title: Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: a retrospective study.
abstract: BACKGROUND
  The majority of patients with stage III-IV epithelial ovarian cancer (EOC) relapse after initially responding to platinum-based chemotherapy, and develop resistance. The genomic features involved in drug resistance are unknown. To unravel some of these features, we investigated the mutational profile of genes involved in pathways related to drug sensitivity in a cohort of matched tumors obtained at first surgery (Ft-S) and second surgery (Sd-S).
  
  
  METHODS
  Matched biopsies (33) taken at Ft-S and Sd-S were selected from the 'Pandora' tumor tissue collection. DNA libraries for 65 genes were generated using the TruSeq Custom Amplicon kit and sequenced on MiSeq (Illumina). Data were analyzed using a high-performance cluster computing platform (Cloud4CARE project) and independently validated.
  
  
  RESULTS
  A total of 2270 somatic mutations were identified (89.85% base substitutions 8.19% indels, and 1.92% unknown). Homologous recombination (HR) genes and TP53 were mutated in the majority of Ft-S, while ATM, ATR, TOP2A and TOP2B were mutated in the entire dataset. Only 2% of mutations were conserved between matched Ft-S and Sd-S. Mutations detected at second surgery clustered patients in two groups characterized by different mutational profiles in genes associated with HR, PI3K, miRNA biogenesis and signal transduction.
  
  
  CONCLUSIONS
  There was a low level of concordance between Ft-S and Sd-S in terms of mutations in genes involved in key processes of tumor growth and drug resistance. This result suggests the importance of future longitudinal analyses to improve the clinical management of relapsed EOC.
authors.affiliation: Department of Oncology, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: L
authors.initials: L
authors.lastname: Beltrame
authors.affiliation: Department of Oncology, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: M
authors.initials: M
authors.lastname: Di Marino
authors.affiliation: Clinic of Obstetrics and Gynecology, University of Milano-Bicocca, San Gerardo Hospital, Monza.
authors.forename: R
authors.initials: R
authors.lastname: Fruscio
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.
authors.forename: E
authors.initials: E
authors.lastname: Calura
authors.affiliation: Bioinformatics Core, Harvard School of Public Health, Boston, USA.
authors.forename: B
authors.initials: B
authors.lastname: Chapman
authors.affiliation: Department of Oncology, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: L
authors.initials: L
authors.lastname: Clivio
authors.affiliation: Clinic of Obstetrics and Gynecology, University of Milano-Bicocca, San Gerardo Hospital, Monza.
authors.forename: F
authors.initials: F
authors.lastname: Sina
authors.affiliation: Department of Molecular Medicine Laboratory, Immunology and Genetic of Rare Diseases and Organ Transplantation, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: C
authors.initials: C
authors.lastname: Mele
authors.affiliation: Department of Molecular Medicine Laboratory, Immunology and Genetic of Rare Diseases and Organ Transplantation, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: P
authors.initials: P
authors.lastname: Iatropoulos
authors.affiliation: Clinic of Obstetrics and Gynecology, University of Milano-Bicocca, San Gerardo Hospital, Monza.
authors.forename: T
authors.initials: T
authors.lastname: Grassi
authors.affiliation: PhD Program in Experimental Medicine, University of Pavia, Pavia.
authors.forename: V
authors.initials: V
authors.lastname: Fotia
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.
authors.forename: C
authors.initials: C
authors.lastname: Romualdi
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Martini
authors.affiliation: Department of Molecular Medicine Laboratory, Immunology and Genetic of Rare Diseases and Organ Transplantation, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: M
authors.initials: M
authors.lastname: Noris
authors.affiliation: Department of Oncology, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: L
authors.initials: L
authors.lastname: Paracchini
authors.affiliation: Department of Oncology, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: I
authors.initials: I
authors.lastname: Craparotta
authors.affiliation: Gynecologic Oncology Unit, Catholic University of the Sacred Heart, Rome.
authors.forename: M
authors.initials: M
authors.lastname: Petrillo
authors.affiliation: Clinic of Obstetrics and Gynecology, University of Milano-Bicocca, San Gerardo Hospital, Monza.
authors.forename: R
authors.initials: R
authors.lastname: Milani
authors.affiliation: Department of Pathology, University of Milano-Bicocca, San Gerardo Hospital, Monza.
authors.forename: P
authors.initials: P
authors.lastname: Perego
authors.affiliation: Division of Gynecologic Oncology, 'Angelo Nocivelli' Institute of Molecular Medicine, University of Brescia, Brescia.
authors.forename: A
authors.initials: A
authors.lastname: Ravaggi
authors.affiliation: Unit of Medical Oncology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo.
authors.forename: A
authors.initials: A
authors.lastname: Zambelli
authors.affiliation: Laboratory of Experimental Oncology and Pharmacogenomics, IRCCS Salvatore Maugeri Foundation, Pavia, Italy.
authors.forename: E
authors.initials: E
authors.lastname: Ronchetti
authors.affiliation: Department of Oncology, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano maurizio.dincalci@marionegri.it.
authors.forename: M
authors.initials: M
authors.lastname: D'Incalci
authors.affiliation: Department of Oncology, Centro di Ricerche Cliniche per le Malattie Rare 'ALDO e CELE DACCO'', IRCCS 'Mario Negri' Institute for Pharmacological Research, Milano.
authors.forename: S
authors.initials: S
authors.lastname: Marchini
mesh_terms: D018262:Adenocarcinoma, Clear Cell / Q000235:genetics* / Q000401:mortality / Q000556:secondary / Q000628:therapy; D002288:Adenocarcinoma, Mucinous / Q000235:genetics* / Q000401:mortality / Q000556:secondary / Q000628:therapy; D000328:Adult; D000368:Aged; D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use; D001706:Biopsy; D003131:Combined Modality Therapy; D018284:Cystadenocarcinoma, Serous / Q000235:genetics* / Q000401:mortality / Q000556:secondary / Q000628:therapy; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D016889:Endometrial Neoplasms / Q000235:genetics* / Q000401:mortality / Q000556:secondary / Q000628:therapy; D005260:Female; D005500:Follow-Up Studies; D052138:Genes, Neoplasm / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D059765:Homologous Recombination; D006801:Humans; D008137:Longitudinal Studies; D008207:Lymphatic Metastasis; D008875:Middle Aged; D009154:Mutation / Q000235:genetics*; D060787:Neoplasm Grading; D009364:Neoplasm Recurrence, Local / Q000235:genetics / Q000401:mortality / Q000473:pathology / Q000628:therapy; D009367:Neoplasm Staging; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology / Q000628:therapy; D011379:Prognosis; D012189:Retrospective Studies; D015996:Survival Rate
keywords: NGS; epithelial ovarian cancer; matched tumor biopsies