title: Integrated RNA and DNA sequencing improves mutation detection in low purity tumors.
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.
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA mwilkers@med.unc.edu.
authors: Matthew D
authors: MD
authors: Wilkerson
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA The Genome Institute at Washington University, St. Louis, MO 63108, USA.
authors: Christopher R
authors: CR
authors: Cabanski
authors: Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Wei
authors: W
authors: Sun
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Katherine A
authors: KA
authors: Hoadley
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Vonn
authors: V
authors: Walter
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Lisle E
authors: LE
authors: Mose
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Melissa A
authors: MA
authors: Troester
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors: Peter S
authors: PS
authors: Hammerman
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Joel S
authors: JS
authors: Parker
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors: Charles M
authors: CM
authors: Perou
authors: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA mwilkers@med.unc.edu.
authors: D Neil
authors: DN
authors: Hayes
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D005260:Female; D052138:Genes, Neoplasm; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D059645:Mutation Rate; D009369:Neoplasms / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*