BACKGROUND: Cancer pharmacogenetic studies use @entity5 samples as a DNA source when germline DNA is unavailable. Genotyping DNA from @entity2300 ( @entity2300 ) 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 @entity2300 DNA and demonstrate analytical validity of @entity2300 genotyping of candidate single nucleotide polymorphisms (SNPs) for pharmacogenetic analyses. METHODS: Cancer pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in DNA harvested from matched @entity2300 , FFPE lymph node (FFPE-LN), and whole blood leukocyte samples obtained from @entity0 @entity1 . No- and discordant-call rates were calculated for each tissue type and SNP. Analytical validity was defined as any SNP with <5% discordance between @entity2300 and blood and <10% discordance plus no-calls. RESULTS: Matched samples from 114 @entity1 were genotyped for 247 SNPs. No-call rate in @entity2300 was greater than FFPE-LN and blood (4.3% vs. 3.0% vs. 0.5%, p < 0.001). Discordant-call rate between @entity2300 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 @entity2300 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 @entity2300 on our Sequenom platform. @entity2300 is a viable DNA source for prospective-retrospective pharmacogenetic analyses of clinical trial cohorts.

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

@entity5 :: ('MESH:D009369', 'Disease') :: ['archival tumor'] @entity1 :: ('9606', 'Species') :: ['patients'] @entity2300 :: ('MESH:D011681', 'Disease') :: ['formalin-fixed paraffin embedded tumors', 'FFPE-T'] @entity0 :: ('MESH:D001943', 'Disease') :: ['breast cancer']
@entity0 :: (MESH:D001943,Disease) :: ['breast tumor']
