title: Mutation Analysis of Nine Chordoma Specimens by Targeted Next-Generation Cancer Panel Sequencing.
abstract: BACKGROUND
  Chordoma is a rare primary malignant bone tumour. Treatment options are mainly restricted to surgical excision, since chordomas are largely resistant to conventional ionising radiation and chemotherapy. Thus, there is a strong need to gain more thorough insights into the molecular biology and genetics of chordoma to allow for the development of new therapeutic options. We performed an ultra-deep sequencing analysis to find novel mutations in cancer associated genes in chordomas to date unseen with Sanger sequencing.
  
  
  METHODS
  Nine chordomas (skull base (n=3), mobile spine (n=4), and sacrum/coccyx (n=2) were screened for mutations in 48 cancer genes using the Hot Spot Cancer Panel (Illumina). All putative mutations were compared against multiple databases (e.g. NCBI, COSMIC, PolyPhen, EGB, SIFT) and published Copy Number Variation (CNV) data for chordoma.
  
  
  RESULTS
  Our results showed mutations with a frequency above 5% in tumorsuppressor- and onco-genes, revealing new possible driver genes for chordomas. We detected three different variants accounting for 11 point mutations in three cancer associated genes (KIT, KDR and TP53). None of the detected mutations was found in all samples investigated. However, all genes affected interact or are connected in pathway analysis. There were no correlations to already reported CNVs in the samples analysed.
  
  
  CONCLUSIONS
  We identified mutations in the associated genes KIT, KDR, and TP53. These mutations have been described previously and have been predicted to be tolerated. Further results on a larger series are warranted. The driver mechanisms of chordoma still have to be identified.
authors.affiliation: 1. Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
authors.forename: Carina
authors.initials: C
authors.lastname: Fischer
authors.affiliation: 3. University College London Cancer Institute, 72 Huntley Street, London, WC1 6BT, UK. ; 5. Department of Orthopaedic Surgery, Medical University of Graz, Auenbruggerplatz 5, 8036 Graz, Austria.
authors.forename: Susanne
authors.initials: S
authors.lastname: Scheipl
authors.affiliation: 1. Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
authors.forename: Agnes
authors.initials: A
authors.lastname: Zopf
authors.affiliation: 1. Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
authors.forename: Norbert
authors.initials: N
authors.lastname: Niklas
authors.affiliation: 4. Division of Hematology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 38D, 8036 Graz, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Deutsch
authors.affiliation: 3. University College London Cancer Institute, 72 Huntley Street, London, WC1 6BT, UK.
authors.forename: Mette
authors.initials: M
authors.lastname: Jorgensen
authors.affiliation: 5. Department of Orthopaedic Surgery, Medical University of Graz, Auenbruggerplatz 5, 8036 Graz, Austria.
authors.forename: Birgit
authors.initials: B
authors.lastname: Lohberger
authors.affiliation: 5. Department of Orthopaedic Surgery, Medical University of Graz, Auenbruggerplatz 5, 8036 Graz, Austria.
authors.forename: Elke Verena
authors.initials: EV
authors.lastname: Froehlich
authors.affiliation: 5. Department of Orthopaedic Surgery, Medical University of Graz, Auenbruggerplatz 5, 8036 Graz, Austria.
authors.forename: Andreas
authors.initials: A
authors.lastname: Leithner
authors.affiliation: 1. Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Gabriel
authors.affiliation: 6. Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, 8036 Graz, Austria.
authors.forename: Bernadette
authors.initials: B
authors.lastname: Liegl-Atzwanger
authors.affiliation: 2. Center for Medical Research, Cell Culture Facility, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
authors.forename: Beate
authors.initials: B
authors.lastname: Rinner
keywords: cancer panel; chordoma; copy number; next-generation sequencing; somatic mutations