title: Clinical actionability enhanced through deep targeted sequencing of solid tumors.
abstract: BACKGROUND
  Further advances of targeted cancer therapy require comprehensive in-depth profiling of somatic mutations that are present in subpopulations of tumor cells in a clinical tumor sample. However, it is unclear to what extent such intratumor heterogeneity is present and whether it may affect clinical decision-making. To study this question, we established a deep targeted sequencing platform to identify potentially actionable DNA alterations in tumor samples.
  
  
  METHODS
  We assayed 515 formalin-fixed paraffin-embedded (FFPE) tumor samples and matched germline DNA (475 patients) from 11 disease sites by capturing and sequencing all the exons in 201 cancer-related genes. Mutations, indels, and copy number data were reported.
  
  
  RESULTS
  We obtained a 1000-fold mean sequencing depth and identified 4794 nonsynonymous mutations in the samples analyzed, of which 15.2% were present at <10% allele frequency. Most of these low level mutations occurred at known oncogenic hotspots and are likely functional. Identifying low level mutations improved identification of mutations in actionable genes in 118 (24.84%) patients, among which 47 (9.8%) otherwise would have been unactionable. In addition, acquiring ultrahigh depth also ensured a low false discovery rate (<2.2%) from FFPE samples.
  
  
  CONCLUSIONS
  Our results were as accurate as a commercially available CLIA-compliant hotspot panel but allowed the detection of a higher number of mutations in actionable genes. Our study reveals the critical importance of acquiring and utilizing high sequencing depth in profiling clinical tumor samples and presents a very useful platform for implementing routine sequencing in a cancer care institution.
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Ken
authors.initials: K
authors.lastname: Chen
authors.affiliation: Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX; Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Surgical Oncology.
authors.forename: Funda
authors.initials: F
authors.lastname: Meric-Bernstam
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX;
authors.forename: Qingxiu
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX;
authors.forename: Nader
authors.initials: N
authors.lastname: Ezzeddine
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX;
authors.forename: Lin-Ya
authors.initials: LY
authors.lastname: Tang
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Qi
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Yong
authors.initials: Y
authors.lastname: Mao
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Tenghui
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Zechen
authors.initials: Z
authors.lastname: Chong
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Wanding
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Department of Bioinformatics and Computational Biology and.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX;
authors.forename: Amber
authors.initials: A
authors.lastname: Johnson
authors.affiliation: Department of Pathology.
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Aldape
authors.affiliation: Department of Hematopathology.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Routbort
authors.affiliation: Department of Hematopathology.
authors.forename: Rajyalakshmi
authors.initials: R
authors.lastname: Luthra
authors.affiliation: Department of GI Medical Oncology.
authors.forename: Scott
authors.initials: S
authors.lastname: Kopetz
authors.affiliation: Department of Melanoma Medical Oncology.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Davies
authors.affiliation: Department of Neuro Oncology.
authors.forename: John
authors.initials: J
authors.lastname: de Groot
authors.affiliation: Department of Breast Medical Oncology, and.
authors.forename: Stacy
authors.initials: S
authors.lastname: Moulder
authors.affiliation: Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX;
authors.forename: Ravi
authors.initials: R
authors.lastname: Vinod
authors.affiliation: Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC;
authors.forename: Carol J
authors.initials: CJ
authors.lastname: Farhangfar
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX;
authors.forename: Kenna Mills
authors.initials: KM
authors.lastname: Shaw
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX;
authors.forename: John
authors.initials: J
authors.lastname: Mendelsohn
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Systems Biology, MD Anderson Cancer Center, Houston, TX.
authors.forename: Gordon B
authors.initials: GB
authors.lastname: Mills
authors.affiliation: Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Systems Biology, MD Anderson Cancer Center, Houston, TX. aketerovic@mdanderson.org.
authors.forename: Agda Karina
authors.initials: AK
authors.lastname: Eterovic
mesh_terms: D004273:DNA, Neoplasm / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D004273:DNA, Neoplasm