Heritability of MI/CAD explained by three genomic compartment sets.

Heritability estimates were inferred independently first in MIGen and WTCCC CAD from a single model involving three variance components (“genic coding”, “genic noncoding” and “intergenic”) using the GCTA software [22,23]. Heritability estimates shown here are from a meta-analysis of the Variance and standard error (V-SE) from these models using as weights the inverse variance from these models.
1Variance and V-SE are estimates from the ratio of genetic variance to phenotypic variance for the specified variance component whereas the P value (V-P) is from the likelihood ratio test of a reduce model with the specified genetic variance component dropped from the full model, from the restricted maximum likelihood method in the GCTA software [22,23].
2Enrichment of variance was calculated as the % variance of total divided by % SNPs of total. MI, myocardial infarction; CAD, coronary artery disease; SNP, single nucleotide polymorphism.
3P value from difference in the observed variance minus the expected variance (variance of whole genome as sum multiplied by % SNPs of total). Genic coding, variants that code amino acid sequence within ±10 kilobases of the 3′ or 5′ untranslated regions of a gene. Genic noncoding, variants that do not code amino acid sequence within ±10 kilobases of the 3′ or 5′ untranslated regions of a gene. Intergenic, variants that are beyond ±10 kilobases of the 3′ or 5′ untranslated regions of a gene.
We calculated the SNP-heritability in three genomic compartment sets for MI/CAD in a meta-analysis of the MIGen and WTCCC CAD studies using the Genome-wide Complex Trait Analysis (GCTA) software. We observed increased enrichment in variance in both “genic coding” and “genic noncoding” regions.