Extended Data Fig. 5: Top mutated genes carrying VUSO and 96 base substitution profiles of ten hypermutated cfDNA samples.
From: High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
(a) Frequency of genomic alterations in cfDNA of 47 non-cancer controls and 124 cancer patients. The genes were sorted by their frequency of alterations in the tumor. The colors indicate whether the alterations were biopsy-matched, detected in the tumor but below the threshold of the MSK-IMPACT assay (biopsy-subthreshold), or were specific to cfDNA (i.e. variants of unknown source, VUSO). (b) Correlation of the number of VUSO per gene and per patient (y-axis) in the ten hypermutated and 114 non-hypermutated cancer patients against the length of the coding region sequenced (x-axis) of each target gene. (c-e) Heat maps showing the top mutated genes harboring somatic variants detected in plasma cfDNA that are neither tumor-matched (biopsy-matched or subthreshold) nor WBC-matched across each cohort in (c) 47 non-cancer controls, (d) 114 non-hypermutated and (e) 10 hypermutated cancer patients. The numbers in the cells indicate the number of patients. (f) 96 base substitution profiles of the 10 hypermutated patients. For each patient, the number of C>A, C>G, C>T, T>A, T>C and T>G substitutions together with the sequence context immediately 3′ and 5′ are expressed as a percentage of the total number of substitutions.
