Analysis of Somatic Copy Number Alterations in Biliary Tract Carcinoma Using a Single Nucleotide Polymorphism Array

Abstract

Aim: Biliary tract carcinoma (BTC), including gall bladder carcinoma (GBC) and biliary duct carcinoma (BDC), has a poor prognosis. Comprehensive genomic profiling has important roles in evaluation of the carcinogenesis of BTC. Materials & methods: We examined somatic copy number alterations (SCNAs) using a single nucleotide polymorphism array system to analyze 36 BTC samples (11 GBCs and 25 BDCs). Results: In hierarchical cluster analysis, two clusters were identified (subgroup 1 with low SCNAs and subgroup 2 with high SCNAs). GBC was predominant in subgroup 1, whereas BDC was predominant in subgroup 2, suggesting that GBC and BDC had different genetic backgrounds in terms of SCNAs. Conclusion: These findings could be helpful for establishing the molecular carcinogenesis of BTCs.

Lay abstract

Biliary tract carcinoma, including gall bladder carcinoma (GBC) and biliary duct carcinoma (BDC), has a poor prognosis. Comprehensive genomic (single nucleotide polymorphism-array) profiling plays important roles in evaluation of the carcinogenesis of biliary tract carcinoma. In the hierarchical cluster analysis, two clusters were identified (subgroup 1 with low somatic copy number alterations [SCNAs] and subgroup 2 with high SCNAs); GBC was found to be predominant in subgroup 1, whereas BDC was predominant in subgroup 2. These findings suggested that GBC and BDC had different genetic backgrounds in terms of SCNAs.

Keywords:

• bile duct cancer
• biliary tract carcinoma
• carcinogenesis
• cluster analysis
• crypt isolation method
• gall bladder cancer
• molecular alteration
• prognosis
• single nucleotide polymorphism array
• somatic copy number alteration

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2144/fsoa-2021-0057

Author contributions

Y Shioi, who is the first author, collected the samples. T Sugai, who is the corresponding author, contributed to the preparation of the manuscript, including all aspects of the data collection and analysis. M Osakabe performed all data collection and statistical analyses. N Yanagawa helped with interpretation of the pathological findings. H Nitta and A Sasaki provided clinical support during the preparation of the manuscript.

Acknowledgments

We gratefully acknowledge the technical assistance of E Sugawara and C Ishikawa. We also thank the members of the Department of Molecular Diagnostic Pathology, Iwate Medical University for their support.

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

Informed consent was obtained from each patient according to institutional guidelines, and the research protocols were approved by the ethics committee of Iwate Medical University Hospital (reference no.: HG20–22).

Availability of data & materials

The data that support the findings of this study are available on request from the corresponding author.