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T. Zayats, J. A. Guggenheim; Mouthwash DNA Quality for Genomewide Molecular Genetic Analysis: Experience From the United Kingdom Family Study of Myopia. Invest. Ophthalmol. Vis. Sci. 2007;48(13):4637.
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Molecular genetics is playing an increasingly important role in vision research. To allow vision scientists to build on recent advances of genetics, it is essential to provide an effective method of obtaining DNA samples that can be applied in large-scale genomewide linkage and association studies. An attractive approach is to use buccal cells, as their collection is non-invasive and can be carried out by post. We assessed the quality of DNA obtained from mouthwashes. In Experiment 1, we investigated whether poor quality mouthwash DNA was subject-specific or a random occurrence. In Experiment 2, we investigated the above issue, plus the effect of a time delay between mouthwash rinsing and DNA extraction (mimicking that experienced by posted samples).
Experiment 1). Three hundred and one participants of the Family Study of Myopia and 10 volunteers each provided 2 mouthwashes. DNA was extracted on the day of arrival. Experiment 2). Six volunteers each provided 1 mouthwash per day on 12 separate days. The mouthwashes were stored at 18-22°C for zero, one, two, or three days before being processed. DNA quality was assessed by agarose gel electrophoresis and q-PCR. Contingency tables and logistic regression (LR) were used to examine associations between DNA quality and potential explanatory variables.
Experiment 1). The frequency of DNA sample degradation was 0.10 (95% CI: 0.08-0.13). The odds of DNA degradation in a second mouthwash sample given degradation of the first was significantly different from zero (OR = 4.7; 95% CI: 1.55-13.49) and Fisher's test for this association was also significant (p=0.002). Experiment 2). Time delay had no significant effect on mouthwash quality (LR, p=0.8). However, particular subjects were associated with degraded mouthwash DNA (Chi-square, p<0.01).
We found evidence that mouthwash DNA quality may be subject-dependent. A delay between the mouthwash rinsing procedure and the sample being processed was ruled out as a potential cause of DNA degradation (confirming that mailing is a practicable method of mouthwash collection). Our findings suggest that certain subjects provide mouthwash samples in which the DNA may already be degraded, and thus unsuitable for genetic analysis.
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