Evaluation of Quality of DNA Extracted from Buccal Swabs for Microarray Based Genotyping

Abstract

Buccal cell usage has been shown by many to be a cost effective and safe method to isolate DNA for various biological experiments especially large epidemiological studies (Garcia-Closas et al. Cancer Epidemiol Biomarkers Prev 10:687-696, 2001). Non-invasive DNA collection methods are preferred over phlebotomy in order to increase study participation and compliance in research centers and for sick patients in hospital settings. There have been conflicting reports about the methodology and results obtained from using buccal DNA. It is not very clear if phlebotomy can be confidently replaced by buccal cell DNA. It is often left for the user to take an intelligent decision. To address this issue, we compared the performance of buccal and blood DNA from same subjects in a genotyping experiment and this paper reports the results. Cotton swab derived buccal cells were scraped from the inner side of cheeks from 16 subjects, and blood was also drawn from the same 16 subjects participating in a genotypic association study of a lipid disease. The DNA quality was assessed by resolving on agarose gels, checking purity (A260/A280) and finally by microarray hybridization. This study showed that DNA degradation affects the total yield and performance of the buccal DNA when compared to the blood DNA in microarray based genotyping. Genotyping results can be seriously compromised if care is not taken to check the quality and yields of such specimens.

Differences in AMY1 Gene Copy Numbers Derived from Blood, Buccal Cells and Saliva Using Quantitative and Droplet Digital PCR Methods: Flagging the Pitfall

“…Recently, a study also showed that saliva collected using the Oragene kit yielded high quantity and high quality DNA for genetic studies [ 17 ]. However, there are still concerns over using DNA extracted from saliva samples or buccal cyto-brushes for genotyping [ 18 , 19 ] due to possible bacterial contamination which may affect yield and quality of DNA [ 20 ]. Furthermore, there is lack of data on whether different biological samples can be used interchangeably for the genotyping of a specific gene of interest, especially for complex genes like the AMY1 gene.…”

World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project: III. Fluid biospecimen collection, processing, and storage in endometriosis research

“…Several methods are available for collecting saliva for DNA, including “swish and spit,” saliva collection kits for DNA (e.g., Oragene ® , DNAgard ® , Norgen ® ), or swabs. The swish and spit method or Oragene ® kits are recommended as standard in EPHect, providing the best DNA quality and yield (51–53) . For general biomarker studies, the “passive drool” method for sample collection is preferred over other methods that stimulate saliva production (e.g., chewing on cotton), as the latter can alter hormone levels (50) .…”

Oxidative Stress Levels in Buccal Cells Using MAWI Collection Tubes

“…Although buccal cells provides a smaller amount of DNA than blood, recently developed methods of genotyping use very small amounts of DNA (2-10 ng per assay) and thus allow the use of buccal cells as a source of DNA. Importantly, the use of non-invasive DNA collection methods has been shown to increase study participation rates [7].…”

“…DNA buccal swabs have been specifically designed to increase study participation and compliance in research centers and for sick patients in hospital settings. In fact, the cotton swab has long been a basic and essential tool for collecting DNA evidence for forensic casework analysis [7].…”