Dataset Information

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.

SUBMITTER: Shioi Y

PROVIDER: S-EPMC8656348 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Publications

Analysis of somatic copy number alterations in biliary tract carcinoma using a single nucleotide polymorphism array.

Shioi Yoshihiro Y Osakabe Mitsumasa M Yanagawa Naoki N Nitta Hiroyuki H Sasaki Akira A Sugai Tamotsu T

Future science OA 20211115 1

<h4>Aim</h4>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.<h4>Materials & methods</h4>We examined somatic copy number alterations (SCNAs) using a single nucleotide polymorphism array system to analyze 36 BTC samples (11 GBCs and 25 BDCs).<h4>Results</h4>In hierarchical cluster analysis, two clusters were identified (subgrou ...[more]

PMID: 34900340

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Project description:Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. We conducted longitudinal whole-genome sequencing of 37 tumor samples from 8 patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and a metastatic or relapse site. Subclonal copy-number alterations were identified in all patients except one. In 5 patients, subclones from the primary tumor emerged and dominated at subsequent relapses. MYC gain/amplification was enriched in the treatment-resistant clones in 6 of 7 patients with multiple clones. Amplifications in other potential driver genes, such as CCNE1, RAD21, VEGFA, and IGF1R, were also observed in the resistant copy-number clones. A chromosomal duplication timing analysis revealed that complex genomic rearrangements typically occurred prior to diagnosis, supporting a macroevolutionary model of evolution, where a large number of genomic aberrations are acquired over a short period of time followed by clonal selection, as opposed to ongoing evolution. A mutational signature analysis of recurrent tumors revealed that homologous repair deficiency (HRD)-related SBS3 increases at each time point in patients with recurrent disease, suggesting that HRD continues to be an active mutagenic process after diagnosis. Overall, by examining the clonal relationships between temporally and spatially separated samples from patients with relapsed/refractory osteosarcoma, this study sheds light on the intratumor heterogeneity and potential drivers of treatment resistance in this disease.SignificanceThe chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

Dataset Information

Analysis of somatic copy number alterations in biliary tract carcinoma using a single nucleotide polymorphism array.

Aim

Materials & methods

Results

Conclusion

Publications

Analysis of somatic copy number alterations in biliary tract carcinoma using a single nucleotide polymorphism array.

Similar Datasets

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