Whole genome amplification of buccal cell DNA: genotyping concordance before and after multiple displacement amplification
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Miles D. Thompson
Abstract
While buccal cells provide an easily accessible source of genomic DNA, the amount extracted may be insufficient for many studies. Whole genome amplification (WGA) using multiple displacement amplification (MDA) may optimize buccal cell genomic DNA yield. We compared the usefulness, in epidemiological surveys, of DNA derived from buccal cells collected by alcohol mouthwash and amplified by WGA protocol and standard protocols. Buccal cell collection kits were mailed to 300 randomly selected members of a large cohort study, and 189 subjects returned buccal cell samples. We determined: (i) which QIAamp ® DNA Blood Mini Kit extraction protocol (tissue or blood) produced more DNA; and (ii) whether it is feasible to use MDA to prepare DNA for single nucleotide polymorphism (SNP) genotyping of markers such as the methylenetetrahydrofolate reductase ( MTHFR) and vitamin D receptor ( VDR) genes. The two DNA extraction protocols were tested on 20 different patient samples each. The tissue protocol yielded more DNA than the blood protocol (15.4±8.6 vs. 7.6±7.1μg, p<0.0001). The 20 DNA samples extracted using the tissue protocol were then subjected to pre- and post-MDA genotyping using amplicons for the MTHFR SNP at C677T and the intron 8 VDR SNP. No genotyping discrepancies were detected in pair-wise comparisons of pre- and post-MDA. Genotyping DNA from MDA-based WGA is indistinguishable from routine polymerase chain reaction and offers a stable DNA source for genomic research and clinical diagnosis.
References
1 Lench N, Stanier P, Williamson R. Simple non-invasive method to obtain DNA for gene analysis. Lancet 1988; 1: 1356–8. 10.1016/S0140-6736(88)92178-2Search in Google Scholar
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. 10.1002/ajhb.10177Search in Google Scholar
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. 10.1289/ehp.99107517Search in Google Scholar
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. 10.1023/A:1025614231190Search in Google Scholar
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. 10.1006/bmme.1996.0017Search in Google Scholar
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. 10.1016/0022-1759(86)90269-3Search in Google Scholar
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. 10.1002/cyto.990130802Search in Google Scholar
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. Search in Google Scholar
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. 10.5858/2001-125-0127-UOBCCISearch in Google Scholar
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 Biomark 10: 687–96. Search in Google Scholar
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. Search in Google Scholar
12 Katakura Y, Alam S, Shirahata S. Immortalization by gene transfection. Methods Cell Biol 1998; 57: 69–91. 10.1016/S0091-679X(08)61573-3Search in Google Scholar
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. 10.1073/pnas.89.13.5847Search in Google Scholar PubMed PubMed Central
14 Barrett MT, Reid BJ, Joslyn G. Genotypic analysis of multiple loci in somatic cells by whole genome amplification. Nucleic Acids Res 1995; 23: 3488–92. 10.1093/nar/23.17.3488Search in Google Scholar
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. 10.1073/pnas.93.25.14676Search in Google Scholar
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. 10.1093/nar/gnf125Search in Google Scholar
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. 10.1093/clinchem/42.9.1382Search in Google Scholar
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. 10.1073/pnas.082089499Search in Google Scholar
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. 10.1016/S0021-9258(18)53833-3Search in Google Scholar
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. 10.1016/S0021-9258(18)81883-XSearch in Google Scholar
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. 10.1101/gr.816903Search in Google Scholar PubMed PubMed Central
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. 10.1023/A:1024173909401Search in Google Scholar
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. 10.1079/PHN2002362Search in Google Scholar PubMed
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. 10.1111/j.1432-2277.2004.00021.xSearch in Google Scholar
25 Peltekova VD, Cole DE, Pavlova A, Rubin LA. Improved method for direct haplotyping at the vitamin D receptor gene locus. Clin Biochem 1998; 31: 191–4. 10.1016/S0009-9120(98)00005-8Search in Google Scholar
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. 10.1186/CVM-2-3-141Search in Google Scholar
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. 10.1016/S0361-090X(03)00103-XSearch in Google Scholar
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. 10.1136/jcp.2003.014704Search in Google Scholar
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. Search in Google Scholar
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. 10.1016/S0002-9440(10)65254-6Search in Google Scholar
©2005 by Walter de Gruyter Berlin New York
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Articles in the same Issue
- Quality control for SELDI analysis
- Immunobead multiplex RT-PCR detection of carcinoembryonic genes expressing cells in the blood of colorectal cancer patients
- Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling
- Simultaneous determination of HIV antibodies, hepatitis C antibodies, and hepatitis B antigens in dried blood spots –a feasibility study using a multi-analyte immunoassay
- Hematopoietic cytokines in the sera of patients with pancreatic cancer
- Modulation of translation factor's gene expression by histone deacetylase inhibitors in breast cancer cells
- Whole genome amplification of buccal cell DNA: genotyping concordance before and after multiple displacement amplification
- Y-Chromosome short tandem repeat (STR) haplotypes in a Campania population sample
- TaqMan assays for genotyping of single nucleotide polymorphisms present at a disease susceptibility locus on chromosome 6
- The secretion of ibuprofen metabolites interferes with the capillary chromatography of urinary homovanillic acid and 4-hydroxy-3-methoxymandelic acid in neuroblastoma diagnosis
- Selective measurement of HCHO in urine using direct liquid-phase fluorimetric analysis
- A spectrophotometric micromethod for determining erythrocyte protoporphyrin-IX in whole blood or erythrocytes
- Simultaneous analysis of MDR1 C3435T, G2677T/A, and C1236T genotypes by multiplexed mutagenically separated PCR
- Measurement of reticulocyte and red blood cell indices in patients with iron deficiency anemia and β-thalassemia minor
- Chitotriosidase activity in colostrum from African and Caucasian women
- Integration between point-of-care cardiac markers in an emergency/cardiology department and the central laboratory: methodological and preliminary clinical evaluation
- Controlled storage conditions prolong stability of biochemical components in whole blood
- Poor knowledge and faulty thinking regarding hemolysis and potassium elevation
- Delayed effects of short-term transdermal application of 7-oxo-dehydroepiandrosterone on its metabolites, some hormonal steroids and relevant proteohormones in healthy male volunteers
- Evaluation of a novel semi-automated HPLC procedure for whole blood cyclosporin A confirms equivalence to adjusted monoclonal values from Abbott TDx
- Evaluation of the Bio-Rad VARIANT™ II HbA 2/HbA 1C Dual Program for measurement of hemoglobin concentrations and detection of variants
- Interferences in coagulation tests – evaluation of the 570-nm method on the Dade Behring BCS analyser
- No evidence for involvement of the human inducible nitric oxide synthase gene in susceptibility to coronary artery disease
- National survey on the use of measurement of cholinesterase activity in serum
