Fig. 1: Comparative analysis of mutational signatures and method overview.
From: The mutREAD method detects mutational signatures from low quantities of cancer DNA
a Cosine similarity (y-axis) of whole-genome sequencing (WGS)-derived mutational signatures for EAC samples (n = 129 independent patients) and signatures derived from random subsets of mutations with increasing number of mutations (x-axis). Data are shown as boxplots, where the bold line at the center indicates the median and the upper and lower hinges extend to the 25th and 75th percentile, respectively. The upper/lower whisker extends from the upper/lower hinge to the largest/smallest value no further than 1.5 times the interquartile range from the upper/lower hinge. Samples outside this range are indicated as points. Only samples having sufficient number of mutations (at least the number indicated on the x-axis) contribute to the boxes. b Cosine similarity (y-axis) of WGS-derived mutational signatures for EAC samples (n = 129 independent patients) and signatures derived from subsets of mutations simulating different sequencing approaches (x-axis). Data are represented as mean cosine similarity values ± standard deviation. Different enzyme combinations were simulated for RR-seq, each shown as a different point. For the simulated 10x sWGS samples, the mean (n = 21 independent patients) is given as dashed horizontal line and the standard deviation is given as dotted line. RR-Seq, reduced representation sequencing; 10× sWGS, 10× shallow whole-genome sequencing; WES, whole-exome sequencing; expanded WES, whole-exome sequencing expanded to untranslated regions and miRNAs. c Schematic overview of the individual steps in mutREAD. Details for each step are given in the “Methods” section. SB, sample barcode; UMI, unique molecular identifier; RE, restriction enzyme. d Comparison of the mutational signature profiles for three EAC samples across different sequencing methods (x-axis). Each bar indicates the contribution of the mutational signature (y-axis) to the overall mutational spectrum. Pairwise cosine similarities to WGS for mutREAD, WES and 10× sWGS are indicated above the bars.
