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.]]>
Participants are recruited from urban, suburban, and rural populations across the United States and in selected sites abroad. Individuals suffering from schizophrenia or bipolar disorder are ascertained as in-patients in acute care or chronic care settings, out-patients, or community dwelling. All subject will be 18 or older. Both males and females will be actively recruited, including pregnant females and hospitalized patients. All cases meet lifetime diagnostic criteria for schizophrenia (any subtype) in accordance with the OPCRIT algorithms for DSM-IV and/or ICD-10 criteria. Control participants are drawn from the same geographic area as case participants, either within health care facilities or as community volunteers. Both potential cases (patients suffering with schizophrenia and bipolar disorder) and controls (unaffected participants) were asked to complete a questionnaire (Appendix: Screening Questionnaire) to assess their psychiatric history.]]>
The University of Southern California (USC Center for Genomic Psychiatry), the Massachusetts General Hospital (MGH), the Broad Institute (Stanley Center) and a nation-wide network of academic medical centers have created the Genomic Psychiatry Cohort (GPC). GPC is a large clinical cohort of patients with schizophrenia, bipolar disorder and controls, comprised of nearly equal numbers of European-Ancestry, African-Ancestry and Latino-Ancestry, that will be prospectively followed in order to allow ongoing careful assessment of phenotype and the possibility of future nested case-control studies. Members of the cohort are long-term patients that have agreed to participate in studies related to understanding the genetic and environmental risks for these disorders. This type of population study is critical to understanding risk, helping develop treatments, and understanding prevention of this major illness.]]>