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Cancer genetics
Comprehensive somatic genome alterations of urachal carcinoma
  1. Seungchul Lee1,
  2. Jingu Lee1,
  3. Sung Hoon Sim2,3,
  4. Yeonghun Lee1,
  5. Kyung Chul Moon4,
  6. Cheol Lee4,
  7. Woong-Yang Park5,6,7,
  8. Nayoung KD Kim5,
  9. Se-Hoon Lee2,6,8,
  10. Hyunju Lee1
  1. 1 School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, South Korea
  2. 2 Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, South Korea
  3. 3 Center for Breast Cancer, National Cancer Center, Gyeonggi-do, South Korea
  4. 4 Department of Pathology, Seoul National University Hospital, Seoul, South Korea
  5. 5 Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
  6. 6 Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea
  7. 7 Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
  8. 8 Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
  1. Correspondence to Professor Se-Hoon Lee, Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, 81 Irwon-Ro Gangnam-gu, Seoul 06351, South Korea; sehoon.lee119{at}gmail.com and Professor Hyunju Lee, School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, South Korea; hyunjulee{at}gist.ac.kr

Abstract

Background 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.

Methods 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).

Results 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.

Conclusions Our genome-wide analysis of urachal cancer suggests that molecular characteristics may be important for the treatment of urachal cancer.

  • Urachal cancer
  • Whole exome sequencing
  • Somatic mutations
  • Somatic copy number aberrations
  • MAPK signalling pathway

https://doi.org/10.1136/jmedgenet-2016-104390

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    Footnotes

    • Contributors Study conception and design: HL and SHL. Acquisition of data: SHS, KCM, CL, WYP and NKDK. Data analysis and interpretation: SCL, JGL, SHS, YHL, SHL and HL. Writing of the manuscript: SCL, JGL, SHS, YHL, SHL and HL. Study supervision: HL and SHL. All authors read and approved the final manuscript.

    • Funding This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) (NRF-2016R1A2B2013855), and supported by the MSIP (The Ministry of Science, ICT and Future Planning), Korea and Microsoft Research, under ICT/SW Creative research programme supervised by the IITP (Institute for Information & Communications Technology Promotion) (IITP-2015-R2212-15-0012).

    • Competing interests None declared.

    • Patient consent For the use of tissues obtained since February 2013, the documented consent was obtained from the patients.

    • Ethics approval The study protocol was reviewed and approved by the Institutional Review Board of Seoul National University Hospital (an approval number: H-1312-100-544). According to the revised law of Bioethics and Safety Act in Korea, the use of human tissue specimen obtained before February 2013 was exempt from informed consent.

    • Provenance and peer review Not commissioned; externally peer reviewed.