Fig. 1: Design, characterization, and validation of MSK-ACCESS.
a The MSK-ACCESS panel was designed using data from 25,000 tumors analyzed using MSK-IMPACT tumor sequencing assay to identify at least one mutation in 94% of lung cancers, 91% of breast, and 84% of all cancers. b The laboratory workflow includes the extraction of cfDNA from plasma and genomic DNA from WBC originating from the same tube of blood. The addition of UMIs during library construction enables the identification of original cfDNA molecules during analysis and error suppression. c The analysis pipeline is modified from the standard MSK-IMPACT pipeline to incorporate UMI clipping and the generation of simplex and duplex consensus reads. d The sequencing of healthy donors to a mean raw coverage of 18,818× yielded a mean duplex coverage of 1103× and a mean simplex coverage of 658× across 47 samples. e The background error rate of non-reference sites demonstrates the reduction of overall and substitution specific errors via consensus read generation. Only the genomic position with non-reference reads are used; error rate is defined as the percentage of reads that support non-reference alleles. N = 47 for each boxplot. f A heatmap of error rate at all positions demonstrates how effective consensus read generation is at decreasing the error to zero at over 85% of sites. g Comparison of orthogonal and validated testing (expected VAF) to MSK-ACCESS (observed VAF) in the accuracy analysis showed high concordance (R2 = 0.98). All boxplots show the median (center line) and 25th and 75th percentiles (bounding box) along with the 1.5 interquartile range (whiskers).
