Whole genome amplication of buccal cytobrush DNA collected for molecular epidemiology studies

L. E. Moore, A. W. Bergen, K. A. Haque, Y. Qi, P. Castle, S. J. Chanock, K. Egan, P. Newcomb, L. Titus-Ernstoff, J. Alguacil, N. Rothman, M. Garcia-Closas

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

When cytobrush buccal cell samples have been collected as a genomic DNA (gDNA) source for an epidemiological study, whole genome amplification (WGA) can be critical to maintain sufficient DNA for genotyping. We evaluated REPLI-g™ WGA using gDNA from two paired cytobrushes (cytobush 'A' kept in a cell lysis buffer, and 'B' dried and kept at room temperature for 3 days, and frozen until DNA extraction) in a pilot study (n=21), and from 144 samples collected by mail in a breast cancer study. WGA success was assessed as the per cent completion/concordance of STR/SNP genotypes. Locus amplification bias was assessed using quantitative PCR of 23 human loci. The pilot study showed ≥ 98% completion but low genotype concordance between cytobrush wgaDNA and paired blood gDNA (82% and 84% for cytobrushes A and B, respectively). Substantial amplification bias was observed with significantly lower human gDNA amplification from cytobrush B than A. Using cytobrush gDNA samples from the breast cancer study (n=20), an independent laboratory demonstrated that increasing template gDNA to the REPLI-g reaction improved genotype performance for 49 SNPs; however, average completion and concordance remained below 90%. To reduce genotype misclassification when cytobrush wgaDNA is used, inclusion of paired gDNA/wgaDNA and/or duplicate wgaDNA samples is critical to monitor data quality.

Original languageEnglish (US)
Pages (from-to)303-312
Number of pages10
JournalBiomarkers
Volume12
Issue number3
DOIs
StatePublished - May 1 2007
Externally publishedYes

Keywords

  • Genetic susceptibility
  • Genotyping
  • Molecular epidemiology
  • Multiple displacement amplification
  • TaqMan® assay
  • Whole genome amplification

ASJC Scopus subject areas

  • Biochemistry
  • Clinical Biochemistry
  • Health, Toxicology and Mutagenesis

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  • Cite this

    Moore, L. E., Bergen, A. W., Haque, K. A., Qi, Y., Castle, P., Chanock, S. J., Egan, K., Newcomb, P., Titus-Ernstoff, L., Alguacil, J., Rothman, N., & Garcia-Closas, M. (2007). Whole genome amplication of buccal cytobrush DNA collected for molecular epidemiology studies. Biomarkers, 12(3), 303-312. https://doi.org/10.1080/13547500601162011