Figures 1c and 1d show Bland-Altman plots comparing the agreement of normalized gene expression intensities across extract replicates associated with a single representative subject.
Figures 1a and 1b show Bland-Altman plots comparing the agreement of normalized gene expression intensities across a set of technical replicates associated with a single representative tissue sample for the 1.5 K (1a) and 24K (1b) panels.
To illustrate the impact adjusting for PS can have on identifying disease susceptibility loci, we intersected the HLC eQTLs with the set of SNPs in the public GWAS databases identified and replicated as associated with common human disease [16].
Among these studies, the APOE gene has emerged as the only consistently replicated locus associated with human lifespan.
Then, we replicated the associated SNP rs1128334 in the Ningxia cohort of 352 cases and 400 matched controls.
Finally, we also used a recently available database [ 11] to understand whether our T2D EWAS hit and the eight replicated were associated with any gene expression level.
As described by several authors, the OS5 rSNP3383 SNP is still the most robustly replicated polymorphism associated with OA and the only locus successfully validated across diverse Asian and European populations.
To date, the most consistently replicated polymorphism associated with alcohol metabolism is the SNP rs671 in the ALDH2 gene, which is mapped to chromosome 12q24.2 and encodes the mitochondrial ALDH isozyme ALDH2.
Although transcription factor 7-like 2 (TCF7L2) gene is the strongest and most widely replicated locus associated with type 2 diabetes (1– 5), there are very few studies that have examined the association between genetic variation in this gene and cardiovascular disease (6– 9).
Non-candidate gene approaches recently revealed a robustly replicated locus associated with the response to metformin on chromosome 11 [ 51, 82, 83], with subsequent follow-up work pointing to the Npat and Atm genes as the likely causal genes (E. R. Pearson, R. McCrimmon, M. McCarthy, unpublished data).
