FFPE-derived Reference Standards are ideal tools used to test the full integrity of a molecular assay workflow from extraction through to quantification to molecular testing and data analysis.
Laboratories often assume that a failed assay is as a result of a failed analytical step, however root cause analysis often shows that problems with DNA extraction or issues with DNA quantification are really at fault (e.g. over-estimating sample DNA concentration leading to the assay being under loaded). Analyzing the cause of a failed assay is a particular challenge for laboratories not used to handling FFPE samples, or for laboratories using quantification methodologies that tend to overestimate the amount of DNA in a sample when measuring concentrations below 20 ng per microliter (e.g. NanoDrop).
Mutant cell lines embedded in FFPE are all heterozygotes, and in the majority of cases this means there is a single mutant allele and a single normal allele. Where the copy number is 2N, a 100% mutant gDNA sample indicates that 100% of the cells the DNA was extracted from contained the mutation, however as only one of the two copies of the gene from that cell will actually contain the mutation, the sample actually will have an allelic frequency of 50% for that mutation. Mutant and “normal” cell lines can be precisely blended to generate samples with specific allelic frequencies typically ranging between 1% and 50%.
Sources of variabitlity within a standard molecular assay workflow
Also available as Genomic DNA.
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