title: Exome-wide Sequencing Shows Low Mutation Rates and Identifies Novel Mutated Genes in Seminomas.
abstract: BACKGROUND
  Testicular germ cell tumors are the most common cancer diagnosed in young men, and seminomas are the most common type of these cancers. There have been no exome-wide examinations of genes mutated in seminomas or of overall rates of nonsilent somatic mutations in these tumors.
  
  
  OBJECTIVE
  The objective was to analyze somatic mutations in seminomas to determine which genes are affected and to determine rates of nonsilent mutations.
  
  
  METHODS
  Eight seminomas and matched normal samples were surgically obtained from eight patients.
  
  
  METHODS
  DNA was extracted from tissue samples and exome sequenced on massively parallel Illumina DNA sequencers. Single-nucleotide polymorphism chip-based copy number analysis was also performed to assess copy number alterations.
  
  
  METHODS
  The DNA sequencing read data were analyzed to detect somatic mutations including single-nucleotide substitutions and short insertions and deletions. The detected mutations were validated by independent sequencing and further checked for subclonality.
  
  
  CONCLUSIONS
  The rate of nonsynonymous somatic mutations averaged 0.31 mutations/Mb. We detected nonsilent somatic mutations in 96 genes that were not previously known to be mutated in seminomas, of which some may be driver mutations. Many of the mutations appear to have been present in subclonal populations. In addition, two genes, KIT and KRAS, were affected in two tumors each with mutations that were previously observed in other cancers and are presumably oncogenic.
  
  
  CONCLUSIONS
  Our study, the first report on exome sequencing of seminomas, detected somatic mutations in 96 new genes, several of which may be targetable drivers. Furthermore, our results show that seminoma mutation rates are five times higher than previously thought, but are nevertheless low compared to other common cancers. Similar low rates are seen in other cancers that also have excellent rates of remission achieved with chemotherapy.
  
  
  RESULTS
  We examined the DNA sequences of seminomas, the most common type of testicular germ cell cancer. Our study identified 96 new genes in which mutations occurred during seminoma development, some of which might contribute to cancer development or progression. The study also showed that the rates of DNA mutations during seminoma development are higher than previously thought, but still lower than for other common solid-organ cancers. Such low rates are also observed among other cancers that, like seminomas, show excellent rates of disease remission after chemotherapy.
authors.affiliation: Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore; Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.
authors.forename: Ioana
authors.initials: I
authors.lastname: Cutcutache
authors.affiliation: Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore; Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Medical Oncology, National Cancer Centre Singapore, Singapore; Genome Institute of Singapore, A*STAR, Singapore.
authors.forename: Iain Beehuat
authors.initials: IB
authors.lastname: Tan
authors.affiliation: Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore; Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.
authors.forename: Subhashini
authors.initials: S
authors.lastname: Ramgopal
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.
authors.forename: Shenli
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.
authors.forename: Kalpana
authors.initials: K
authors.lastname: Ramnarayanan
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore; Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.
authors.forename: Anna
authors.initials: A
authors.lastname: Gan
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore; Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.
authors.forename: Heng Hong
authors.initials: HH
authors.lastname: Lee
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.
authors.forename: Su Ting
authors.initials: ST
authors.lastname: Tay
authors.affiliation: Laboratory of Interdisciplinary Renal Oncology, Van Andel Research Institute, Grand Rapids, MI, USA.
authors.forename: Aikseng
authors.initials: A
authors.lastname: Ooi
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.
authors.forename: Choon Kiat
authors.initials: CK
authors.lastname: Ong
authors.affiliation: Division of Urology, Spectrum Health Hospital System, Grand Rapids, MI, USA.
authors.forename: Jonathan T
authors.initials: JT
authors.lastname: Bolthouse
authors.affiliation: Division of Urology, Spectrum Health Hospital System, Grand Rapids, MI, USA.
authors.forename: Brian R
authors.initials: BR
authors.lastname: Lane
authors.affiliation: Division of Urology, Spectrum Health Hospital System, Grand Rapids, MI, USA.
authors.forename: John G
authors.initials: JG
authors.lastname: Anema
authors.affiliation: Division of Urology, Spectrum Health Hospital System, Grand Rapids, MI, USA.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Kahnoski
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore; Genome Institute of Singapore, A*STAR, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore. Electronic address: gmstanp@duke-nus.edu.sg.
authors.forename: Patrick
authors.initials: P
authors.lastname: Tan
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore; Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore. Electronic address: teh.bin.tean@singhealth.com.sg.
authors.forename: Bin Tean
authors.initials: BT
authors.lastname: Teh
authors.affiliation: Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore; Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore. Electronic address: steve.rozen@duke-nus.edu.sg.
authors.forename: Steven G
authors.initials: SG
authors.lastname: Rozen
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics; D000293:Adolescent; D000328:Adult; D015820:Cadherins / Q000235:genetics; D016022:Case-Control Studies; D047390:Casein Kinase II / Q000235:genetics; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics; D056915:DNA Copy Number Variations; D004265:DNA Helicases / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D059472:Exome / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D059645:Mutation Rate; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics; D018239:Seminoma / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013736:Testicular Neoplasms / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D000251:Adenosine Triphosphatases; D015820:Cadherins; D047390:Casein Kinase II; D002868:Chromosomal Proteins, Non-Histone; D004265:DNA Helicases; D004268:DNA-Binding Proteins; D019869:Phosphatidylinositol 3-Kinases; D019009:Proto-Oncogene Proteins c-kit; D016283:Proto-Oncogene Proteins p21(ras); D025521:Tumor Suppressor Proteins; C490584:CDH17 protein, human; C117307:KRAS protein, human; C067857:MCC protein, human; C560566:phosphoinositol-3 kinase regulatory subunit 2, human; C570325:CSNK2A1 protein, human; C409462:SMARCA5 protein, human; C080359:CHD1 protein, human
keywords: Copy number; Exome sequencing; Germ cell tumor; KIT; KRAS; Somatic mutation; Testicular cancer