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Effects of Electron-Beam Irradiation on Whole Genome Amplification

¹ Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD; ² Core Genotyping Facility, Advanced Technology Center, National Cancer Institute, Gaithersburg, Maryland; ³ Intramural Research Support Program, Science Applications International Corporation, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, Maryland; and ⁴ Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD

Requests for reprints: Andrew W. Bergen, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, Bethesda, MD 20892-7236. Phone: 301-435-7614; Fax: 301-402-4489. E-mail: bergena{at}mail.nih.gov

Electron-beam (E-beam) irradiation, currently being used to sterilize mail addressed to selected ZIP codes in the United States, has significant negative effects on the genomic integrity of DNA extracted from buccal-cell washes. We investigated the yield, composition, and genotyping performance of whole genome amplified DNA (wgaDNA) derived from 24 matched samples of E-beam–irradiated and nonirradiated genomic DNA (gDNA) as a model for the effects of degraded gDNA on the performance of whole genome amplification. gDNA was amplified using the Multiple Displacement Amplification method. Three methods of DNA quantification analysis were used to estimate the yield and composition of wgaDNA, and 65 short tandem repeat and single nucleotide polymorphism genotyping assays were used to evaluate the genotyping performance of irradiated and nonirradiated gDNA and wgaDNA. Compared with wgaDNA derived from nonirradiated gDNA, wgaDNA derived from irradiated gDNA exhibited a significantly reduced yield of wgaDNA and significantly reduced short tandem repeat and single nucleotide polymorphism genotyping completion and concordance rates (P < 0.0001). Increasing the amount of irradiated gDNA input into whole genome amplification improved genotyping performance of wgaDNA but not to the level of wgaDNA derived from nonirradiated gDNA. Multiple Displacement Amplification wgaDNA derived from E-beam–irradiated gDNA is not suitable for genotyping analysis.

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