Whole genome amplification of buccal cytobrush DNA collected for molecular epidemiology studies

Abstract

When cytobrush buccal cell samples have been collected as a genomic DNA (gDNA) source for an epidemiological study, whole genome amplification (WGA) can be critical to maintain sufficient DNA for genotyping. We evaluated REPLI-g™ WGA using gDNA from two paired cytobrushes (cytobush ‘A’ kept in a cell lysis buffer, and ‘B’ dried and kept at room temperature for 3 days, and frozen until DNA extraction) in a pilot study (n=21), and from 144 samples collected by mail in a breast cancer study. WGA success was assessed as the per cent completion/concordance of STR/SNP genotypes. Locus amplification bias was assessed using quantitative PCR of 23 human loci. The pilot study showed > 98% completion but low genotype concordance between cytobrush wgaDNA and paired blood gDNA (82% and 84% for cytobrushes A and B, respectively). Substantial amplification bias was observed with significantly lower human gDNA amplification from cytobrush B than A. Using cytobrush gDNA samples from the breast cancer study (n =20), an independent laboratory demonstrated that increasing template gDNA to the REPLI-g reaction improved genotype performance for 49 SNPs; however, average completion and concordance remained below 90%. To reduce genotype misclassification when cytobrush wgaDNA is used, inclusion of paired gDNA/wgaDNA and/or duplicate wgaDNA samples is critical to monitor data quality.

Keywords: :

• Whole genome amplification
• multiple displacement amplification
• genetic susceptibility
• molecular epidemiology
• genotyping
• TaqMan® assay

Acknowledgements

This research was supported by the Intramural Research Program of the NIH, NCI and the Molecular Epidemiology Committee, DCEG, NCI (protocol OH00-C-N018). We would like to thank Karen Pitt and Jackie King from Biolreliance (Rockville, MD, USA) for providing assistance with laboratory contractual agreements with Molecular Staging, study design and field work. We thank Seiyu Hosono and Michael Egholm from Molecular Staging (New Heaven, CT, USA) for their advice and performance of WGA and genotyping assays.