Skip to main content

Advertisement

SpringerLink
Log in

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

  • Original Article
  • Published:
Indian Journal of Clinical Biochemistry Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Garcia-Closas M, Egan KM, Abruzzo J, Newcomb PA, Titus-Ernstoff L, Franklin T, et al. Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. Cancer Epidemiol Biomarkers Prev. 2001;10(6):687–96.

    PubMed  CAS  Google Scholar 

  2. Freeman B, Powell J, Ball D, Hill L, Craig I, Plomin R. DNA by mail: an inexpensive and noninvasive method for collecting DNA samples from widely dispersed populations. Behav Genet. 1997;27(3):251–7.

    Article  PubMed  CAS  Google Scholar 

  3. Harty LC, Garcia-Closas M, Rothman N, Reid YA, Tucker MA, Hartge P. Collection of buccal cell DNA using treated cards. Cancer Epidemiol Biomarkers Prev. 2000;9(5):501–6.

    PubMed  CAS  Google Scholar 

  4. Le Marchand L, Lum-Jones A, Saltzman B, Visaya V, Nomura AM, Kolonel LN. Feasibility of collecting buccal cell DNA by mail in a cohort study. Cancer Epidemiol Biomarkers Prev. 2001;10(6):701–3.

    PubMed  CAS  Google Scholar 

  5. Herraez DL, Stoneking M. High fractions of exogenous DNA in human buccal samples reduce the quality of large-scale genotyping. Anal Biochem. 2008;383(2):329–31.

    Article  PubMed  CAS  Google Scholar 

  6. Feigelson HS, Rodriguez C, Robertson AS, Jacobs EJ, Calle EE, Reid YA, et al. Determinants of DNA yield and quality from buccal cell samples collected with mouthwash. Cancer Epidemiol Biomarkers Prev. 2001;10(9):1005–8.

    PubMed  CAS  Google Scholar 

  7. Quinque D, Kittler R, Kayser M, Stoneking M, Nasidze I. Evaluation of saliva as a source of human DNA for population and association studies. Anal Biochem. 2006;353(2):272–7.

    Article  PubMed  CAS  Google Scholar 

  8. Bergen AW, Haque KA, Qi Y, Beerman MB, Garcia-Closas M, Rothman N, et al. Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources. Hum Mutat. 2005;26(3):262–70.

    Article  PubMed  CAS  Google Scholar 

  9. Kirov G, Nikolov I, Georgieva L, Moskvina V, Owen MJ, O’Donovan MC. Pooled DNA genotyping on Affymetrix SNP genotyping arrays. BMC Genomics. 2006;7:27.

    Article  PubMed  Google Scholar 

  10. Chang ML, Terrill RL, Bautista MM, Carlson EJ, Dyer DJ, Overall KL, et al. Large-scale SNP genotyping with canine buccal swab DNA. J Hered. 2007;98(5):428–37.

    Article  PubMed  CAS  Google Scholar 

  11. Woo JG, Sun G, Haverbusch M, Indugula S, Martin LJ, Broderick JP, et al. Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500K GeneChip. BMC Genet. 2007;8:79.

    Article  PubMed  Google Scholar 

  12. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001;29(4):365–71.

    Article  PubMed  CAS  Google Scholar 

  13. Fan JB, Gunderson KL, Bibikova M, Yeakley JM, Chen J, Wickham Garcia E, et al. Illumina universal bead arrays. Methods Enzymol. 2006;410:57–73.

    Article  PubMed  CAS  Google Scholar 

  14. Zayats T, Young TL, Mackey DA, Malecaze F, Calvas P, Guggenheim JA. Quality of DNA extracted from mouthwashes. PLoS One. 2009;4(7):e6165.

    Article  PubMed  Google Scholar 

  15. Rudney JD, Chen R. The vital status of human buccal epithelial cells and the bacteria associated with them. Arch Oral Biol. 2006;51(4):291–8.

    Article  PubMed  CAS  Google Scholar 

  16. King IB, Satia-Abouta J, Thornquist MD, Bigler J, Patterson RE, Kristal AR, et al. Buccal cell DNA yield, quality, and collection costs: comparison of methods for large-scale studies. Cancer Epidemiol Biomarkers Prev. 2002;11(10 Pt 1):1130–3.

    PubMed  Google Scholar 

  17. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43(11):5721–32.

    Article  PubMed  Google Scholar 

  18. Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, et al. Bacterial diversity in human subgingival plaque. J Bacteriol. 2001;183(12):3770–83.

    Article  PubMed  CAS  Google Scholar 

  19. Haffajee AD, Socransky SS. Relationship of cigarette smoking to the subgingival microbiota. J Clin Periodontol. 2001;28(5):377–88.

    Article  PubMed  CAS  Google Scholar 

  20. Shiloah J, Patters MR, Waring MB. The prevalence of pathogenic periodontal microflora in healthy young adult smokers. J Periodontol. 2000;71(4):562–7.

    Article  PubMed  CAS  Google Scholar 

  21. Glei M, Habermann N, Osswald K, Seidel C, Persin C, Jahreis G, et al. Assessment of DNA damage and its modulation by dietary and genetic factors in smokers using the Comet assay: a biomarker model. Biomarkers. 2005;10(2–3):203–17.

    Article  PubMed  CAS  Google Scholar 

  22. Konig KG. Diet and oral health. Int Dent J. 2000;50(3):162–74.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We greatly appreciate the support of the study subjects and their families who participated in this project. This work was supported by the Ministry of Science, Technology and Innovation (MOSTI), the government of Malaysia. The authors thank the staff of UM, UMMC and INFOVALLEY® for their timely help during the subject recruitment and sample collection.

Author information

Authors and Affiliations

  1. INFOVALLEY ® Life Sciences Sdn. Bhd., Unit 1.1, Level 1, Block B, MINES Waterfront Business Park, No. 3, Jalan Tasik, 43300, MINES Resort City, Selangor, Malaysia

    Alex Livy, Sayhean Lye, Chahil K. Jagdish, Nurul Hanis, Velapasamy Sharmila, Lian Wee Ler & Bagali Pramod

Authors
  1. Alex Livy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sayhean Lye
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chahil K. Jagdish
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nurul Hanis
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Velapasamy Sharmila
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lian Wee Ler
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Bagali Pramod
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alex Livy.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Livy, A., Lye, S., Jagdish, C.K. et al. Evaluation of Quality of DNA Extracted from Buccal Swabs for Microarray Based Genotyping. Ind J Clin Biochem 27, 28–33 (2012). https://doi.org/10.1007/s12291-011-0154-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12291-011-0154-y

Keywords

Search

Navigation