Buccal DNA Collection: Comparison of Buccal Swabs with FTA Cards

Abstract

Collection and analysis of DNA, most commonly from blood or buccal cells, is becoming more common in epidemiologic studies. Buccal samples, which are painless to take and relatively easily collected, are often the preferred source. There are several buccal cell collection methods: swabs, brushes, mouthwash, and treated cards, such as FTA or IsoCode cards. Few studies have systematically compared methods of buccal cell collection with respect to DNA yield and amplification success under similar conditions. We compared buccal DNA collection and amplification using buccal swabs and FTA cards in 122 control subjects from our Australian case-control study of childhood acute lymphoblastic leukaemia. Buccal DNA was quantified using a real-time PCR for B-actin and genotyped at the loci of three polymorphisms (MTHFR 677C>T, ACE I/D, and XPD 1012G>A). PCR was successful with DNA from buccal swabs for 62% to 89% of subjects and from FTA cards for 83% to 100% of subjects, depending on the locus. The matched pair odds ratios (95% confidence interval) comparing success of FTA cards with buccal swabs are as follows: MTHFR 677C>T using PCR-RFLP, 12.5 (11.6-13.5) and using real-time PCR, 130.0 (113.1-152.8); ACE I/D using PCR-amplified fragment length polymorphism, 3.36 (3.2-3.5); XPD 1012G>A using real-time PCR,. FTA cards are a robust DNA collection method and generally produce DNA suitable for PCR more reliably than buccal swabs. There are, however, technical challenges in handling discs punched from FTA cards that intending users should be aware of. (Cancer Epidemiol Biomarkers Prev 2006;15(4):816 -9)

Folate Pathway Gene Polymorphisms, Maternal Folic Acid Use, and Risk of Childhood Acute Lymphoblastic Leukemia

“…Mothers completed a questionnaire detailing folic acid supplement use with dose in the 3 months before and during pregnancy. Blood samples for DNA analysis were collected from case children and their parents at the treating hospital, while buccal cell samples were collected from control children and their parents at home using FTA cards (43). Case children also provided a buccal sample using this method.…”

“…Case children also provided a buccal sample using this method. Punches taken from the cards were prepared for PCR as previously described (43), and samples were then subjected to whole genome amplification using the GenomiPhi V2 DNA Amplification Kit (GE Healthcare) according to the manufacturer's instructions.…”

Efficiency of Buccal DNA Sampling Device in the Mortuary

“…More recently, increasing focus has been placed on buccal epithelial cells as an alternative DNA source [8][9][10][11][12][13][14][15], offering an easy-to-collect, non-invasive method [7,[10][11][12]16,17] with no reliance on medical staff [9,10,12]. Various methods have been described for the collection of buccal cells, including saliva [11,16,17], mouthwash [8,13,14,17], cytobrushes [13,14,17] and swabs [8][9][10][11]15]. Numerous studies have reported on the differences in DNA yield and quality between these collection methods.…”

Elimination of False-Positive Polymerase Chain Reaction Results Resulting from Hole Punch Carryover Contamination

“…In method 4 (bleach, tap water, ethanol), no detectable amplification was obtained with PCR of the precut control (Fig. 4, lane 1 Many studies used hole punches to excise material dried on filter paper [2][3][4]7,9,[12][13][14]16,18,20 ; however, only a few reports mention any protocols for detecting possible carryover or detection of false positives in filter-paperbased PCR methods. 9,11 Furthermore, many published studies overlooked any consideration for the possibility of such contamination.…”

“…9,11 Furthermore, many published studies overlooked any consideration for the possibility of such contamination. 2,3,7,12,14,18 Quality assurance methods to avoid such contamination were reported by some investigators. 4,9,13,16,17,20 Some laboratories report punching holes in blank paper between samples to remove possible contaminants.…”