Assessing the utility of whole genome amplified DNA as a template for DMET Plus array.

Background: Large amounts of high quality DNA are typically required for high-throughput genotyping arrays but sometimes study participant DNA is in limited supply. Multiple displacement amplification (MDA)-based whole genome amplification is an in vitro technique that permits the genetic analysis of limited amounts of high molecular weight genomic DNA (gDNA).

Methods: The performance of MDA-whole genome amplified DNA (wgaDNA) as a template for DMET Plus (Affymetrix) was assessed. wgaDNA was generated from gDNA from three HapMap CEU cell lines and 11 breast cancer patients. One HapMap sample and three patient samples were randomly selected for replication to assess reproducibility. Accuracy was assessed by comparing the wgaDNA genotypes with gDNA genotypes. The kappa (κ) statistic was used to measure genotype concordance between paired gDNA-wgaDNA and wgaDNA-wgaDNA samples. Copy number variants (CNV) were not included in concordance analysis in this study.

Results: A good genotype call rate of 98.8%±1.06% (mean±standard deviation, 1931 markers) was observed for all 18 wgaDNA samples with three samples having call rates lower than 98%. High genotype concordance rates were observed between four HapMap wgaDNA-gDNA pairs (98.5%, κ=0.9817, p<0.0001, 1931 markers) and 14 patient wgaDNA-gDNA pairs (100%, κ=1.00, p<0.0001, 19 markers among CYP2D6 and CYP2C19). Excellent genotype concordance was also observed between four independently amplified duplicate samples (98.0%, κ=0.9745; p<0.0001, 1931 markers).

Conclusions: MDA-produced wgaDNA provides accurate and reproducible genotypes with the DMET Plus array and is therefore a suitable template for this targeted pharmacogenetic genotyping array.