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- Study Description
This study is part of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Program. TOPMed is part of a broader Precision Medicine Initiative, which aims to provide disease treatments that are tailored to an individual's unique genes and environment. TOPMed will contribute to this initiative through the integration of whole-genome sequencing (WGS) and other -omics (e.g., metabolic profiles, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data. In doing so, this program aims to uncover factors that increase or decrease the risk of disease, to identify subtypes of disease, and to develop more targeted and personalized treatments. Two genotype call sets derived from WGS are now available, one called Freeze 4 (GRCh37) and another called Freeze 5b (GRCh38), with largely overlapping sample sets. Information about how to identify other TOPMed WGS accessions for cross-study analysis, as well as descriptions of TOPMed methods of data acquisition, data processing and quality control, are provided in the accompanying documents, "TOPMed Whole Genome Sequencing Project - Freeze 4, Phase 1" and "TOPMed Whole Genome Sequencing Project - Freeze 5b, Phases 1 and 2". Please check the study list at the top of each of these methods documents to determine whether it applies to this study accession.
The San Antonio Family Heart Study (SAFHS) is a complex pedigree-based mixed longitudinal study designed to identify low frequency or rare variants influencing susceptibility to cardiovascular disease, using whole genome sequence (WGS) information from 3,000 individuals in large Mexican American pedigrees from San Antonio, Texas. The major objectives of this study are to identify low frequency or rare variants in and around known common variant signals for CVD, as well as to find novel low frequency or rare variants influencing susceptibility to CVD.
WGS of the SAFHS cohort has been obtained through three efforts. Approximately 600 WGS were performed commercially at 50X by Complete Genomics, Inc (CGI) as part of the large T2D-GENES Project. The phenotype and genotype data for this group is available at dbGaP under accession number phs000462. An additional 631 WGS at 30X were obtained through Illumina as part of the R01HL113322 "Whole Genome Sequencing to Identify Causal Genetic Variants Influencing CVD Risk" project. Finally, 1,200 WGS at 30X WGS were obtained through Illumina funded by a supplement as part of the NHLBI's TOPMed program.
Extensive phenotype data are provided for 3,000 individuals primarily obtained from the P01HL45522 "Genetics of Atherosclerosis in Mexican Americans" for adults and R01HD049051 for children in these same families. Phenotype information was collected between 1991 and 2016. SAFHS participants may have information from up to 5 visits. The clinical variables reported are coordinated with TOPMed and include major adverse cardiac events (MACE), T2D status and age at diagnosis, glycemic traits (fasting glucose and insulin), blood pressure, blood lipids (total cholesterol, HDL cholesterol, calculated LDL cholesterol and triglycerides). Additional phenotype data include the medication status at each visit, classified in four categories as any current use of diabetes, hypertension or lipid-lowering medications, and, for females, current use of female hormones. Anthropometric measurements include age, sex, height, weight, hip circumference, waist circumference and derived ratios. PBMC derived gene expression assays for a subset of individuals (n=1240) obtained using the Illumina Sentrix-6 chip is also available from the baseline examination. The WGS data from these three different efforts have been jointly called and are available in the current TOPMed accession (phs001215).
- Authorized Access
- Publicly Available Data (Public ftp)
Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.
- Study Inclusion/Exclusion Criteria
The SAFHS began in 1991, and included 1,431 individuals in 42 extended families at baseline. Probands were 40 to 60 year old low-income Mexican Americans selected at random without regard to presence or absence of disease, almost exclusively from Mexican American census tracts in San Antonio, Texas. All first, second, and third degree relatives of the proband and of the proband's spouse, aged 16 years or above, were eligible to participate in the study. As part of our ongoing studies, we have recruited new family members from the original families, expanding the cohort to almost 3,000 individuals.
The first T2D-GENES sequencing effort chose the twenty largest pedigrees from SAFHS, constituting approximately 600 individuals. Sequencing in the R01HL113322 "Whole Genome Sequencing to Identify Causal Genetic Variants Influencing CVD Risk" project selected the next largest pedigrees and participants most informative for imputation, a total of 931 individuals. Finally, sequencing of the remaining SAFHS participants (1199 individuals) was supported by the TOPMed program.
- Molecular Data
Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Whole Genome Sequencing Illumina HiSeq X Ten N/A N/A
- Selected publications
- Diseases/Traits Related to Study (MESH terms)
- Links to Related Resources
- Authorized Data Access Requests
- Study Attribution