Buccal Swabs: A Complete Guide to Collecting & Analyzing DNA
Buccal Swabs: A Complete Guide to Collecting & Analyzing DNA

Buccal Swabs: A Complete Guide to Collecting & Analyzing DNA

Young female medical student taking samples from mouth with buccal cotton swab from her colleague.

What are buccal swabs and how are they collected?

Buccal swabs, also known as buccal smears, are a method of collecting DNA from the cells on the inside of a person's cheek. The word "buccal" refers to the cheek or mouth area. To perform a buccal swab, a healthcare provider gently rubs a small sponge or brush (swab) against the inside of the cheek to collect buccal epithelial cells. This is a relatively non-invasive way to collect DNA samples for genetic testing or forensic analysis.

Buccal swab collection kits typically contain cotton, foam, or flocked swabs, collection tubes, gloves, labels, and instructions. The inside of the cheek is swabbed and rubbed for 5-10 seconds to collect cells, taking care not to touch the swab tip to any surface besides the inner cheek. The swab is then placed in a collection tube, allowed to air dry, and labeled. Buccal swab collection can be done by a healthcare provider or by the individual themselves following simple instructions. It is fast, painless, and collects high quality DNA.

What types of samples and downstream analyses are buccal swabs used for?

Buccal swabs are commonly used for DNA-based testing and analysis in clinical, forensic, and research settings. In the clinic, buccal swabs provide DNA for genetic tests such as newborn screening, paternity testing, oncology risk testing, and pharmacogenetic testing. They are easy to collect from adults and children of any age. In forensics, touch DNA from buccal swabs can include or exclude suspects when matched to DNA collected from a crime scene. Buccal swabs are also widely used in biomedical research studies involving genetics, epigenetics, gene expression, and proteomics.

The high quality DNA collected by buccal swabs is compatible with a wide range of downstream applications including PCR, microarrays, sequencing, genotyping, and mass spectrometry. Compared to blood samples, buccal swabs provide more pure epithelial cell DNA with lower leukocyte contamination. The intact, high molecular weight DNA isolated from buccal swabs performs excellently in techniques like long-range PCR.

What are the advantages of using buccal swabs?

Buccal swabs have many advantages that make them a preferred method for collecting DNA samples:

    • 1. Non-invasive and painless. Swabbing the inner cheek is easy and comfortable.
    • 2. Convenient and simple. Samples can be self-collected following basic instructions.
    • 3. Safe for all ages. Buccal swabs can be used on adults, children, infants, and the elderly.
    • 4. Pure DNA. Buccal cells yield high quality DNA with less cellular heterogeneity than blood.
    • 5. Stable storage. DNA from buccal swabs remains stable at room temperature for transport and storage.
    • 6. Large DNA yields. Vigorous swabbing maximizes recovered epithelial cells and DNA quantity.
    • 7. PCR compatibility. Intact, high molecular weight DNA performs very well in PCR and sequencing.
    • 8. Cost-effective. Buccal swab collection has lower costs compared to blood draws or biopsies.

The non-invasive nature, convenience, and excellent DNA yields make buccal swabs the preferred method for most DNA collection applications.

How do buccal swabs compare to other sources of DNA?

While buccal swabs are widely used, researchers often have to choose between buccal swabs, blood, saliva, or other DNA sources. Key factors that distinguish buccal swabs include:

  1. 1. Cell composition: Buccal swabs provide pure epithelial cell DNA with low leukocyte contamination unlike blood. Saliva also contains a mix of buccal epithelial cells and leukocytes.
  2. 2. DNA quality: High molecular weight DNA from buccal swabs performs very well in PCR, sequencing, and other downstream applications. DNA from other sources can be more fragmented.
  3. 3. Sample collection: Buccal swabs involve non-invasive rubbing inside the cheek. Blood requires venipuncture and saliva involves spitting into a tube.
  4. 4. Sample stability: DNA from buccal swabs remains stable at room temperature for transport and storage, unlike saliva. Blood sample DNA also degrade over time if not properly stored.
  5. 5. Subject comfort: Blood draws can be uncomfortable for subjects. Buccal swabbing and saliva collection are relatively comfortable.

For most applications, the epithelial cell purity, excellent DNA quality, stability, and subject comfort make buccal swabs the preferred choice over blood or saliva for collecting DNA samples. However, saliva may be preferred for studies involving proteomics or metabolites.

What factors can impact DNA yield and quality from buccal swabs?

While buccal swabs provide high quality DNA, some precautions must be taken to maximize DNA yield and purity:

    • 1. Swabbing technique: Firm pressure and rubbing maximizes cell collection and DNA yields. Light swabbing recovers less cells.
    • 2. Swab type: Flocked or foam swabs collect and release more cells than traditional cotton swabs.
    • 3. Oral health: Inflammation from gingivitis can increase leukocyte contamination in buccal samples.
    • 4. Eating/drinking before collection: Food debris can contaminate swab samples so subjects should not eat or drink beforehand.
    • 5. Smoking: Chemicals from smoking precipitate and fragment DNA so buccal samples should be collected at least 30 minutes after smoking.
    • 6. Sample handling: Allowing swabs to air dry prevents DNA degradation before further processing.

Following best practices for buccal swab collection, handling, and processing ensures maximum DNA purity and yields for downstream analysis.

What techniques are used to isolate DNA from buccal swabs?

Two main approaches are used for DNA extraction and purification from buccal swabs:

Traditional DNA extraction kits utilize proteinase K digestion followed by alcohol precipitation or column absorption to isolate DNA. While effective, these kits involve multiple tubes and steps.

Newer kits use novel solid-phase chemistry to extract DNA in a single step directly from swabs, reducing hands-on time and plastic waste. For example, Echoloation extraction technology lyses cells and binds DNA to a matrix in one step, eliminating the need for hazardous chaotropes.

In both traditional and novel kits, purified DNA is eluted into a low salt buffer compatible with downstream applications like PCR and sequencing. Choosing optimized DNA purification strategies maximizes DNA yield and quality from buccal swabs.

How are buccal swabs utilized in pharmacogenetic testing?

Pharmacogenetic testing analyzes how genetic differences impact drug response, allowing for individualized medicine. Buccal swabs provide a convenient DNA source for pharmacogenetic tests. For example, testing for HLA-B*57:01 uses buccal swab DNA to screen for hypersensitivity to the HIV drug abacavir. Additional pharmacogenetic tests screen for warfarin sensitivity, opioid metabolism, and risk of carbamazepine adverse effects using buccal swab DNA samples. The non-invasive collection and excellent DNA makes buccal swabs an ideal choice over blood for pharmacogenetic analyses.

What considerations are important for using buccal swabs in research?

Buccal swabs are widely used in biomedical research, but some factors should be considered:

  • - Cellular heterogeneity in buccal samples can confound epigenetic, gene expression, and proteomic studies. Microscopic evaluation or bioinformatic methods can help account for cell type differences.
  • - DNA yields vary between subjects depending on swabbing technique and oral health. Standardizing collection methods is important.
  • - Stabilizing reagents can help preserve RNA and proteins in buccal samples if proteomic analysis is planned.
  • - DNA extraction methods should be optimized to maximize yields and purity. Novel single-step DNA extraction kits save time and plastic waste.

Accounting for cellular heterogeneity, optimizing collection and stabilization methods, and choosing effective DNA purification strategies allows buccal swabs to provide high quality DNA for diverse research applications.

Buccal swabs provide a simple, non-invasive way to collect high quality DNA samples. Their excellent DNA purity and yields make buccal swabs ideal for diverse genetic, epigenetic, forensic, pharmacogenetic, and biomedical research applications. Following optimized buccal swab collection and processing protocols allows researchers and clinicians to easily obtain DNA samples for precise, personalized analysis and treatment.

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References

  1. 1. Kittelmann S, Kirk MR, Jonker A, McCulloch A, Janssen PH. Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen. Appl Environ Microbiol. 2015 Nov;81(21):7470-83. doi: 10.1128/AEM.02385-15. Epub 2015 Aug 14. PMID: 26276109; PMCID: PMC4592876.
  2. 2. Cascella R, Stocchi L, Strafella C, Mezzaroma I, Mannazzu M, Vullo V, Montella F, Parruti G, Borgiani P, Sangiuolo F, Novelli G, Pirazzoli A, Zampatti S, Giardina E. Comparative analysis between saliva and buccal swabs as source of DNA: lesson from HLA-B*57:01 testing. Pharmacogenomics. 2015;16(10):1039-46. doi: 10.2217/pgs.15.59. Epub 2015 Jul 31. PMID: 26230858.
  3. 3. Theda, C., Hwang, S.H., Czajko, A. et al. Quantitation of the cellular content of saliva and buccal swab samples. Sci Rep 8, 6944 (2018). https://doi.org/10.1038/s41598-018-25311-0
  4. 4. Ang, J.S., Aloise, M.N., Dawes, D. et al. Evaluation of buccal swabs for pharmacogenetics. BMC Res Notes 11, 382 (2018). https://doi.org/10.1186/s13104-018-3476-5

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