All DNA samples go through the same rigorous quality control process before and after genotype generation, so we see no difference in data quality based on source of DNA. Affymetrix GeneChip 6.0 platform and Illumina OmniQuad Express platform are well validated platforms for genotyping. Detailed QC pipeline was described in ref. 18. Briefly, the standard QC measures for SNPs (HWE P>0.001; MAF>0.01; genotype call rate>0.95; misshap test>1× 10-9) and subjects (genotype success rate>0.95; genotype-derived gender concordant with reported gender, excess inter/intra-heterozygosity) were applied. The top hits of the genotype data were successfully replicated in another independent dataset18. For the whole genome sequencing data, base quality score recalibration was performed using the GATK BQSR and the empirical calibration of the variant quality was done using GATK pipeline. Variants were further filtered for minimum read depth (DP), variant calling confidence score (QD), VQSLOD and mapping and variant quality scores (MQ, GQ). For the methylation data, we applied both probe-level (detection P≥0.01 across all samples; not cross-hybridize with the sex chromosomes; not overlapped with known SNPs with MAF≥0.01 within 10 bp region) and
