RT Journal Article
SR Electronic
T1 Successful Genome-Wide Scan in Paired Blood and Buccal Samples
JF Cancer Epidemiology Biomarkers & Prevention
JO Cancer Epidemiol Biomarkers Prev
FD American Association for Cancer Research
SP 1023
OP 1025
DO 10.1158/1055-9965.EPI-06-0859
VO 16
IS 5
A1 Feigelson, Heather Spencer
A1 Rodriguez, Carmen
A1 Welch, Robert
A1 Hutchinson, Amy
A1 Shao, Wen
A1 Jacobs, Kevin
A1 Diver, W. Ryan
A1 Calle, Eugenia E.
A1 Thun, Michael J.
A1 Hunter, David J.
A1 Thomas, Gilles
A1 Chanock, Stephen J.
YR 2007
UL http://cebp.aacrjournals.org/content/16/5/1023.abstract
AB 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)