Multi ethnic genotyping array v2 15070954 a2

The expanded Illumina Multi‐Ethnic Genotyping Array (MEGA) v2 15070954 A2 (genome build 37) that contains over 2 million Single Nucleotide Polymorphisms and over 60,000 rare variants selected from populations of African origin was used for genotyping. Genotyping was carried out on 3,347 samples which included 3,198 unique samples and 70 duplicates. HapMap controls (70 unique samples and 9 duplicates) were also genotyped as part of the quality control process.

Demographic information (age, sex, and residential location) and limited exposure information were obtained. Saliva specimens were collected using the Oragene saliva kit, de-identified and shipped to the Butali laboratory at the University of Iowa. DNA was extracted from the saliva using the standard Oragene saliva DNA extraction protocol and quantified using Qubit (http://www.invitrogen.com/site/us/en/home/brands/Product-Brand/Qubit.html;Thermo Fisher Scientific,Grand Island, NY). As part of internal QC, Taqman XY genotyping was used for sex confirmation. Subsequently, aliquoted DNA was sent to the Center for Inherited Disease Research (Baltimore, Maryland, USA) for genotyping. The Illumina Multi-Ethnic Genotyping Array MEGA v2 15070954 A2 (genome build 37), which has over 2 million variants including over 60 000 rare variants selected from populations of African origin, was used for the genotyping. Details on genotyping and QC measures have been previously published^{38 (link)}.