Clinical Exome Gene Panel Analysis of a Cohort of Urothelial Bladder Cancer Patients from Sri Lanka

Malalasekera, Ajith; Neththikumara, Nilaksha; Somasundaram, Praveenan; Pathirana, Sajeewani; Ediriweera, Chathumadavi; Ediriweera, Dileepa; Goonewardena, Serozsha AS; Perera, Neville D; Abeygunasekara, Anuruddha; Jayasekara, Rohan W; Wettasinghe, Kalum; Lokuhetty, M Dilani S; Dissanayeke, Vajira H W

doi:10.31557/APJCP.2023.24.5.1533

Clinical Exome Gene Panel Analysis of a Cohort of Urothelial Bladder Cancer Patients from Sri Lanka

Document Type : Research Articles

Authors

¹ Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.

² Department of Biology, The University of Akron, OH, USA.

³ Health Data Science Unit, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.

⁴ Department of Urology, National Hospital of Sri Lanka, Colombo, Sri Lanka.

⁵ Department of Urology, Colombo South Teaching Hospital, Kalubowila, Sri Lanka.

⁶ Department of Pathology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.

10.31557/APJCP.2023.24.5.1533

Abstract

Background: Bladder cancer has a high rate of recurrence and high mortality rates in those who progress to muscle invasive disease. Biomarkers and molecular sub classification of tumours beyond standard histopathology has been proposed to address therapeutic dilemmas. The Cancer Genome Atlas project and other studies have contributed to the enhanced knowledge base of the mutational landscape of urothelial bladder cancer. Once again, these are mostly from Caucasian and Chinese patients, with data from the rest of Asia and Sri Lanka being sparse. The objective of this study was to assess the genomic variations of a cohort of urothelial bladder cancer patients in Sri Lanka. Methods: The molecular genetic study was conducted on formalin fixed paraffin embedded tumour samples of 24 patients, prospectively enrolled from 2013 to 2017. The samples were sequenced and variant distribution performed based on a 70-gene panel. Results: Total number of filtered mutations in the 24 patients was 10453. Median mutations per patient were 450 (range 22-987). The predominant mutational change was C>T and G>A. The top 5 mutated genes in our cohort were SYNE1, SYNE2, KMT2C, LRP2, and ANK2. The genes were clustered into 3 groups dependent on the number of mutations per patient per gene. The genes of cluster 1 and 2 mapped to Chromatin modifying enzymes and Generic Transcription Pathway. The chromatin remodelling pathway accounted for the largest proportion (22%) of mutations. Conclusions: Clinical exome sequencing utilising a gene panel yielded a high mutation rate in our patients. The predominant mutational change was C>T and G>A. Three clusters of genes were identified. SYNE1 was the gene with the most mutations. The mutations comprised predominantly of genes of the chromatin remodelling pathway.

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