Extended Data Fig. 5: Immune evasion mechanisms and TMB. | Nature Genetics

Extended Data Fig. 5: Immune evasion mechanisms and TMB.

From: Genetic immune escape landscape in primary and metastatic cancer

Extended Data Fig. 5

a) Analogous to Fig. 7a, but restricted to (from left to right) non-small cell lung cancer, breast cancer and colorectal cancer patients. Top panels represent the total number of bucket-assigned (white bars with a black contouring line) and GIE-positive (pink bars with pink contouring lines) samples across the ten evenly arranged TMB buckets. bottom panel, representation of observed (pink) and simulated (gray) GIE frequency across these buckets. For the observed GIE values, average (represented as pink dots) and standard deviation (std, vertical error bars and shaded pink area) values are computed using 1,000 bootstraps from the total number of cancer type samples classified into each bucket (from the top panel). For the simulated GIE values, average (gray triangle) and standard deviation (std, vertical bars and shaded gray area) values are computed from 100 GIE simulations using the total number of cancer type samples assigned into each bucket. b) Analogous to panel a) but using the entire cohort (N=6,319) and twenty evenly arranged buckets as well as clonal TMB (left) and subclonal TMB (right) as baseline. c) Equivalent to panel a) but using the entire cohort (N=6,319) and twenty evenly arranged buckets and grouping GIE events according to the assigned GIE pathway. Label number represents the assigned immune escape pathway (from Fig. 1a) d) Similar to panel c) but using the number of predicted neoepitopes as baseline for the buckets. Bottom labels, number of estimated neoantigens as a relative percentage (1% and 5%) of the number of predicted neoepitopes in the bucket. N, number of samples. Muts/Mb, mutations per megabase. ICI, immune checkpoint inhibitor.

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