This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Paynter, R. A. Articles by Smith, M. T. Search for Related Content PubMed PubMed Citation Articles by Paynter, R. A. Articles by Smith, M. T.

Accuracy of Multiplexed Illumina Platform-Based Single-Nucleotide Polymorphism Genotyping Compared between Genomic and Whole Genome Amplified DNA Collected from Multiple Sources

¹ School of Public Health, University of California, Berkeley, California and ² Department of Epidemiology and Biostatistics, University of California, San Francisco, California

Requests for reprints: Randi A. Paynter, Division of Environmental Health Sciences, School of Public Health, University of California, 140 Earl Warren Hall #7360, Berkeley, CA 94720-7360. Phone: 510-643-5346; Fax: 510-642-0427. E-mail: randi{at}post.harvard.edu

Association studies designed to identify the genetic determinants underlying complex disease increasingly require sustainable high-quality DNA resources for large-scale single-nucleotide polymorphism (SNP) genotyping. Recent studies have shown that genomic DNA (gDNA) suitable for SNP genotyping can be obtained from buccal cells and from dried blood spots on Guthrie cards. Further, successful SNP genotyping has been done using the reaction product of multiple displacement amplification of gDNA. We evaluated genotype consistency on the Illumina genotyping platform for 717 to 1,744 SNP loci between replicate samples of gDNA and whole genome amplified DNA (wgaDNA) from a variety of sources. Nine healthy adults provided peripheral blood via venipuncture and buccal cells by mouth rinse. DNA was also obtained from urothelial cells in urine samples from five of the nine subjects. gDNA was extracted from all samples, wgaDNA was generated from each gDNA, and all samples were genotyped. To assess SNP genotyping accuracy of DNA obtained from dried blood spots, gDNA was extracted, amplified, and genotyped from peripheral blood samples and paired Guthrie card samples were obtained from eight childhood leukemia patients. Call rates and replicate concordances for all sample types, regardless of amplification, were >97%, with most sample types having call rates and replicate concordances >99%. Using the gDNA from blood samples as the reference for concordances calculated for all other sample types, we observed concordances >98% regardless of sample type or amplification. We conclude that highly multiplexed Illumina genotyping may be done on gDNA and wgaDNA obtained from whole blood, buccal samples, dried blood spots on Guthrie cards, and possibly even urine samples, with minimal misclassification. (Cancer Epidemiol Biomarkers Prev 2006;15(12):2533–6)

This article has been cited by other articles:

				A. Gusev, J. K. Lowe, M. Stoffel, M. J. Daly, D. Altshuler, J. L. Breslow, J. M. Friedman, and I. Pe'er Whole population, genome-wide mapping of hidden relatedness Genome Res., February 1, 2009; 19(2): 318 - 326. [Abstract] [Full Text] [PDF]

				M. Nakashima, M. Tsuda, A. Kinoshita, T. Kishino, S. Kondo, O. Shimokawa, N. Niikawa, and K.-i. Yoshiura Precision of High-Throughput Single-Nucleotide Polymorphism Genotyping with Fingernail DNA: Comparison with Blood DNA Clin. Chem., October 1, 2008; 54(10): 1746 - 1748. [Full Text] [PDF]

				J. M. Cunningham, T. A. Sellers, J. M. Schildkraut, Z. S. Fredericksen, R. A. Vierkant, L. E. Kelemen, M. Gadre, C. M. Phelan, Y. Huang, J. G. Meyer, et al. Performance of Amplified DNA in an Illumina GoldenGate BeadArray Assay Cancer Epidemiol. Biomarkers Prev., July 1, 2008; 17(7): 1781 - 1789. [Abstract] [Full Text] [PDF]

				D. T. Croft Jr, R. M. Jordan, H. L. Patney, C. D. Shriver, M. N. Vernalis, T. J. Orchard, and D. L. Ellsworth Performance of Whole-Genome Amplified DNA Isolated from Serum and Plasma on High-Density Single Nucleotide Polymorphism Arrays J. Mol. Diagn., May 1, 2008; 10(3): 249 - 257. [Abstract] [Full Text] [PDF]

				A. Hazra, S. Chanock, E. Giovannucci, D. G. Cox, T. Niu, C. Fuchs, W. C. Willett, and D. J. Hunter Large-Scale Evaluation of Genetic Variants in Candidate Genes for Colorectal Cancer Risk in the Nurses' Health Study and the Health Professionals' Follow-up Study Cancer Epidemiol. Biomarkers Prev., February 1, 2008; 17(2): 311 - 319. [Abstract] [Full Text] [PDF]