Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays

Author:

Dagnall, Casey

Morton, Lindsay M

Hicks, Belynda

Li, Shengchao

Zhou, Weiyin

Karlins, Eric

Teshome, Kedest

Chowdhury, Salma

Lashley, Kerrie S

Sampson, Joshua N

Robison, Leslie L

Armstrong, Gregory T

Bhatia, Smita

Radloff, Gretchen A

Davies, Stella M

Tucker, Margaret A

Yeager, Meredith

Chanock, Stephen J
Author Address

Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA. dagnallc@mail.nih.gov., Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA. dagnallc@mail.nih.gov., Department of Epidemiology and Cancer Control, St. Jude Children 39;s Research Hospital, Memphis, TN, USA., Department of Population Sciences, City of Hope, Duarte, CA, USA., Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA., Department of Pediatrics, Cincinnati Children 39;s Hospital Medical Center, Cincinnati, OH, USA.,

Abstract:

The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input. Our results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.

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Author Address