Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses

Daniel L. Hertz, Kelley M. Kidwell, Jacklyn N. Thibert, Christina Gersch, Meredith M. Regan, Todd C. Skaar, N. Lynn Henry, Daniel F. Hayes, Catherine H. Van Poznak, James M. Rae

Research output: Contribution to journalArticle

9 Scopus citations


Background: Cancer pharmacogenetic studies use archival tumor samples as a DNA source when germline DNA is unavailable. Genotyping DNA from formalin-fixed paraffin embedded tumors (FFPE-T) may be inaccurate due to FFPE storage, genetic aberrations, and/or insufficient DNA extraction. Our objective was to assess the extent and source of genotyping inaccuracy from FFPE-T DNA and demonstrate analytical validity of FFPE-T genotyping of candidate single nucleotide polymorphisms (SNPs) for pharmacogenetic analyses. Methods: Cancer pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in DNA harvested from matched FFPE-T, FFPE lymph node (FFPE-LN), and whole blood leukocyte samples obtained from breast cancer patients. No- and discordant-call rates were calculated for each tissue type and SNP. Analytical validity was defined as any SNP with <5% discordance between FFPE-T and blood and <10% discordance plus no-calls. Results: Matched samples from 114 patients were genotyped for 247 SNPs. No-call rate in FFPE-T was greater than FFPE-LN and blood (4.3% vs. 3.0% vs. 0.5%, p < 0.001). Discordant-call rate between FFPE-T and blood was very low, but greater than that between FFPE-LN and blood (1.1% vs. 0.3%, p < 0.001). Samples with heterozygous genotypes were more likely to be no- or discordantly-called in either tissue (p < 0.001). Analytical validity of FFPE-T genotyping was demonstrated for 218 (88%) SNPs. Conclusions: No- and discordant-call rates were below concerning thresholds, confirming that most SNPs can be accurately genotyped from FFPE-T on our Sequenom platform. FFPE-T is a viable DNA source for prospective-retrospective pharmacogenetic analyses of clinical trial cohorts.

Original languageEnglish (US)
Pages (from-to)1868-1876
Number of pages9
JournalMolecular Oncology
Issue number9
StatePublished - Nov 2015



  • Cancer
  • FFPE
  • Formalin-fixed paraffin embedded
  • Germline genome
  • Pharmacogenetics
  • Somatic genome

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Oncology
  • Cancer Research

Cite this

Hertz, D. L., Kidwell, K. M., Thibert, J. N., Gersch, C., Regan, M. M., Skaar, T. C., Henry, N. L., Hayes, D. F., Van Poznak, C. H., & Rae, J. M. (2015). Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses. Molecular Oncology, 9(9), 1868-1876.