Whole genome amplification of buccal cell DNA: Genotyping concordance before and after multiple displacement amplification

Miles D. Thompson, Raffick A.R. Bowen, Betty Y.L. Wong, Joan Antal, Zhanqin Liu, Helen Yu, Katherine Siminovitch, Nancy Kreiger, Tom E. Rohan, David E.C. Cole

Research output: Contribution to journalArticle

20 Scopus citations

Abstract

While buccal cells provide an easily accessible source of genomic DNA, the amount extracted may be insufficient for many studies. Whole genome amplification (WGA) using multiple displacement amplification (MDA) may optimize buccal cell genomic DNA yield. We compared the usefulness, in epidemiological surveys, of DNA derived from buccal cells collected by alcohol mouthwash and amplified by WGA protocol and standard protocols. Buccal cell collection kits were mailed to 300 randomly selected members of a large cohort study, and 189 subjects returned buccal cell samples. We determined: (i) which QIAamp® DNA Blood Mini Kit extraction protocol (tissue or blood) produced more DNA; and (ii) whether it is feasible to use MDA to prepare DNA for single nucleotide polymorphism (SNP) genotyping of markers such as the methylenetetrahydrofolate reductase (MTHFR) and vitamin D receptor (VDR) genes. The two DNA extraction protocols were tested on 20 different patient samples each. The tissue protocol yielded more DNA than the blood protocol (15.4±8.6 vs. 7.6±7.1 μg, p<0.0001). The 20 DNA samples extracted using the tissue protocol were then subjected to pre- and post MDA genotyping using amplicons for the MTHFRSNP at C677T and the intron 8 VDR SNP. No genotyping discrepancies were detected in pair-wise comparisons of pre- and post-MDA. Genotyping DNA from MDA-based WGA is indistinguishable from routine polymerase chain reaction and offers a stable DNA source for genomic research and clinical diagnosis.

Original languageEnglish (US)
Pages (from-to)157-162
Number of pages6
JournalClinical Chemistry and Laboratory Medicine
Volume43
Issue number2
DOIs
StatePublished - Mar 29 2005

Keywords

  • Buccal cell
  • DNA
  • Methylenetetrahydrofolate reductase
  • Multiple displacement amplification
  • Single nucleotide polymorphisms
  • Vitamin D receptor
  • Whole genome amplification

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

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    Thompson, M. D., Bowen, R. A. R., Wong, B. Y. L., Antal, J., Liu, Z., Yu, H., Siminovitch, K., Kreiger, N., Rohan, T. E., & Cole, D. E. C. (2005). Whole genome amplification of buccal cell DNA: Genotyping concordance before and after multiple displacement amplification. Clinical Chemistry and Laboratory Medicine, 43(2), 157-162. https://doi.org/10.1515/CCLM.2005.026