Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms†

摘要: Highly accurate and high-throughput SNP genotyping platforms are increasingly popular but the performance of suboptimal DNA samples remains unclear. The aim our study was to determine best platform, amplification technique, loading concentration maximize genotype accuracy call rate using degraded samples. We amplified high-molecular weight genomic recently extracted from whole blood 50-year-old patient sera. Two whole-genome (WGA) methodologies were used: an isothermal multiple displacement method (MDA) a fragmentation-PCR-based (GenomePlex [GPLEX]; Sigma-Aldrich, St. Louis, MO). Duplicate runs performed on genome-wide dense arrays (Nsp-Mendel; Affymetrix) custom based molecular inversion probes (Targeted Genotyping [TG]; BeadArray technology (Golden Gate [GG]; Illumina). Miscalls no-calls Mendel correlated with each other, confidence scores Bayesian calling algorithm, average probe intensity. Degraded MDA gave low rates concordance across all at standard concentrations. GG improved when 5 x used. GPLEX high for higher concentrations both TG platforms. Based these analyses, after filtering sample performance, we able achieve mean 99.7% by 2 concentration. These findings may be useful investigators planning case-control association studies quality.