Protocol detail

Genotyping and Imputation of Genomic Data

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SNP genotype data were acquired on the Illumina Human660W-Quadv1_A (eMERGE), Illumina HumanOmni1-Quad (VESPA), HumanOmni5-Quad (VESPA) and Affymetrix 6.0 SNP array (ARIC) platforms. Quality control (QC) steps for the EHR data sets were performed per the published protocols established by the eMERGE Genomics Working Group.^{23 (link)} For imputation, palindromic alleles were aligned to the positive strand using allele frequency information from the 1000 Genomes Project. SNPs were pre-phased using SHAPEIT,^{24 (link)} and data were imputed using IMPUTE2^{25 (link)} and the 10/2014 release of the 1000 Genomes cosmopolitan reference haplotypes. QC for the ARIC data set followed the guidelines accompanying the dbGaP release including removing SNPs with chromosomal anomalies and with >5 discordant calls in replicate samples, and using a predefined subset of unrelated subjects. QC analyses used PLINK v1.07.^{26 (link)} After filtering for a sample missingness rate<2.0%, a SNP missingness rate<2.0% and a SNP deviation from Hardy-Weinberg<0.001, there were 627,580 SNPs with MAF>1.0%. The merged intersection of the ARIC and imputed EHR data sets contained 488,525 SNPs with MAF>1.0%.

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Mosley J.D., Van Driest S.L., Wells Q.S., Shaffer C.M., Edwards T.L., Bastarache L., McCarty C.A., Thompson W., Chute C.G., Jarvik G.P., Crosslin D.R., Larson E.B., Kullo I.J., Pacheco J.A., Peissig P.L., Brilliant M.H., Linneman J.G., Denny J.C, & Roden D.M. (2016). Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile using Historical Data. Circulation. Cardiovascular genetics, 9(6), 521-530.

Publication 2016

Human660W-Quadv1_A 6.0 SNP array

Alleles Chromosomal anomalies Genomes Genotype Haplotypes Rate Replicate Snps

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Protocol cited in 2 other protocols

Variable analysis

independent variables

SNP genotype data acquired on Illumina Human660W-Quadv1_A (eMERGE), Illumina HumanOmni1-Quad (VESPA), HumanOmni5-Quad (VESPA) and Affymetrix 6.0 SNP array (ARIC) platforms

dependent variables

Not explicitly mentioned

control variables

Positive and negative controls not explicitly mentioned
Quality control (QC) steps for the EHR data sets were performed per the published protocols established by the eMERGE Genomics Working Group
QC for the ARIC data set followed the guidelines accompanying the dbGaP release including removing SNPs with chromosomal anomalies and with >5 discordant calls in replicate samples, and using a predefined subset of unrelated subjects
QC analyses used PLINK v1.07

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