NHLBI TOPMed: San Antonio Family Heart Study

Description

The description below was taken directly from the NCBI database of Genotypes and Phenotypes (dbGaP):

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).

General information

phs#	Study abbreviation	Study type	Parent phs#
phs001215	SAFS	Family	phs000462