tsoppy input standardization - 6. TMB, MSI, GIS

[danielvo]

Inputs considered so far:

• Dragen TSO500 analysis pipeline v. 2.6.2
  • the information below is based on output generated for samples sequenced with TSO500 assay version 2, but the current
  • unclear: is the Dragen server version a factor?
    • OUS assumes it does not, and both OUS and UNN use the same Dragen server version.
      • It looks like both assay v1 and assay v2 samples can now be analyzed with the same Dragen software.
    • Dragen server version [07.021.624.]3.11.2 was used when generating the output referenced in the text below
    • UNN utilizes the same Dragen server version and Dragen TSO500 analysis pipeline version
    • unclear: When analyzing samples with ICA (Illumina Cconnected Analysis), can one pick exactly the same Dragen server version and TSO500 pipeline version?
  • unclear: can the analysis output structure vary based on the sample sheet content/format choices?
    • different Pair_ID and Sample_ID values were used when generating the output referenced in the text below
    • we should aim to standardize the sample sheets across InPreD nodes either way
• Local App version 2.2.0.12
  • the sample sheet content/format (e.g., the Pair_ID value choice) can impact the analysis output structure
    • different Pair_ID and Sample_ID values were used when generating the output referenced in the text below

6. TMB, MSI, GIS

TMB (Tumor Mutational Burden), MSI (Micro-Satellite Instability) and GIS (Genomic Instability Score) are numerical metrics that represent how many changes of a certain type a given tumor has accumulated. InPreD currently wishes to use all three metrics as they are calculated and presented by the Local App and/or Dragen pipelines. All tsoppy needs to do is to look up the respective metric values (together with the available related metrics that can provide information about the reliability of the TMB, MSI and GIS measures for a given sample).

All the values can be extracted from Local App-/Dragen-generated *_CombinedVariantOutput.tsv files, as described in #19.