Whole genome amplification of buccal cell DNA: Genotyping concordance before and after multiple displacement amplification

Clinical Chemistry and Laboratory Medicine

Volumn 43, Issue 2, 2005, Pages 157-162

  Thompson, Miles D ^a   Bowen, Raffick A R ^a   Wong, Betty Y L ^a,b   Antal, Joan ^a   Liu, Zhanqin ^b   Yu, Helen ^b   Siminovitch, Katherine ^b,c   Kreiger, Nancy ^a,d   Rohan, Tom E ^e   Cole, David E C ^a,b,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY HEALTH NETWORK   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d CANCER CARE ONTARIO   (Canada)

^e ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

Buccal cell; DNA; Methylenetetrahydrofolate reductase; Multiple displacement amplification; Single nucleotide polymorphisms; Vitamin D receptor; Whole genome amplification

Indexed keywords

CELL DNA; METHYLENETETRAHYDROFOLATE REDUCTASE (NADPH2); VITAMIN D RECEPTOR;

AMPLICON; ARTICLE; CHEEK; CONTROLLED STUDY; DNA EXTRACTION; DNA SEQUENCE; FEMALE; GENE AMPLIFICATION; GENOME; GENOTYPE; HUMAN; HUMAN CELL; HUMAN TISSUE; INTRON; MALE; MOUTHWASH; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; CHEEK; COHORT STUDIES; DNA; GENOME; GENOTYPE; HUMANS; MALE; METHYLENETETRAHYDROFOLATE REDUCTASE (NADPH2); MOUTH MUCOSA; MOUTHWASHES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, CALCITRIOL; SENSITIVITY AND SPECIFICITY;

EID: 20144382347     PISSN: 14346621     EISSN: None     Source Type: Journal    
DOI: 10.1515/CCLM.2005.026     Document Type: Article

References (30)

1. Lench N, Stanier P, Williamson R. Simple non-invasive method to obtain DNA for gene analysis. Lancet 1988;1:1356-8.
2. Vandenbergh DJ, Anthony K, Whitfield KE. Optimizing DNA yield from buccal swabs in the elderly: attempts to promote buccal cell growth in culture. Am J Hum Biol 2003;15:637-42.
3. Walker AH, Najarian D, White DL, Jaffe JF, Kanetsky PA, Rebbeck TR. Collection of genomic DNA by buccal swabs for polymerase chain reaction-based biomarker assays. Environ Health Perspect 1999;107:517-20.
4. Freeman B, Powell J, Ball D, Hill L, Craig I, Plomin R. DNA by mail: an inexpensive and noninvasive method for collecting DNA samples from widely dispersed populations. Behav Genet 1997;27:251-7.
5. Therrell BL, Hannon WH, Pass KA, Lorey F, Brokopp C, Eckman J, et al. Guidelines for the retention, storage, and use of residual dried blood spot samples after newborn screening analysis: statement of the Council of Regional Networks for Genetic Services. Biochem Mol Med 1996;57:116-24.
6. Long WJ, McGuire W, Palombo A, Emini EA. Enhancing the establishment efficiency of hybridoma cells. Use of irradiated human diploid fibroblast feeder layers. J Immunol Methods 1986;86:89-93.
7. Darzynkiewicz Z, Bruno S, Del Bino G, Gorczyca W, Hotz MA, Lassota P, et al. Features of apoptotic cells measured by flow cytometry. Cytometry 1992;13:795-808.
8. Lum A, Le Marchand L. A simple mouthwash method for obtaining genomic DNA in molecular epidemiological studies. Cancer Epidemiol Biomarkers Prev 1998; 7:719-24.
9. Heath EM, Morken NW, Campbell KA, Tkach D, Boyd EA, Strom DA. Use of buccal cells collected in mouthwash as a source of DNA for clinical testing. Arch Pathol Lab Med 2001;125:127-33.
10. Garcia-Closas M, Egan KM, Abruzzo J, Newcomb PA, Titus-Ernstoff L, Franklin T, et al. Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. Cancer Epidemiol Biomarkers Prev 2001;10:687-96.
11. Feigelson HS, Rodriguez C, Robertson AS, Jacobs EJ, Calle EE, Reid YA, et al. Determinants of DNA yield and quality from buccal cell samples collected with mouthwash. Cancer Epidemiol Biomarkers Prev 2001;10:1005-8.
12. Katakura Y, Alam S, Shirahata S. Immortalization by gene transfection. Methods Cell Biol 1998;57:69-91.
13. Zhang L, Cui X, Schmitt K, Hubert R, Navidi W, Arnheim N. Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci USA 1992;89:5847-51.
14. Barrett MT, Reid BJ, Joslyn G. Genotypic analysis of multiple Ioci in somatic cells by whole genome amplification. Nucleic Acids Res 1995;23:3488-92.
15. Cheung VG, Nelson SF. 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 1996;93:14676-9.
16. Grant SF, Steinlicht S, Nentwich U, Kern R, Burwinkel B, Tolle R. SNP genotyping on a genome-wide amplified DOP-PCR template. Nucleic Acids Res 2002;30:e125.
17. Paunio T, Reima I, Syvanen AC. Preimplantation diagnosis by whole-genome amplification, PCR amplification, and solid-phase minisequencing of blastomere DNA. Clin Chem 1996;42:1382-90.
18. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 2002;99:5261-6.
19. Esteban JA, Salas M, Blanco L. Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J Biol Chem 1993; 268:2719-26.
20. Blanco L, Bernad A, Lazaro JM, Martin G, Garmendia C, Salas M. Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 1989;264:8935-40.
21. Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, et al. Unbiased whole-genome amplification directly from clinical samples. Genome Res 2003;13:954-64.
22. Tranah GJ, Lescault PJ, Hunter DJ, De Viro, I. Multiple displacement amplification prior to single nucleotide polymorphism genotyping in epidemiologic studies. Biotechnol Lett 2003;25:1031-6.
23. Jain MG, Rohan TE, Soskolne CL, Kreiger N. Calibration of the dietary questionnaire for the Canadian Study of Diet, Lifestyle and Health cohort. Public Health Nutr 2003;6:79-86.
24. Miriuka SG, Langman LJ, Evrovski J, Miner SE, D'Mello N, Delgado DH, et al. Genetic polymorphisms predisposing to hyperhomocysteinemia in cardiac transplant patients. Transplant Int 2005;18:29-35.
25. Peltekova VD, Cole DE, Pavlova A, Rubin LA. Improved method for direct haplotyping at the vitamin D receptor gene Iocus. Clin Biochem 1998;31:191-4.
26. Ray JG, Langman LJ, Vermeulen MJ, Evrovski J, Yeo EL, Cole DE. Genetics University of Toronto Thrombophilia Study in Women (GUTTSI): genetic and other risk factors for venous thromboembolism in women. Curr Control Trials Cardiovasc Med 2001;2:141-9.
27. Cao W, Hashibe M, Rao JY, Morgenstern H, Zhang ZF. Comparison of methods for DNA extraction from paraffin-embedded tissues and buccal cells. Cancer Detect Prev 2003;27:397-404.
28. Mai M, Hoyer JD, McClure RF. Use of multiple displacement amplification to amplify genomic DNA before sequencing of the alpha and beta haemoglobin genes. J Clin Pathol 2004;57:637-40.
29. Zheng S, Ma X, Buffler PA, Smith MT, Wiencke JK. Whole genome amplification increases the efficiency and validity of buccal cell genotyping in pediatric populations. Cancer Epidemiol Biomarkers Prev 2001; 10:697-700.
30. Dietmaier W, Hartmann A, Wallinger S, Heinmoller E, Kerner T, Endl E, et al. Multiple mutation analyses in single tumor cells with improved whole genome amplification. Am J Pathol 1999;154:83-95.