title: Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response.
abstract: BACKGROUND
  In triple negative breast cancers (TNBC) the initial response to chemotherapy is often favorable, but relapse and chemotherapy resistance frequently occur in advanced disease. Hence there is an urgent need for targeted treatments in this breast cancer subtype. In the current study we deep sequenced DNA of tumors prior to chemotherapy to search for predictors of response or resistance.
  
  
  METHODS
  Next generation sequencing (NGS) was performed for 1,977 genes involved in tumorigenesis. DNA from 56 pre-treatment TNBC-biopsies was sequenced, as well as matched normal DNA. Following their tumor biopsy, patients started neoadjuvant chemotherapy with doxorubicin and cyclophosphamide. We studied associations between genetic alterations and three clinical variables: chemotherapy response, relapse-free survival and BRCA proficiency.
  
  
  RESULTS
  The mutations observed were diverse and few recurrent mutations were detected. Most mutations were in TP53, TTN, and PIK3CA (55 %, 14 %, and 9 %, respectively). The mutation rates were similar between responders and non-responders (average mutation rate 9 vs 8 mutations). No recurrent mutations were associated with chemotherapy response or relapse. Interestingly, PIK3CA mutations were exclusively observed in patients proficient for BRCA1. Samples with a relapse had a higher copy number alteration rate, and amplifications of TTK and TP53BP2 were associated with a poor chemotherapy response.
  
  
  CONCLUSIONS
  In this homogenous cohort of TNBCs few recurrent mutations were found. However, PIK3CA mutations were associated with BRCA proficiency, which can have clinical consequences in the near future.
authors.affiliation: Department of Molecular Pathology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. e.lips@nki.nl.|Department of Pathology, Amsterdam, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. e.lips@nki.nl.
authors.forename: Esther H
authors.initials: EH
authors.lastname: Lips
authors.affiliation: Department of Molecular Carcinogenesis, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. m.michaut@nki.nl.
authors.forename: Magali
authors.initials: M
authors.lastname: Michaut
authors.affiliation: Department of Molecular Carcinogenesis, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. m.hoogstraat@nki.nl.|Department of Medical Oncology, UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands. m.hoogstraat@nki.nl.
authors.forename: Marlous
authors.initials: M
authors.lastname: Hoogstraat
authors.affiliation: Department of Molecular Pathology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. l.mulder@nki.nl.
authors.forename: Lennart
authors.initials: L
authors.lastname: Mulder
authors.affiliation: Department of Medical Oncology, UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands. n.besselink-2@umcutrecht.nl.
authors.forename: Nicolle J M
authors.initials: NJ
authors.lastname: Besselink
authors.affiliation: Department of Medical Oncology, UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands. m.j.koudijs@umcutrecht.nl.
authors.forename: Marco J
authors.initials: MJ
authors.lastname: Koudijs
authors.affiliation: Department of Medical Genetics, UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands. e.cuppen@hubrecht.eu.
authors.forename: Edwin
authors.initials: E
authors.lastname: Cuppen
authors.affiliation: Department of Medical Oncology, UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands. e.voest@nki.nl.|Department of Medical Oncology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. e.voest@nki.nl.
authors.forename: Emile E
authors.initials: EE
authors.lastname: Voest
authors.affiliation: Department of Molecular Carcinogenesis, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. r.bernards@nki.nl.
authors.forename: Rene
authors.initials: R
authors.lastname: Bernards
authors.affiliation: Department of Pathology, Amsterdam, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. p.nederlof@nki.nl.
authors.forename: Petra M
authors.initials: PM
authors.lastname: Nederlof
authors.affiliation: Department of Molecular Pathology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. j.wesseling@nki.nl.|Department of Pathology, Amsterdam, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. j.wesseling@nki.nl.
authors.forename: Jelle
authors.initials: J
authors.lastname: Wesseling
authors.affiliation: Department of Medical Oncology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. s.rodenhuis@nki.nl.
authors.forename: Sjoerd
authors.initials: S
authors.lastname: Rodenhuis
authors.affiliation: Department of Molecular Carcinogenesis, the Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. l.wessels@nki.nl.|Department of EEMCS, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands. l.wessels@nki.nl.
authors.forename: Lodewyk F A
authors.initials: LF
authors.lastname: Wessels
mesh_terms: D000328:Adult; D000368:Aged; D000970:Antineoplastic Agents / Q000494:pharmacology* / Q000627:therapeutic use; D058534:Class I Phosphatidylinositol 3-Kinases; D064211:Connectin / Q000235:genetics; D004252:DNA Mutational Analysis; D019008:Drug Resistance, Neoplasm; D005260:Female; D018628:Gene Dosage; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008875:Middle Aged; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D015398:Signal Transduction; D064726:Triple Negative Breast Neoplasms / Q000188:drug therapy / Q000235:genetics*; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D055815:Young Adult
chemical_list: D000970:Antineoplastic Agents; D064211:Connectin; C495901:TP53 protein, human; C577285:TTN protein, human; D016159:Tumor Suppressor Protein p53; D019869:Phosphatidylinositol 3-Kinases; D058534:Class I Phosphatidylinositol 3-Kinases; C484760:PIK3CA protein, human