Abstract
Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is currently the most popular technology; however, this yields low sensitivity in low purity tumors. RNA sequencing (RNA-seq) covers the expressed exome with depth proportional to expression. We hypothesized that integrating DNA-WES and RNA-seq would enable superior mutation detection versus DNA-WES alone. We developed a first-of-its-kind method, called UNCeqR, that detects somatic mutations by integrating patient-matched RNA-seq and DNA-WES. In simulation, the integrated DNA and RNA model outperformed the DNA-WES only model. Validation by patient-matched whole genome sequencing demonstrated superior performance of the integrated model over DNA-WES only models, including a published method and published mutation profiles. Genome-wide mutational analysis of breast and lung cancer cohorts (n = 871) revealed remarkable tumor genomics properties. Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES. RNA provided greater mutation signal than DNA in expressed mutations. Compared to earlier studies on this cohort, UNCeqR increased mutation rates of driver and therapeutically targeted genes (e.g. PIK3CA, ERBB2 and FGFR2). In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors.
Highlights
Acquired sequence mutations fuel the initiation and progression of cancer [1]
In cancer profiling projects such as The Cancer Genome Atlas (TCGA) [4,6] and in clinical sequencing [2,19], DNAWES is utilized for mutation detection while RNA sequencing (RNA-seq) [20] is performed for gene expression, fusion transcript and splicing analyses
DNA whole exome sequencing (DNA-WES) and RNA-seq alignments in BAM [31] format for 176 lung squamous cell carcinoma cases and for 695 breast cancer cases were acquired from TCGA at https://cghub.ucsc.edu (Supplementary Table S1)
Summary
Acquired sequence mutations (nucleotide substitutions, insertions and deletions) fuel the initiation and progression of cancer [1]. In cancer profiling projects such as The Cancer Genome Atlas (TCGA) [4,6] and in clinical sequencing [2,19], DNAWES is utilized for mutation detection while RNA sequencing (RNA-seq) [20] is performed for gene expression, fusion transcript and splicing analyses Beyond those applications, RNA-seq provides an observation of the underlying tumor DNA sequence, via transcription, and can be used to detect sequence variants [21]. RNA-seq has challenges including dependency on gene expression, which limits the genes that can be measured for sequence mutations, and quality control requirements, which when not considered result in abundant false positive variants [11,21,28,29,30]. Genome-wide analysis of UNCeqR mutations led to novel discoveries in tumor genomics
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