Multiple displacement amplification prior to single nucleotide polymorphism genotyping in epidemiologic studies
We assessed the whole genome amplification strategy, known as multiple displacement amplification (MDA), for use with the TaqMan genotyping platform for DNA samples derived from two case-control studies nested in the Nurses' Health Study and the Physicians' Health Study. Our objectives were to (1) quantify DNA yield from samples of varying starting concentrations and (2) assess whether MDA products give an accurate representation of the original genomic sequence. Multiple displacement amplification yielded a mean 23 000-fold increase in DNA quantity and genotyping results demonstrate 99.95% accuracy across six SNPs from four genes for 352 samples included in this study. These results suggest that MDA will provide a sufficiently robust amplification of limiting samples of genomic DNA that can be used for SNP genotyping in large case-control studies of complex diseases.
Unable to display preview. Download preview PDF.
- Barrett M, Reid B, Joslyn G (1995) Genotypic analysis of multiple loci in somatic cells by whole genome amplification. Nucl. Acids Res. 23: 3488–3492.Google Scholar
- Cheung V, Nelson S (1996) Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc. Natl. Acad. Sci. USA 93: 14676–14679.Google Scholar
- Dean F, Hosono S, Fang L, Wu X, Faruqi A, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore S, Egholm M, Lasken R (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99: 5261–5266.Google Scholar
- Eckert K, Kunkel T (1991) DNA polymerase fidelity and the polymerase chain reaction. PCR Meth. Appl. 1: 17–24.Google Scholar
- Esteban J, Salas M, Blanco L (1993) Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J. Biol. Chem. 268: 2719–2726.Google Scholar
- Marchand LL, Lum-Jones A, Saltzman B, Visaya V, Nomura AM, Kolonel LN (2001) Feasibility of collecting buccal cell DNA by mail in a cohort study. Cancer Epidemiol. Biomarkers Prev. 10: 701–703.Google Scholar
- Olivier M, Chuang LM, Chang MS, Chen YT, Pei D, Ranade K, de Witte A, Allen J, Tran N, Curb D, Pratt R, Neefs H, de Arruda Indig M, Law S, Neri B, Wang L, Cox DR (2002) High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucl. Acids Res. 30: e53.Google Scholar
- Paunio T, Reima I, Syvanen AC (1996) Preimplantation diagnosis by whole-genome amplification, PCR amplification, and solid-phase minisequencing of blastomere DNA. Clin. Chem. 42: 1382–1390.Google Scholar
- Ranade K, Chang MS, Ting CT, Pei D, Hsiao CF, Olivier M, Pesich R, Hebert J, Chen YD, Dzau VJ, Curb D, Olshen R, Risch N, Cox DR, Botstein D (2001) High-throughput genotyping with single nucleotide polymorphisms. Genome Res. 11: 1262–1268.Google Scholar
- Snabes MC, Chong SS, Subramanian SB, Kristjansson K, DiSepio D, Hughes MR (1994) Preimplantation single-cell analysis of multiple genetic loci by whole-genome amplification. Proc. Natl. Acad. Sci. USA 91: 6181–6185.Google Scholar
- Telenius H, Carter NP, Bebb CE, Nordenskjold M, Ponder BA, Tunnacliffe A (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13: 718–725.Google Scholar
- Zhang L, Cui X, Schmitt K, Hubert R, Navidi W, Arnheim N (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl. Acad. Sci. USA 89: 5847–5851.Google Scholar