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 Skaar, N. Lynn Henry, Daniel F. Hayes, Catherine H. Van Poznak, James M. Rae

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

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

Original languageEnglish (US)
Pages (from-to)1868-1876
Number of pages9
JournalMolecular Oncology
Volume9
Issue number9
DOIs
StatePublished - Nov 1 2015

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Paraffin
Formaldehyde
Breast Neoplasms
Single Nucleotide Polymorphism
DNA
Neoplasms
Pharmacogenetics
Pharmacogenomic Testing
Leukocytes
Lymph Nodes

Keywords

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

ASJC Scopus subject areas

  • Cancer Research
  • Genetics
  • Molecular Medicine

Cite this

Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses. / Hertz, Daniel L.; Kidwell, Kelley M.; Thibert, Jacklyn N.; Gersch, Christina; Regan, Meredith M.; Skaar, Todd; Henry, N. Lynn; Hayes, Daniel F.; Van Poznak, Catherine H.; Rae, James M.

In: Molecular Oncology, Vol. 9, No. 9, 01.11.2015, p. 1868-1876.

Research output: Contribution to journalArticle

Hertz, DL, Kidwell, KM, Thibert, JN, Gersch, C, Regan, MM, Skaar, T, Henry, NL, Hayes, DF, Van Poznak, CH & Rae, JM 2015, 'Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses', Molecular Oncology, vol. 9, no. 9, pp. 1868-1876. https://doi.org/10.1016/j.molonc.2015.07.002
Hertz, Daniel L. ; Kidwell, Kelley M. ; Thibert, Jacklyn N. ; Gersch, Christina ; Regan, Meredith M. ; Skaar, Todd ; Henry, N. Lynn ; Hayes, Daniel F. ; Van Poznak, Catherine H. ; Rae, James M. / Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses. In: Molecular Oncology. 2015 ; Vol. 9, No. 9. pp. 1868-1876.
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AU - Gersch, Christina

AU - Regan, Meredith M.

AU - Skaar, Todd

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