Extended Data Fig. 7: Somatic mutations occurring at high sequencing depth in cfDNA.
From: High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
Somatic mutations detected at sequencing depth >10,000 in cfDNA occur mostly in hypermutated samples and are related to sample level mean target collapsed depth which is itself a function of the amount of input DNA used for library preparation. (a) Number of somatic mutations occurring at >10,000 sequence depth (n=215) per patient and categorized into WBC-matched, VUSO or Tumor-matched where the latter category is composed of Biopsy-matched and Biopsy-subthreshold mutations. (b) Variant level collapsed depth for all somatic mutations detected in cfDNA categorized into Tumor-matched, VUSO or WBC-matched and grouped according to the amount of input DNA used for library preparation. (c) Variant level collapsed depth for all somatic mutations detected in cfDNA against sample level mean collapsed target depth. (d) variant level collapsed depth for all somatic mutations against modeled VAF in cfDNA. 121 of 215 (56.3%) somatic mutations detected at sequencing depth >10,000 in cfDNA occurred in the hypermutated patient MSK-VB-0023. (e, f) Log2 ratios of (e) tumor biopsy and (f) cfDNA of patient MSK-VB-0023. The tumor biopsy and cfDNA showed similar copy number alterations (i.e. 1q+ and 16q-). No high-level copy number amplifications were observed in either the tumor biopsy or the cfDNA which could explain the high sequencing depth. Three replicate sequencing of cfDNA and WBC were available for that patient. (g) and (h) Pairwise comparisons of VAF for the 121 mutations detected at depth >10,000 using version V1 of the assay. In (a), ‘1’ denotes hypermutated samples. In (b), the midpoint indicates the median whilst the violins extent to the full range of the data. In (b–d), the sequencing depths of somatic variants for the cohort of n=124 cancer patients are shown. In (e) and (f), the grey points represent the raw Log2 ratios and are ordered according to their genomic coordinates. The solid red lines indicate the segmented values. In (g) and (h), the variants are shape coded based on their origin (i.e. whether they were also detected in the matched tumor biopsy and color coded according to their category; whether they were called in both replicates and assigned to similar source categories, namely VUSO, WBC-matched or noise).
