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

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.

Analysis of common genetic mutations in a cohort of children with salt wasting form of Congenital Adrenal Hyperplasia.

INTRODUCTION: Steroid hydroxylase deficiency due to CYP21A2 gene mutation is the most common cause of Congenital Adrenal Hyperplasia (CAH). Mutation spectrum in Sri Lankan CAH patients has not been investigated adequately. OBJECTIVES: This study attempted to study the spectrum of mutations in CYP21A2 gene in 30 patients with salt wasting form of CAH in Sri Lanka. METHODS: Allele specific polymerase chain reaction was carried out using mutation site specific primers for eight mutations (P30L, I2G, 8bp deletion, I172N, E6 cluster, V281L, Q318X and R356W) reported as frequently occurring in other populations. RESULTS: Fourteen patients had homozygous mutations; six patients were compound heterozygotes as determined by investigating parents of the patients, one patient had a large gene deletion which was previously reported and the remaining patients had at least one heterozygous mutation. The following allele frequencies were observed for each mutation P30L-10%, I2G- 40%, 8bp-18.33%, I172N-3.33%, E6 cluster- 5%, Q318X-40% and R356W-3.33%. V281L mutation was not observed in the study cohort. DNA sequencing revealed a novel mutation G292S in one patient. CONCLUSION: This is the first report describing a broad spectrum of mutations in CYP21A2 gene in Sri Lankan patients with CAH. Mutation frequencies did not vary from other ethnic groups reported around the world.