This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to classify samples into high and low Tumor mutational burden?

I actually wanted to calculate TMB (tumor mutational burden) for TCGA breast cancer samples. But I see that mutational load is available here Mutation Load - mutation-load-updated.txt for PAN CANCER data. So, From here I took the mutational load for TCGA BRCA data and it looks like below:

Cohort   Patient_ID     Tumor_Sample_ID  Silent per Mb   Non-silent per Mb
BRCA    TCGA-A2-A0CO    TCGA-A2-A0CO-01     0                  0
BRCA    TCGA-A2-A3KC    TCGA-A2-A3KC-01     0                  0
BRCA    TCGA-A2-A3XS    TCGA-A2-A3XS-01     0                  0
BRCA    TCGA-A2-A3XY    TCGA-A2-A3XY-01     0                  0
BRCA    TCGA-A2-A4RW    TCGA-A2-A4RW-01     0                  0
BRCA    TCGA-A2-A4RX    TCGA-A2-A4RX-01     0                  0
BRCA    TCGA-A2-A4RY    TCGA-A2-A4RY-01     0                  0
BRCA    TCGA-A2-A4S0    TCGA-A2-A4S0-01     0                  0
BRCA    TCGA-A7-A13H    TCGA-A7-A13H-01     0                  0
BRCA    TCGA-A7-A3IY    TCGA-A7-A3IY-01     0                  0
BRCA    TCGA-EW-A1P1    TCGA-EW-A1P1-01 0.028660581       0.028660581
BRCA    TCGA-PL-A8LY    TCGA-PL-A8LY-01 0.021965099       0.021965099
BRCA    TCGA-A2-A25F    TCGA-A2-A25F-01 0.029637804       0.059275609
BRCA    TCGA-LL-A440    TCGA-LL-A440-01     0             0.045303438
BRCA    TCGA-AO-A03U    TCGA-AO-A03U-01 0.086896254       0.115861671
BRCA    TCGA-A2-A0EP    TCGA-A2-A0EP-01 0.021402315       0.107011574
BRCA    TCGA-A2-A3XW    TCGA-A2-A3XW-01 0.043349112       0.108372779
BRCA    TCGA-OL-A5RY    TCGA-OL-A5RY-01 0.023244128            0
BRCA    TCGA-AR-A2LQ    TCGA-AR-A2LQ-01 0.058017267       0.203060434
BRCA    TCGA-OL-A5RV    TCGA-OL-A5RV-01 0.045425394       0.158988878
BRCA    TCGA-A2-A0ES    TCGA-A2-A0ES-01 0.135797917       0.217276667

Using this information how can I divide samples into High TMB and Low TMB? Is there a cutoff? Any help is appreciated. thanq.

wes genome mutation tcga tumor mutational burden

1 answer

There is no consensus regarding cutoffs and it's probably best to use as continuous covariate when possible.

https://www.ncbi.nlm.nih.gov/pubmed/30643254

Log in to answer this question.