Fig. 1: Integrated WES/RNA-seq assay from the same tissue.
From: Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort
a Tissue sample processing workflow. b Tumor/normal variant calling and RNA confirmation in TP53 exons; reference (blue) and mutant (red) alleles shown. Sample integrity confirmed via SNV concordance and HLA genotype. c Proportion of read types in optimized DNA and RNA sequencing. d Dependence of variability of detected transcripts on total read numbers per sample (n = 10). Box plots show the interquartile range. e Dependence of coefficient of variance (CV) of single gene expression (log2TPM) on the expression level. f Schema showing the three-step validation approach for different biomarker groups. g Schema of experiment to develop comprehensive somatic references for COLO829, HCC1143, HCC1395, HCC1937, and NCI-H1770 cell lines. h Scatter plot of VAF and coverage for all variants (n = 500) in COLO829 (100% purity); true positives (purple), RNA-confirmed (yellow), and filtered false positives (pink). Dashed line marks filtering threshold. Somatic (i) and germline (j) variant calling F1-scores by coverage and tumor purity (i) or genotypes (j); shading shows s.e.m. from 10 samples per dilution (n = 60). Dependence of coverage completeness (k), BAF variance (pink dots, left y-axis), and tumor/normal depth ratio variance (purple dots, right y-axis) (l) on median sample coverage (n = 250).
