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CHS Genetic Data Overview

 

How to Access CHS Genetic Data:

Access to CHS phenotype and genotype data requires the same protocol required for accessing all other CHS data in accordance with the CHS data distribution policy.

CHS Genetic data have been collected as part of the main study (apoE data) as well as by various ancillary studies, from single CHS cohort studies to large multi-cohort consortia. Ancillary study investigators who collect genetic data in CHS are given an exclusive opportunity to analyze, present and publish those data under the auspices of the ancillary study.  After a reasonable time (in general, 12 months after data collection and cleaning are complete), the ancillary study data will be made available for additional uses by other investigators. Collaboration with the ancillary study investigators who collected the data is encouraged.

When submitting a CHS paper proposal that involves selected SNPs, researchers will need to provide a list of RS numbers from the websites below.   
 

Where to find the latest listing of available CHS Genetic Data

  1. On the Internal CHS Website:

Individual single-nucleotide polymorphisms (SNP) lists from a variety of ancillary studies are posted on the internal website. The list includes both completed and approved, proposed assays. 

  • "Summary of CHS Genetic Assays" (as of September, 2008)  
  • "Search Databases" menu - Search the list of approved CHS ancillary studies
  1. On dbGaP (NIH NCBI database of Genotypes and Phenotypes) Note that both phenotype and genotype data are available on dbGap.  The participant idnumbers on dbGap are not the same as those used in the study, so data need to come from one source or the other.

Large-scale genotyping efforts using CHS data:

  • GWAS  Whole Genome Association study to identify genetic variants associated with CV events in CHS, Bruce Psaty, PI. (CHS Study #187).

Whole Genome Genotyping, # of oligos/SNPs =370,404 . Chip = ILLUMINA HumanCNV370v1

Most investigators who wish to use these data are involved in multi-cohort consortia where each cohort analyzes their own data and results are subsequently meta-analyzed.  The CHS analyses have been done by Dr. Psaty’s research group, and we advise investigators to communicate with Dr. Psaty.

This GWAS dataset has also been uploaded to dbGaP along with phenotype data. It is important to note that ID numbers used by dbGap differ from those used internally, so investigators are advised to obtain both phenotype and genotype data from the same source.

Additionally, over one million SNPs for African Americans in the CHS cohort have been genotyped on the Illumina Omni1M chip. 

  • CARe NHLBI’s Candidate Gene Association Resource (CARe) Study, Russell Tracy, PI (CHS Study #206).

To request CARe data: Genotype data must be requested through CARe or dbGap. The phenotype will also need to be requested through CARe in order to match participant id numbers.

Targeted Region Genotyping , # of SNPs = 49094.
Chip = ILLUMINA CVDSNP55v1_A
See the dbGaP Location or the CARe home page for more details.

  • Exome:  There are 2 large funded ancillary studies in CHS:
  1. Next steps in gene discovery:  building upon CHARGE (‘CHARGE-S’). Bruce Psaty, P.I. (CHS Study #238)
  2. Large scale sequencing in a consortium of US cohorts (‘HeartGO/ESP’). Bruce Psaty, P.I. (CHS Study #239).

These 2 projects include all CHS participants with available DNA and appropriate consents. Exome data (rare-variant calls) are available for local analysis and meta-analysis.

The above projects focus on GWAS hits with targeted sequencing of not only the exons but also the introns, promoter regions, 3’-untranslated regions, and some inter-genic regions.  These projects are complementary to MESA AS#140 Rich, Human Exome Variation and Subclinical Atherosclerosis Risk in MESA (1RC2HL103010-01), which sequences all exomes and only the exomes via high throughput DNA sequencing of human exons (Human Exome Project) in 4,100 samples from MESA and correlate distribution of variant genotypes with phenotypes related to subclinical atherosclerosis and related phenotypes, as part of a four-cohort Consortium (MESA, Framingham, Jackson and CARDIA).

  • Whole Genome Sequencing

Whole-genome Sequencing in CHS. Bruce Psaty, P.I. (CHS Study #281).

Evaluations of genome-wide or exome-wide associations between genetic variants and Alzheimers Disease in the full CHS cohort as part of NIA/NHGRI Alzheimer Disease Sequencing Project (ADSP).  Sequencing at Human Genome Sequencing Center at Baylor College of Medicine (Richard Gibbs, PI), Broad Institute Genome Center (Eric Lander, PI), and Washington University Genome Institute (Richard Wilson, PI).

 

See also:

 

Contact Information:

Tony Wilsdon, CHS Data Manager