title: Determining the origin of synchronous multifocal bladder cancer by exome sequencing.
abstract: BACKGROUND
  Synchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration (clonal) or spontaneous transformation of multiple cells by carcinogens (field effect). It is unclear which model is correct, with several studies supporting both hypotheses. A potential cause of this uncertainty may be the small number of genetic mutations previously used to quantify the relationship between these tumours.
  
  
  METHODS
  To better understand the genetic lineage of these tumours we conducted exome sequencing of synchronous multifocal pTa urothelial bladder cancers at a high depth, using multiple samples from three patients.
  
  
  RESULTS
  Phylogenetic analysis of high confidence single nucleotide variants (SNV) demonstrated that the sequenced multifocal bladder cancers arose from a clonal origin in all three patients (bootstrap value 100 %). Interestingly, in two patients the most common type of tumour-associated SNVs were cytosine mutations of TpC* dinucleotides (Fisher's exact test p < 10(-41)), likely caused by APOBEC-mediated deamination. Incorporating these results into our clonal model, we found that TpC* type mutations occurred 2-5× more often among SNVs on the ancestral branches than in the more recent private branches (p < 10(-4)) suggesting that TpC* mutations largely occurred early in the development of the tumour.
  
  
  CONCLUSIONS
  These results demonstrate that synchronous multifocal bladder cancers frequently arise from a clonal origin. Our data also suggests that APOBEC-mediated mutations occur early in the development of the tumour and may be a driver of tumourigenesis in non-muscle invasive urothelial bladder cancer.
authors.affiliation: Department of Urology, School of Medicine, Koc University, Istanbul, Turkey. oacar@kuh.ku.edu.tr.|Department of Urology, VKF American Hospital, Istanbul, Turkey. oacar@kuh.ku.edu.tr.
authors.forename: Ömer
authors.initials: Ö
authors.lastname: Acar
authors.affiliation: Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. ezgi140@gmail.com.
authors.forename: Ezgi
authors.initials: E
authors.lastname: Özkurt
authors.affiliation: Department of Computer Engineering, Bilkent University, Ankara, Turkey. demirgulfem@gmail.com.
authors.forename: Gulfem
authors.initials: G
authors.lastname: Demir
authors.affiliation: School of Medicine, Koc University, Istanbul, Turkey. hsarac@ku.edu.tr.
authors.forename: Hilal
authors.initials: H
authors.lastname: Saraç
authors.affiliation: Department of Computer Engineering, Bilkent University, Ankara, Turkey. calkan@cs.bilkent.edu.tr.
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.affiliation: Department of Urology, School of Medicine, Koc University, Istanbul, Turkey. tesen@ku.edu.tr.|Department of Urology, VKF American Hospital, Istanbul, Turkey. tesen@ku.edu.tr.
authors.forename: Tarık
authors.initials: T
authors.lastname: Esen
authors.affiliation: Department of Biological Sciences, Middle East Technical University, Ankara, Turkey. somel.mehmet@gmail.com.
authors.forename: Mehmet
authors.initials: M
authors.lastname: Somel
authors.affiliation: School of Medicine, Koc University, Istanbul, Turkey. nlack@ku.edu.tr.
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Lack
mesh_terms: D000071479:APOBEC-1 Deaminase; D000368:Aged; D019070:Cell Lineage / Q000235:genetics; D003564:Cytidine Deaminase / Q000235:genetics*; D059472:Exome / Q000235:genetics; D005828:Genetics, Population; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009378:Neoplasms, Multiple Primary / Q000235:genetics* / Q000473:pathology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D001749:Urinary Bladder Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D000071479:APOBEC-1 Deaminase; C000605089:APOBEC1 protein, human; D003564:Cytidine Deaminase