Successful Genome-Wide Scan in Paired Blood and Buccal Samples
- Heather Spencer Feigelson1,
- Carmen Rodriguez1,
- Robert Welch2,3,
- Amy Hutchinson2,3,
- Wen Shao2,
- Kevin Jacobs2,
- W. Ryan Diver1,
- Eugenia E. Calle1,
- Michael J. Thun1,
- David J. Hunter4,6,7,
- Gilles Thomas3,4 and
- Stephen J. Chanock3,4,5
- 1Department of Epidemiology and Surveillance Research, American Cancer Society, NE, Atlanta, Georgia; 2Intramural Research Support Program Science Applications International Corporation-Frederick, National Cancer Institute-Frederick, Frederick, Maryland; 3Core Genotyping Facility, 4Division of Cancer Epidemiology and Genetics, and 5Section on Genomic Variation, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland; and 6Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, and 7Channing Laboratory, Brigham and Women's Hospital, Boston, Massachusetts
- Requests for reprints:
H.S. Feigelson, Department of Epidemiology and Surveillance Research, American Cancer Society, 1599 Clifton Road, NE, Atlanta, GA. Phone: 404-929-6815; Fax: 404-327-6450. E-mail: heather.feigelson{at}cancer.org
Abstract
Interest in genome-wide association studies to identify susceptibility alleles for cancer is growing, and several are currently planned or under way. Although the feasibility of collecting buccal cell samples as an alternative to venous blood samples as a source of genomic DNA has been shown, the validity of using DNA from buccal cells for genome-wide scans has not been assessed. We used 46 paired buffy coat and buccal cell samples to test the feasibility of using DNA from buccal cells for genotyping with the HumanHap300 Bead Chip (v.1.0.0) on the Illumina Infinium II platform. Genotyping was successful in every sample, regardless of DNA yield or sample type. Of the 317,502 genotypes attempted, 315,314 (99.3%) were successfully called. Completion rates were similar for buffy coat and buccal cell samples (99.63% and 99.44%, respectively; P = 0.15). Completion rates <99% were observed in only four samples and did not differ by specimen type. The paired samples showed exceptionally high concordance (99.96%). These results show that buccal cell samples collected and processed under optimal conditions can be used for genome-wide association studies with results comparable to those obtained from DNA extracted from buffy coat. (Cancer Epidemiol Biomarkers Prev 2007;16(5):1023–5)
Footnotes
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The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
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- Accepted February 21, 2007.
- Received October 9, 2006.
- Revision received January 10, 2007.
