WGSPD Project 1: Whole Genome Sequencing for Schizophrenia and Bipolar Disorder
The Center for Genomic Psychiatry at the University of Southern California (USC) and an extensive network of academic medical centers have created the Genomic Psychiatry Cohort (GPC). The GPC consists of a large clinical cohort of patients with schizophrenia, bipolar disorder, and healthy controls. The pilot phase of whole genome sequencing of the GPC has been done in collaboration with the USC and the Broad Institute of MIT and Harvard.
Whole genome sequencing (20X) and analysis of 9,033 well-phenotyped individuals from the Genomic Psychiatry Cohort (GPC), divided among schizophrenia cases, bipolar disorder cases, and psychiatrically normal controls, and comprised of European-Ancestry (EA), African-Ancestry (AA), and Latino individuals. The combination of clinically well-characterized GPC participants and whole genome sequencing with rich functional annotation aims to identify functional variants associated with schizophrenia and bipolar disorder risk. Over half of the sequenced samples are patients with a diagnosis of either schizophrenia or bipolar disorder. The majority of the study participants are of African American ancestry, increasing the diversity of sampling for these important diseases in traditionally understudied populations.
This data set also contains 545 samples that have undergone 10x Genomics Linked-Read Sequencing (169 participants overlapping with the 9,033 participant WGS 20X dataset). In addition to the benefits due to disease phenotyping and ancestry selection that apply to all of the WGSPD Project 1 samples, the 10x Genomics Linked-Read samples, through the use of barcodes that can identify the long input DNA fragment that each sequencing read was generated from, can be used to 1) identify structural variants that are difficult to call with standard short read data, 2) map short reads to repetitive regions of the genome that cannot be assayed with standard short reads, and provide highly accurate phasing information about genetic variants, including rare variants that are more difficult to phase using statistical phasing techniques.
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This study has been divided into the following workspaces by consent codes and optionally the originating laboratory.
|Terra Workspace Name||Consent Code||Disease||Access||Study Design||Data Type||Samples||Participants||Size (TB)|
|AnVIL_NIMH_Broad_WGSPD1_McCarroll_Braff_DS_10XLRGenomes||DS-SZRD-MDS||Schizophrenia cases and controls||Controlled Access||Case-Control||Whole Genome||187||555||11.60|
|AnVIL_NIMH_Broad_WGSPD1_McCarroll_Braff_DS_WGS||DS-SZRD-MDS||Schizophrenia cases and controls||Controlled Access||Case-Control||Whole Genome||864||864||20.10|
|AnVIL_NIMH_Broad_WGSPD1_McCarroll_Escamilla_DS_WGS||DS-MLHLTH-MDS||Schizophrenia cases and controls||Controlled Access||Case-Control||Whole Genome||85||85||3.45|
|AnVIL_NIMH_Broad_WGSPD1_McCarroll_Pato_GRU_10XLRGenomes||GRU||Schizophrenia and Bipolar Disorder cases and co...||Controlled Access||Case-Control||Whole Genome||368||355||21.70|
|AnVIL_NIMH_Broad_WGSPD1_McCarroll_Pato_GRU_WGS||GRU||Schizophrenia and Bipolar Disorder cases and co...||Controlled Access||Case-Control||Whole Genome||0||8,084||120.00|