title: TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen.
abstract: BACKGROUND
  A substantial proportion of cancer cases present with a metastatic tumor and require further testing to determine the primary site; many of these are never fully diagnosed and remain cancer of unknown primary origin (CUP). It has been previously demonstrated that the somatic point mutations detected in a tumor can be used to identify its site of origin with limited accuracy. We hypothesized that higher accuracy could be achieved by a classification algorithm based on the following feature sets: 1) the number of nonsynonymous point mutations in a set of 232 specific cancer-associated genes, 2) frequencies of the 96 classes of single-nucleotide substitution determined by the flanking bases, and 3) copy number profiles, if available.
  
  
  METHODS
  We used publicly available somatic mutation data from the COSMIC database to train random forest classifiers to distinguish among those tissues of origin for which sufficient data was available. We selected feature sets using cross-validation and then derived two final classifiers (with or without copy number profiles) using 80 % of the available tumors. We evaluated the accuracy using the remaining 20 %. For further validation, we assessed accuracy of the without-copy-number classifier on three independent data sets: 1669 newly available public tumors of various types, a cohort of 91 breast metastases, and a set of 24 specimens from 9 lung cancer patients subjected to multiregion sequencing.
  
  
  RESULTS
  The cross-validation accuracy was highest when all three types of information were used. On the left-out COSMIC data not used for training, we achieved a classification accuracy of 85 % across 6 primary sites (with copy numbers), and 69 % across 10 primary sites (without copy numbers). Importantly, a derived confidence score could distinguish tumors that could be identified with 95 % accuracy (32 %/75 % of tumors with/without copy numbers) from those that were less certain. Accuracy in the independent data sets was 46 %, 53 % and 89 % respectively, similar to the accuracy expected from the training data.
  
  
  CONCLUSIONS
  Identification of primary site from point mutation and/or copy number data may be accurate enough to aid clinical diagnosis of cancers of unknown primary origin.
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, DK-2800, Lyngby, Denmark. marquard@cbs.dtu.dk.
authors.forename: Andrea Marion
authors.initials: AM
authors.lastname: Marquard
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, DK-2800, Lyngby, Denmark. njuul@cbs.dtu.dk.|Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK. njuul@cbs.dtu.dk.
authors.forename: Nicolai Juul
authors.initials: NJ
authors.lastname: Birkbak
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, DK-2800, Lyngby, Denmark. cecilia.thomas@cpr.ku.dk.|NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark. cecilia.thomas@cpr.ku.dk.
authors.forename: Cecilia Engel
authors.initials: CE
authors.lastname: Thomas
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, DK-2800, Lyngby, Denmark. favero@cbs.dtu.dk.
authors.forename: Francesco
authors.initials: F
authors.lastname: Favero
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, DK-2800, Lyngby, Denmark. marcin@cbs.dtu.dk.
authors.forename: Marcin
authors.initials: M
authors.lastname: Krzystanek
authors.affiliation: Inserm Unit U981, Gustave Roussy, Villejuif, France. Celine.LEFEBVRE@gustaveroussy.fr.
authors.forename: Celine
authors.initials: C
authors.lastname: Lefebvre
authors.affiliation: Inserm Unit U981, Gustave Roussy, Villejuif, France. Charles.FERTE@gustaveroussy.fr.|Department of Medical Oncology, Gustave Roussy, Villejuif, France. Charles.FERTE@gustaveroussy.fr.
authors.forename: Charles
authors.initials: C
authors.lastname: Ferté
authors.affiliation: Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK. m.jamal-hanjani@ucl.ac.uk.
authors.forename: Mariam
authors.initials: M
authors.lastname: Jamal-Hanjani
authors.affiliation: Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK. gareth.wilson@ucl.ac.uk.
authors.forename: Gareth A
authors.initials: GA
authors.lastname: Wilson
authors.affiliation: Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK. s.shafi@ucl.ac.uk.
authors.forename: Seema
authors.initials: S
authors.lastname: Shafi
authors.affiliation: Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK. c.swanton@ucl.ac.uk.|Cancer Research UK London Research Institute, London, UK. c.swanton@ucl.ac.uk.
authors.forename: Charles
authors.initials: C
authors.lastname: Swanton
authors.affiliation: Inserm Unit U981, Gustave Roussy, Villejuif, France. Fabrice.ANDRE@gustaveroussy.fr.|Department of Medical Oncology, Gustave Roussy, Villejuif, France. Fabrice.ANDRE@gustaveroussy.fr.
authors.forename: Fabrice
authors.initials: F
authors.lastname: André
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, DK-2800, Lyngby, Denmark. zoltan@cbs.dtu.dk.|Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, USA. zoltan@cbs.dtu.dk.
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Szallasi
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, DK-2800, Lyngby, Denmark. eklund@cbs.dtu.dk.
authors.forename: Aron Charles
authors.initials: AC
authors.lastname: Eklund
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D030541:Databases, Genetic; D005260:Female; D052138:Genes, Neoplasm; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D009928:Organ Specificity; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide