Multi-Ethnic Genotyping Array (MEGA)

PAGE II genotyped 50,000 samples using MEGA, an Illumina high density custom exomechip array, to continue emphasis on characterizing population-level disease risks in non-European-descent individuals. Cohorts in PAGE II are: CALiCo (Causal Variants Across the Life Course, a consortium of ARIC, CARDIA, HCHS/SOL, Strong Heart Studies), ISMMS (Mount Sinai BioMe Biobank), MEC (Multiethnic Cohort), and WHI (Women’s Health Initiative). PAGE is investigating anthropometric, cardiovascular, hypertension, kidney, inflammatory, lipid, T2D, and other traits.

You can find information here about Illumina’s MEGA:

• Illumina Infinium Multi-Ethnic Global BeadChip
• News article from GenomeWeb

You can find Illumina two strand translation files here:

• Top to Forward Strand Translation
• Top to AB Strand Translation

You can find the SNP submission file at dbSNP here:

• View MEGA SNP submission batch at dbSNP
• Download MEGA SNP batch data (including original IDs, ssIDs, and rsIDs)

You can also find 637 SNP annotations and 575 Indel annotations for the MEGA loci from WGSA, as well as the PAGEII allele frequencies for each loci and population in PAGE. The package includes tabix formatted files for faster selection. Note that the compressed annotations file is large (2.1GB). The PAGEII_WGSA_MEGA_QC_Filtering.tar.gz file describes sites that were removed before annotation, and quality control workflow applied.