Open pbiology opened 1 year ago
We need samples with high and low TMB. Should be possible to get from Teresita
Just adding this article: https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-022-01348-z which Saliendra from Lund added during the last GMS-BT meeting which focused on TMB.
Is this feature still blocked? And if so, by what?
Need
TMB calculation today in BALSAMIC
The current definition is based on:
TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome examined. https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0424-2 1.1. Non-coding alterations were not counted. 1.2 Alterations listed as known somatic alterations in COSMIC and truncations in tumor suppressor genes were not counted 1.3 Alterations predicted to be germline by the somatic-germline-zygosity algorithm were not counted 1.4 Alterations that were recurrently predicted to be germline in our cohort of clinical specimens were not counted. 1.5 Known germline alterations in dbSNP were not counted. 1.6 To calculate the TMB per megabase, the total number of mutations counted is divided by the size of the coding region of the targeted territory. 1.7 select the table 1 from paper above as a ref for comparison.
Tumor mutation burden (TMB), fraction of copy number–altered genome, and gene alterations were compared among patients with DCB and no durable benefit (NDB). http://ascopubs.org/doi/full/10.1200/JCO.2017.75.3384 2.1 in addition to above, copy number alterations were also counted.
Summary of TMB computation method in BALSAMIC:
Summary of TMB computation method in Hydra pipeline:
https://github.com/hydra-genetics/biomarker/blob/develop/workflow/scripts/tmb.py
(May be updated)
This may require: A. Generating the allele frequency and FFPE artefact databases. B. Fine-tuning the values for the thresholds according to the sequencing-type.
The thresholds are given below: FFPE SNV observations = 1 DP = 200 VD = 10 AF = 0.05-0.45 gnomAD = 0.0001 db1000g = 0.0001 background sd = 5 Non-synonymous correction factor = 0.78 Non-synonymous and synonymous correction factor = 0.57
Samples and Analysis
Seracare TMB samples: gDNA TMB Mix Scores 7, 9, 13, 20, 26.
TMB MEASUREMENTS
Method description from SeraCare for the TMB calculation.
TMB analysis from BALSAMIC
Summary of TMB analysis in Balsamic. The TMB score from Balsamic is taken from file
*tnscope.balsamic_stat
WGS - 2023 (incorrect results /ALY)
TGA - 2023 (incorrect results /ALY)
New SeraSeq TMB reference samples
Seraseq gDNA TMB Mix Score 7 Seraseq gDNA TMB Mix Score 13 Seraseq gDNA TMB Mix Score 26
New reference samples were purchased in 2024 and RC information, sample calculations and order plan is available here.
Information/Articles on TMB
How to improve the calculation
TMB standardization by alignment to reference standards: Phase II of the Friends of Cancer Research TMB Harmonization Project.
Documentation
[ ] For Customers, Include the description of how TMB is calculated and related references in the balsamic readthedocs
Suggested approach
A few sentences about the intended solution
Considered alternatives
Can be closed when
Link the issues needed to be closed for this to be implemented
Blockers
Anything preventing this from happening?