Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping

作者: Kristine L Bucasas , Gagan A Pandya , Sonal Pradhan , Robert D Fleischmann , Scott N Peterson

DOI: 10.1186/1471-2156-10-85

关键词:

摘要: Whole genome amplification (WGA) offers new possibilities for genome-wide association studies where limited DNA samples have been collected. This study provides a realistic and high-precision assessment of WGA genotyping performance from 20-year old archived serum using the Affymetrix Genome-Wide Human SNP Array 6.0 (SNP6.0) platform. Whole-genome amplified 45 replicates 5 fresh sera paired with non-amplified genomic were genotyped in duplicate. All passed imposed QC thresholds quantity quality. In general, produced low call rates (45.00 +/- 2.69%), although reproducibility successfully called markers was favorable (concordance = 95.61 4.39%). Heterozygote dropouts explained majority (>85% technical replicates, 50% genomic/serum samples) discordant results. Genotyping on improved by implementation Corrected Robust Linear Model Maximum Likelihood Classification (CRLMM) algorithm but at loss many which failed to pass its quality threshold. Poor genotype clustering evident that CRLMM confidence We conclude while it is possible extract subsequently perform whole-genome samples, did not well appeared unsuitable high-resolution these arrays.

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