GRCh38 · COSMIC v94

Summary

This section shows a summary for the selected study (COSU identifier) or publication (COSP identifier). Studies may have been performed by the Sanger Institute Cancer Genome Project, or imported from the ICGC/TCGA. You can see more information on the help pages.

Reference
Whole-exome sequencing identified mutational profiles of squamous cell carcinomas of anus.
Paper ID
COSP45172
Authors
Shin S, Park HC, Kim MS, Han MR, Lee SH, Jung SH, Lee SH and Chung YJ
Affiliation
Department of Microbiology, The Catholic University of Korea, Seoul, Republic of Korea; Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, Republic of Korea.
Journal
Human pathology, 2018
ISSN: 1532-8392
PMID: 29555573 (view at PubMed or Europe PMC)
Abstract
Anal squamous cell carcinoma (ASCC), either with human papillomavirus (HPV) (+) or (-), is a neoplastic disease with frequent recurrence and metastasis. To characterize ASCC genomes, we attempted to disclose novel alterations of ASCC genomes as well as other genetic features including mutation signatures. We performed whole-exome sequencing and copy number alteration (CNA) profiling for 8 ASCC samples from 6 patients (2 cases with primary and recurrent/metastatic tumors). We found known ASCC mutations (TP53, CDKN2A and PIK3CA) and CNAs (gains on 3q and 19q and losses on 11q and 13q). In addition, we discovered novel mutations in HRAS and ARID1A and CNAs (gain on 8q and losses 5q, 9p, 10q and 19p) that had not been reported in ASCCs. We identified 4 signature patterns of the mutations (signatures 1 and 2 with deamination of 5-methyl-cytosin, signature 3 with APOBEC and signature 4 with mismatch repair) in the ASCCs. While the signatures 1-3 have been detected in other SCCs, the signature 4 was first identified in ASCCs. In addition, we first found that ASCCs harbored chromothripsis, copy-neutral losses of heterozygosity and focal amplification of KLF5 super-enhancer. Analyses of primary and recurrent/metastatic pair genomes revealed that driver events in development and progression of ASCC might not be uniform. Our data indicate that ASCCs may have similar mutation and CNA profiles to other SCCs, but that there are unique genomic features of ASCCs as well. Our data may provide useful information for ASCC pathogenesis as well as for developing clinical strategies for ASCC.
Paper Status
Curated