Omni5 array

DNA was extracted from peripheral blood using the PureGene system (Gentra Systems, Minneapolis, MN). The MALD study was based on the streamlined panel of 1,509 ancestry informative marker (AIM) single nucleotide polymorphisms (SNPs) genotyped using the Illumina African American admixture panel covering all 22 autosomes and chromosome X. Genome-wide association study (GWAS) data was obtained from the Illumina Omni5 array inclusive of exome chip content. All genotyping was performed in the Center for Genomics and Personalized Medicine Research at WFSM.

A pilot study of 81 MM samples used an Illumina 660 array genotyped at the UCSF Genomics Core Facility. In a second phase, we genotyped 289 MM samples using an Illumina Omni5 array at Expression Analysis (Durham, NC). Of the 370 participants in the GWAS, 52 participants were excluded from the survival analysis as noted above due to either insufficient clinical data (N=10) or due to >2 year time difference between diagnosis and ascertainment (N=42). Of the remaining 318 samples we dropped 12 since they did not pass quality control for genotyping. Eleven were dropped due to high missing genotype values (>5% missing genotypes per sample) and 1 sample was dropped due to potential contamination, leaving 306 patients. We dropped SNPs that had >5% missing values, or were monomorphic. Imputation was performed using IMPUTE2^{34 (link)} (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#home) with all samples from 1000 Genomes dataset (Version 2, May 2011 release^{35 (link)}) as a reference. Imputed SNPs with Information<0.5 or minor allele frequency (MAF)<0.025 were excluded, leaving 8,036,255 SNPs for analysis.