ID
45709
Description
Principal Investigator: John Blangero, PhD, University of Texas Rio Grande Valley, Brownsville, TX, USA MeSH: Cardiovascular Diseases,Body Height,Body Weight,Body Mass Index,Waist Circumference,Blood Glucose,Insulin,Diabetes Mellitus, Type 2,Blood Pressure,Cholesterol,Cholesterol, HDL,Triglycerides https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001215 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 2,590 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 540 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 ~900 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, ~1,150 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 sequenced 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. For this dataset, the SAFHS appellation represents an amalgamation of the original SAFHS participants and an expansion that reexamined families previously recruited for the San Antonio Family Diabetes Study (R01DK042273) and the San Antonio Family Gall Bladder Study (R01DK053889). Due to this substantial examination history, participants may have information from up to five 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 ~1,060 individuals obtained using the Illumina Sentrix-6 chip is also available from the baseline examination. The WGS data have been jointly called and are available in the current TOPMed accession (phs001215).
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Versions (1)
- 5/16/23 5/16/23 - Chiara Middel
Copyright Holder
John Blangero, PhD, University of Texas Rio Grande Valley, Brownsville, TX, USA
Uploaded on
May 16, 2023
DOI
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Creative Commons BY 4.0
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dbGaP phs001215 NHLBI TOPMed: San Antonio Family Heart Study (SAFHS)
This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, sex of subjects, and monozygotic twin IDs.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent data table contains subject IDs, consent group information, and subject aliases.
- This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, sex of subjects, and monozygotic twin IDs.
- This subject sample mapping data table includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- This subject phenotype data table includes sex, ethnicity, age, anthropometric measurements (n=4 variables; height, weight, BMI, waist circumference), type 2 diabetes status and age of diagnosis, systolic and diastolic blood pressure measurements, blood measurements (n=7 variables; cholesterol, triglycerides, HDL, fasting and 2 hour glucose, fasting and 2 hour insulin), smoking status, medications (n=3 variables; diabetes, BP, lipids), and cardiovascular disease (CVD) status.
- This sample attributes table includes body site where sample was collected, analyte type, tumor status, histological type, sequencing center, funding source, TOPMed phase, project, and study name.
Similar models
This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, sex of subjects, and monozygotic twin IDs.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent data table contains subject IDs, consent group information, and subject aliases.
- This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, sex of subjects, and monozygotic twin IDs.
- This subject sample mapping data table includes a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- This subject phenotype data table includes sex, ethnicity, age, anthropometric measurements (n=4 variables; height, weight, BMI, waist circumference), type 2 diabetes status and age of diagnosis, systolic and diastolic blood pressure measurements, blood measurements (n=7 variables; cholesterol, triglycerides, HDL, fasting and 2 hour glucose, fasting and 2 hour insulin), smoking status, medications (n=3 variables; diabetes, BP, lipids), and cardiovascular disease (CVD) status.
- This sample attributes table includes body site where sample was collected, analyte type, tumor status, histological type, sequencing center, funding source, TOPMed phase, project, and study name.
C0030761 (UMLS CUI [1,2])
C0030761 (UMLS CUI [1,2])
C1522602 (UMLS CUI [1,2])