Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses.
作者： Daniel L. Hertz , Kelley M. Kidwell , Jacklyn N. Thibert , Christina Gersch , Meredith M. Regan
DOI: 10.1016/J.MOLONC.2015.07.002
关键词:
摘要: Abstract Background Cancer pharmacogenetic studies use archival tumor samples as a DNA source when germline is unavailable. Genotyping from formalin-fixed paraffin embedded tumors (FFPE-T) may be inaccurate due to FFPE storage, genetic aberrations, and/or insufficient extraction. Our objective was assess the extent and of genotyping inaccuracy FFPE-T demonstrate analytical validity candidate single nucleotide polymorphisms (SNPs) for analyses. Methods pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in harvested matched FFPE-T, lymph node (FFPE-LN), whole blood leukocyte obtained breast cancer patients. No- discordant-call rates calculated each tissue type SNP. Analytical defined any SNP with Results Matched 114 patients 247 SNPs. No-call rate greater than FFPE-LN (4.3% vs. 3.0% 0.5%, p Conclusions below concerning thresholds, confirming that most can accurately on our platform. viable prospective–retrospective analyses clinical trial cohorts.
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