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- Study Description
This substudy phs000420 MESA SHARe contains Affy 6.0 genotypes, produced as part of NHLBI's SNP Health Association Resource (SHARe) project. Summary level phenotypes for the MESA Cohort study participants can be viewed at the top-level study page phs000209 MESA Cohort. Individual level phenotype data and molecular data for all MESA top-level study and substudies are available by requesting Authorized Access to the MESA Cohort study phs000209.
The Multi-Ethnic Study of Atherosclerosis (MESA) contribution to the SNP Health Association Resource (SHARe) Project involves the primary MESA Study (also referred to herein as MESA Classic), newly recruited members of the MESA Family ancillary study cohort, and newly recruited members of the MESA Air Pollution ancillary study cohort. MESA Classic and the two ancillary studies recruited large numbers of subjects, collected biological samples, and gathered extensive phenotype data. These MESA cohorts are perhaps unique among NHLBI cohort studies in combining a highly multi-ethnic cohort (European American, African American, Hispanic American, and Chinese American) recruitment with extremely detailed phenotyping related to subclinical cardiovascular disease. It is these samples and phenotype data that create the MESA SHARe data resource. Additionally, phenotype data from a growing number of MESA ancillary studies are added quarterly to the SHARe data resource.
MESA SHARe extends genome wide SNP genotyping to non-African American MESA Classic participants and includes MESA Family and MESA Air, for a total of 8402 total participants. About one millions SNPs, plus copy number variants are typed using the Affymetrix Genome-Wide Human SNP Array 6.0. Existing GWA data for MESA Classic African American participants, genotyped through the CARe project, were merged with the MESA SHARe data. Genotyping was completed by Affymetrix in September 2009 and released on dbGaP in February 2010.
Original MESA SHARe Participants by Race and Ethnicity
Classic Excl CARe Classic CARe Family Excl Classic Air New Recruits Total Consented 4770 1697 1681 254 8402 Post Genotyping + QC in dbGaP Caucasian 2528 0 0 159 2687 Chinese 775 0 0 2 777 African Am 6 1673 940 39 2658 Hispanic 1449 0 676 51 2176 Total 4758 1673 1616 251 8298 % Utilized 0.997 0.986 0.916 0.988 0.988
- Study Weblink: MESA SHARe
- Study Types: Longitudinal, Family
Number of study subjects that have individual level data available through Authorized Access: 0
- Authorized Access
- Publicly Available Data (Public ftp)
- Study Inclusion/Exclusion Criteria
- only one record per person (duplicates dropped)
- unresolved gender mismatches dropped
- unresolved cryptic duplicates dropped
- call rate < 95% excluded
- other unresolved QC issues excluded
- CARe QC recommendations applied
SNP-level recommended exclusions:
There is a recommended "list_dropped_snps.txt" (distributed with the dbGaP data but not applied) which excludes SNPS:
- monomorphic across all samples
- observed heterozygosity > 53%
- SNP Missing Rate (in total) > 5%
- SNP Missing Rate (with each race) > 5%
No filters on MAF or H-W have been applied.
- Molecular Data
Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Whole Genome Genotyping Affymetrix AFFY_6.0 934940 52074
- Selected publications
- Diseases/Traits Related to Study (MESH terms)
- Authorized Data Access Requests
- Study Attribution