Feasibility of high-throughput genome-wide genotyping using DNA from stored buccal cell samples

Biomarker Insights

Volumn 2010, Issue 5, 2010, Pages 49-55

  Loomis, Stephanie J ^a   Olson, Lana M ^b   Pasquale, Louis R ^a   Wiggs, Janey ^a   Mirel, Daniel ^c   Crenshaw, Andrew ^c   Parkin, Melissa ^c   Rahhal, Brandon ^c   Tetreault, Stephanie ^d   Kraft, Peter ^d   Tworoger, Shelley S ^e   Haines, Jonathan L ^b   Kang, Jae H ^e  

^a MASSACHUSETTS EYE AND EAR INFIRMARY   (United States)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Buccal cell DNA; Genotyping; GWAS; Low concentration DNA; Saliva DNA

Indexed keywords

BIOLOGICAL MARKER; CELL DNA;

ADULT; AGED; ARTICLE; BIOASSAY; BLOOD SAMPLING; CHEEK; CHROMOSOME; COHORT ANALYSIS; FEMALE; GENETIC MARKER; GENOMICS; GENOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; LONGITUDINAL STUDY; NORMAL HUMAN;

EID: 77955207801     PISSN: None     EISSN: 11772719     Source Type: Journal    
DOI: 10.4137/bmi.s5062     Document Type: Article

References (22)

1. Le Marchand L, Lum-Jones A, Saltzman B, Visaya V, Nomura AM, Kolonel LN. Feasibility of collecting buccal cell DNA by mail in a cohort study. Cancer Epidemiol Biomarkers Prev. 2001 Jun;10(6):701-3.
2. 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 Jan;125(1):127-33.
3. Garcia-Closas M, Moore LE, Rabkin CS, et al Quantitation of DNA in buccal cell samples collected in epidemiological studies. Biomarkers. 2006 Sep-Oct;11(5):472-9.
4. Rogers NL, Cole SA, Lan HC, Crossa A, Demerath EW. New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies. Am J Hum Biol. 2007 May-Jun;19(3):319-26.
5. King IB, Satia-Abouta J, Thornquist MD, et al. Buccal cell DNA yield, quality, and collection costs: comparison of methods for large-scale studies. Cancer Epidemiol Biomarkers Prev. 2002 Oct;11(10 Pt 1):1130-3.
6. Agalliu I, Schweitzer PA, Leanza SM, Burk RD, Rohan TE. Illumina DNA test panel-based genotyping of whole genome amplified-DNA extracted from hair samples: performance and agreement with genotyping results from genomic DNA from buccal cells. Clin Chem Lab Med. 2009;47(5):516-22.
7. Herraez DL, Stoneking M. High fractions of exogenous DNA in human buccal samples reduce the quality of large-scale genotyping. Anal Biochem. 2008 Dec 15;383(2):329-31.
8. Paynter RA, Skibola DR, Skibola CF, Buffler PA, Wiemels JL, Smith MT. Accuracy of multiplexed Illumina platform-based single-nucleotide polymorphism genotyping compared between genomic and whole genome amplified DNA collected from multiple sources. Cancer Epidemiol Biomarkers Prev. Dec 2006;15(12):2533-6.
9. Hong J, Leung E, Fraser A, Krissansen GW. Nucleic acid from saliva and salivary cells for noninvasive genotyping of Crohns disease patients. Genet Test. Dec 2008;12(4):587-9.
10. Beckett SM, Laughton SJ, Pozza LD, et al. Buccal swabs and treated cards: methodological considerations for molecular epidemiologic studies examining pediatric populations. Am J Epidemiol. 2008 May 15;167(10):1260-7.
11. He H, Argiro L, Dessein H, Chevillard C. Improved technique that allows the performance of large-scale SNP genotyping on DNA immobilized by FTA technology. Infect Genet Evol. 2007 Jan;7(1):128-32.
12. Feigelson HS, Rodriguez C, Robertson AS, et al. Determinants of DNA yield and quality from buccal cell samples collected with mouthwash. Cancer Epidemiol Biomarkers Prev. 2001 Sep;10(9):1005-8.
13. Swanson JM, Moyzis RK, McGough JJ, et al. Effects of source of DNA on genotyping success rates and allele percentages in the Preschoolers with Attention-Deficit/Hyperactivity Disorder Treatment Study (PATS). J Child Adolesc Psychopharmacol. 2007 Oct;17(5):635-46.
14. Montgomery GW, Campbell MJ, Dickson P, et al. Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues. Twin Res Hum Genet. 2005 Aug;8(4):346-52.
15. Feigelson HS, Rodriguez C, Welch R, et al. Successful genome-wide scan in paired blood and buccal samples. Cancer Epidemiol Biomarkers Prev. 2007 May;16(5):1023-5.
16. Woo JG, Sun G, Haverbusch M, et al. Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500 K GeneChip. BMC Genet. 2007;8:79.
17. Belanger CF, Hennekens CH, Rosner B, Speizer FE. The nurses' health study. Am J Nurs. Jun 1978;78(6):1039-40.
18. Sabeti PC, Varilly P, Fry B, et al. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18; 449(7164):913-8.
19. Sexton DPM,JL, Giles JT, Bush WS, Bradford Y, Haines JL. The Wholegenome Association Study Pipeline (WASP): A Comprehensive Tool for Large-Scale Association Studies. AJHG. 57(413S).
20. Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007 Sep;81(3):559-75.
21. Purcell S. PLINK v 1.07. 2009; http://pngu.mgh.harvard.edu/purcell/plink/
22. Catalog of Published Genome-Wide Association Studies. 2010; http://www.genome.gov/gwastudies/Accessed 2/3/2010, 2009.