Reduce the impact of deamination in low-quality FFPEs

Samples of low quality that exhibit deamination can be analyzed if you increase the minimum allele frequency in an analysis workflow. For example, a minimum allele frequency of 10% for the tumor mutational burden (TMB) calculation can reduce the impact of deamination on the reported TMB value. It is important to consider the tumor content of a given sample when you increase the minimum allele frequency of the TMB calculation.

  • Samples with low tumor content can have many true somatic mutations that are excluded from the tumor mutational burden calculation when a higher minimum allele frequency filter is included in the analysis workflow.

  • The tumor mutational burden values cannot be reliable if you adjust the minimum allele frequency parameters for samples with a high estimated SNP proportion consistent with deamination, (primarily an FFPE number) or a high deamination score, (for example >100).

  • The mean depth and uniformity of the sample as determined by the coverageAnalysis plugin can also indicate sample quality. For more information, see Torrent Suite™ Software Help.

IMPORTANT! Use the default parameter settings unless you are an advanced user.