Journal Article

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

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

2015

Overview

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. 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. 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. 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. •Genotyping DNA from FFPE-T specimens is highly concordant (≈99%) with genotyping germline DNA.•The small loss of genotyping performance is attributable to inadequate DNA yield, not genetic rearrangement.•Analytic validity of genotyping from FFPE-T on our Sequenom array was documented for 218 cancer pharmacogenetics SNPs.•FFPE-T DNA is a viable alternative for prospective–retrospective pharmacogenetic analyses of clinical trials.

• Publisher: Elsevier B.V,John Wiley & Sons, Inc,John Wiley and Sons Inc
• Subject: Blood / Breast - metabolism / Breast - pathology / Breast cancer / Breast Neoplasms - blood / Breast Neoplasms - genetics / Breast Neoplasms - pathology / Cancer / Cancer therapies / Charitable foundations / Clinical trials / Deoxyribonucleic acid / Discordance / DNA / DNA - blood / DNA - genetics / DNA - isolation & purification / Female / FFPE / Formaldehyde / Formaldehyde - chemistry / Formalin-fixed paraffin embedded / Genomes / Genotyping / Genotyping Techniques / Germline genome / Humans / Lymph nodes / Lymphatic system / Medical research / Paraffin / Paraffin Embedding / Patients / Pharmacogenetics / Polymorphism, Single Nucleotide / Single-nucleotide polymorphism / Software / Somatic genome / Tissue Fixation / Tumors / Validity