Background A cost effective, safe and efficient method of obtaining DNA samples is essential in large scale genetic analyses. Buccal cells are an attractive source of DNA, as their collection is non-invasive and can be carried out by mail. However, little attention has been given to the quality of DNA extracted from mouthwashes. Methodology Mouthwash-derived DNA was extracted from 500 subjects participating in a genetic study of high myopia. DNA quality was investigated using two standard techniques: agarose gel electrophoresis and quantitative polymerase chain reaction (qPCR). Principal Findings Whereas the majority of mouthwash-derived DNA samples showed a single band of high molecular weight DNA by gel electrophoresis, 8.9% (95% CI: 7.1–10.7%) of samples contained only a smear of low-to-medium molecular weight, degraded DNA. The odds of DNA degradation in a subject's second mouthwash sample, given degradation of the first, was significantly greater than one (OR = 3.13; 95% CI: 1.22–7.39; Fisher's test P = 0.009), suggesting that DNA degradation was at least partially a subject-specific phenomenon. Approximately 12.4% (95% CI: 10.4–14.4%) of mouthwash-derived DNA failed to PCR amplify efficiently (using an ~200 bp microsatellite marker). However, we found there was no significant difference in amplification success rate between DNA samples judged to be degraded or non-degraded by gel electrophoresis (Fisher's test P = 0.5). Conclusions This study demonstrated that DNA degradation affects a significant minority of saline mouthwashes, and that the phenomenon is partially subject-specific. Whilst the level of degradation did not significantly prevent successful amplification of short PCR fragments, previous studies suggest that such DNA degradation would compromise more demanding applications.
Garcia-Closas M, Egan KM, Abruzzo J, Newcomb PA, Titus-Ernstoff L, et al. (2001) Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. Cancer Epidemiology, Biomarkers and Prevention 10: 687–696.
Le Marchand L, Lum-Jones A, Saltzman B, Visaya V, Nomura AMY, et al. (2001) Feasibility of collecting buccal cell DNA by mail in a cohort study. Cancer Epidemiology Biomarkers and Prevention 10: 701–703.
Freeman B, Powell J, Ball D, Hill L, Craig I, et al. (1997) DNA by mail: An inexpensive and noninvasive method for collecting DNA samples from widely dispersed populations. Behavior Genetics 27: 251–257.
Feigelson HS, Rodriguez C, Robertson AS, Jacobs EJ, Calle EE, et al. (2001) Determinants of DNA yield and quality from buccal cell samples collected with mouthwash. Cancer Epidemiology Biomarkers & Prevention 10: 1005–1008.
King IB, Satia-Abouta J, Thornquist MD, Bigler J, Patterson RE, et al. (2002) Buccal cell DNA yield, quality, and collection costs: Comparison of methods for large-scale studies (vol 11, pg 1130, 2002). Cancer Epidemiology Biomarkers & Prevention 11: 1511–1511.
Bergen AW, Haque KA, Qi Y, Beerman MB, Garcia-Closas M, et al. (2005) Comparison of yield and genotyping performance of multiple displacement OmniPlex (TM) whole genome amplified DNA generated from multiple DNA sources. Human Mutation 26: 262–270.
Farbrother JE, Kirov G, Owen MJ, Pong-Wong R, Haley CS, et al. (2004) Linkage analysis of the genetic loci for high myopia on chromosomes 18p, 12q and 17q in 51 UK families. Investigative Ophthalmology and Visual Science 45: 2879–2885.
Li YJ, Guggenheim JA, Bulusu A, Metlapally R, Abbott D, et al. (2009) An International Collaborative Family-based Whole Genome Linkage Scan for High-grade Myopia. Investigative Ophthalmology and Visual Science. In press (PMID: 19324860).
Glei M, Habermann N, Osswald K, Seidel C, Persin C, et al. (2005) Assessment of DNA damage and its modulation by dietary and genetic factors in smokers using the Comet assay: a biomarker model. Biomarkers 10: 203–217.
D'Souza G, Sugar E, Ruby W, Gravitt P, Gillison M (2005) Analysis of the effect of DNA purification on detection of human papillomavirus in oral rinse samples by PCR. Journal of Clinical Microbiology 43: 5526–5535.
Heath EM, Morken NW, Campbell KA, Tkach D, Boyd EA, et al. (2001) Use of buccal cells collected in mouthwash as a source of DNA for clinical testing. Archives of Pathology & Laboratory Medicine 125: 127–133.