Extended Data Fig. 2: Accuracy of TCRA T cell fraction by copy number and depth.
From: Using DNA sequencing data to quantify T cell fraction and therapy response
a, Simulated log RDR from a sample consisting of 24% T cells, 75% tumour, and 1% non-T cell stroma (TCRA copy number = 1). b, Calculated TCRA T cell fraction versus actual T cell fraction value for simulated data c, Difference between calculated naive T cell fraction and actual fraction for range of tumour purities and local tumour copy number states at the TCRA locus. d, Difference between TCRA T cell fraction and actual fraction for a range of local tumour copy number to the TCRA locus and tumour purities. e,. Downsampling of 5 TRACERx100 samples to different depths. f, Downsampling of simulated data to different depth levels. g, Downsampling of the 5 TRACERx100 samples that with the highest CDR3 read counts to different depths and the resulting CDR3 read counts.
