Axiom precision medicine diversity array

DNA from blood or saliva was extracted and genotyped using Affymetrix Axiom Precision Medicine Diversity Array. Samples with a call rate <95% were excluded from the analysis and SNPs with missing rates >5% were also excluded from the analysis. Genetic ancestry was calculated using principal component analysis in PLINK after linkage disequilibrium pruning (R²<0.1). Imputation was performed using the Michigan Imputation Server with the 1000 Genomes phase3 v5 reference panel. Standard genotyping and quality control procedures were implemented. Variants with minor allele frequency <0.01 were excluded from the analysis.

Californian glioma cases and controls (n_cases = 3150, n_controls = 3154) were selected from the California Childhood Cancer Record Linkage Project, a matched case–control study previously described in detail.^{21 (link)} In short, cases were born in California between 1982 and 2009, with a primary glioma diagnosis made before the age of 15 years registered from 1988 to 2011. California-born cancer-free controls were matched to cases based on date of birth, sex, and self-reported maternal race and/or ethnicity via the California Vital Statistics records. A total of 3150 cases and 3154 controls were included; European-Americans (n_cases = 1583, n_controls = 1592), African-Americans (n_cases = 215, n_controls = 217,), Latino-Americans (n_cases = 1208, n_controls = 1222), and Asian-Americans (n_cases = 238, n_controls = 245). Archived neonatal dried blood spot samples for cases and controls were provided by the California Biobank Program (CBP SIS#311). DNA extraction and processing were performed on the Affymetrix Axiom Precision Medicine Diversity Array. Affymetrix Powertools were used to make genotype calls as previously described.^{22 (link)} This study was approved by the State of California Committee for the Protection of Human Subjects, the University of Southern California, and University of California, Berkeley review board (CPHS IRB Project number 15-05-2005).

Archived DBS were obtained from the California biobank program. DNA extraction, processing, and genotyping were performed as previously described.^{15 (link)} Briefly, DNA was extracted from a 1/3 of DBS using Genfind v3.0 (Beckman) reagents on an Eppendorf robot, and a minimum of 300 ng DNA (using nanodrop for purity and pico-green measurement for DNA quantity) was genotyped on the Affymetrix Axiom Precision Medicine Diversity Array (PMDA). Genotype calls were then extracted with Affymetrix Powertools. Polymorphisms were numbered according to the mitochondrial reference genome Genbank: NC_012920.1.