Comprehensive somatic genome alterations of urachal carcinoma.
- Author : Seungchul Lee#, Jingu Lee#, Sung Hoon Sim#, Yeonghun Lee, Kyung Chul Moon, Cheol Lee, Woong-Yang Park, Nayoung K. D. Kim, Se-Hoon Lee$, and Hyunju Lee$
- Published Date : 2017
- Category : Bioinformatics and Text Mining
- Place of publication : Journal of Medical Genetics
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 characterization 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 OncoScanTM platform (Affymetrix) as follows: tumour-normal paired sequencing (WES, n = 10), tumour-only sequencing (WES, n = 1; targeted deep sequencing, n = 16), and OncoScanTM (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 amplifica tion was highly associated with the patient’s cancer stage. Interestingly, 35% (6/17) of the patients had focal DNA amplifications in FGFR family genes. The integration of somatic SNVs, indels, and SCNAs revealed significant alterations in the MAPK signalling pathways.
Conclusions: Our genome wide analysis of urachal cancer suggests that molecular characteristics may be important for the treatment of urachal cancer.
- Paper: Link