title: Comprehensive somatic genome alterations of urachal carcinoma.
abstract: Urachal cancer is a rare cancer that develops in the urachus. Because of its rarity, standard treatment therapies for urachal cancer are not established, and chemotherapeutic regimens for bladder cancer have been unsuccessful for patients with urachal cancer. Hence, we aim to understand a systematic molecular characterisation of urachal cancer.
  
  
  
  We identified somatic single-nucleotide variations (SNVs)/indels and somatic copy number aberrations (SCNAs) in the 17 patients by using whole-exome sequencing (WES) and OncoScan platform (Affymetrix) as follows: tumour-normal paired sequencing (WES, n=10), tumour-only sequencing (WES, n=1; targeted deep sequencing, n=16), and OncoScan (n=17).
  
  
  
  Our analyses identified 27 genes with somatic SNVs and indels, as well as six genes (APC, COL5A1, KIF26B, LRP1B, SMAD4 and TP53) that were recurrent in at least two patients. By analysing the SCNAs, we found that the extent of chromosomal amplification was highly associated with the patient's cancer stage. Interestingly, 35% (6/17) of the patients had focal DNA amplifications in fibroblast growth factor receptor family genes. The integration of somatic SNVs, indels and SCNAs revealed significant alterations in the mitogen-activated protein kinase signalling pathways.
  
  
  
  Our genome-wide analysis of urachal cancer suggests that molecular characteristics may be important for the treatment of urachal cancer.
authors.affiliation: School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea.
authors.forename: Seungchul
authors.initials: S
authors.lastname: Lee
authors.affiliation: School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea.
authors.forename: Jingu
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, South Korea.|Center for Breast Cancer, National Cancer Center, Gyeonggi-do, South Korea.
authors.forename: Sung Hoon
authors.initials: SH
authors.lastname: Sim
authors.affiliation: School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea.
authors.forename: Yeonghun
authors.initials: Y
authors.lastname: Lee
authors.affiliation: Department of Pathology, Seoul National University Hospital, Seoul, South Korea.
authors.forename: Kyung Chul
authors.initials: KC
authors.lastname: Moon
authors.affiliation: Department of Pathology, Seoul National University Hospital, Seoul, South Korea.
authors.forename: Cheol
authors.initials: C
authors.lastname: Lee
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.|Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea.|Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea.
authors.forename: Woong-Yang
authors.initials: WY
authors.lastname: Park
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.
authors.forename: Nayoung Kd
authors.initials: NK
authors.lastname: Kim
authors.affiliation: Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, South Korea.|Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea.|Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
authors.forename: Se-Hoon
authors.initials: SH
authors.lastname: Lee
authors.affiliation: School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea.
authors.forename: Hyunju
authors.initials: H
authors.lastname: Lee
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D056915:DNA Copy Number Variations / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D055106:Genome-Wide Association Study; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics; D020935:MAP Kinase Signaling System / Q000235:genetics; D008875:Middle Aged; D009367:Neoplasm Staging; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017468:Receptors, Fibroblast Growth Factor / Q000235:genetics*; D001749:Urinary Bladder Neoplasms / Q000235:genetics* / Q000503:physiopathology; D000073359:Exome Sequencing
chemical_list: D017468:Receptors, Fibroblast Growth Factor
keywords: MAPK signalling pathway; Somatic copy number aberrations; Somatic mutations; Urachal cancer; Whole exome sequencing