels < 50 bp) as well as larger structural variants (SVs) including deletions, duplications, inversions, mobile element insertions, complex SVs and multi- allelic copy number variants (CNVs). A secondary goal is to initiate work towards the creation of Community Resources derived from the Freeze2 genome variation map, including publicly available site-frequency catalogs, imputation reference panels and functional constraint annotations. The overall strategy will mirror our successful Freeze1 pilot effort from last year, with modifications to improve comprehensiveness and efficiency.

Public Health Relevance

Freeze2 will consist of all WGS, WES and WGG data generated prior to the June 2018 progress report. The collaborative variant calling activity descried will focus purely on WGS data, however, WES and WGG data will be aggregated on the cloud at the same time and made available for analysis. We estimate that ~55,000 WGS datasets will be available for Freeze2.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project with Complex Structure Cooperative Agreement (UM1)
Project #
3UM1HG008901-03S2
Application #
9704775
Study Section
Special Emphasis Panel (ZHG1)
Program Officer
Felsenfeld, Adam
Project Start
2018-09-12
Project End
2019-11-30
Budget Start
2018-09-12
Budget End
2018-11-30
Support Year
3
Fiscal Year
2018
Total Cost
Indirect Cost

  Institution

Name
New York Genome Center
Department
Type
DUNS #
078473711
City
New York
State
NY
Country
United States
Zip Code
10013

  Publications

Castel, Stephane E; Cervera, Alejandra; Mohammadi, Pejman et al. (2018) Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat Genet 50:1327-1334
Jereb, Saša; Hwang, Hun-Way; Van Otterloo, Eric et al. (2018) Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. Elife 7:
Regier, Allison A; Farjoun, Yossi; Larson, David E et al. (2018) Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. Nat Commun 9:4038
Yuan, Yuan; Xie, Shirley; Darnell, Jennifer C et al. (2018) Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons. Genome Biol 19:117
Mak, Angel C Y; White, Marquitta J; Eckalbar, Walter L et al. (2018) Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med 197:1552-1564
Kim-Hellmuth, Sarah; Bechheim, Matthias; Pütz, Benno et al. (2017) Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. Nat Commun 8:266
Mohammadi, Pejman; Castel, Stephane E; Brown, Andrew A et al. (2017) Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. Genome Res 27:1872-1884
GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group et al. (2017) Genetic effects on gene expression across human tissues. Nature 550:204-213
Stoeckius, Marlon; Hafemeister, Christoph; Stephenson, William et al. (2017) Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 14:865-868
Hwang, Hun-Way; Saito, Yuhki; Park, Christopher Y et al. (2017) cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation. Neuron 95:1334-1349.e5

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