Detection of genome-wide methylation changes in bladder cancer in urinary DNA | LC26

Abstract
Non-invasive urine-based tests for bladder cancer (BC) have the potential to reduce reliance on flexible cystoscopy for both diagnosis and surveillance. Most recent advances in urine testing have focused on targeted detection of genomic and/or epigenomic markers. We hypothesised that long-read whole-genome sequencing of urinary DNA, combined with direct methylation profiling, could enable accurate BC detection while providing insights into disease biology. We now have demonstrated feasibility of this approach: we applied long-read whole-genome sequencing with direct methylation detection to urine cell pellet DNA (ucpDNA) from 21 haematuria clinic patients, including 13 BC cases and 8 non-BC controls. Differentially methylated regions were identified and their ability to discriminate between BC and non-BC samples, as well as the affected cellular pathways, was assessed using principal component analysis, hierarchical clustering, and gene set enrichment analysis. Sequencing of a single ucpDNA sample per flow cell achieved read depths of 18–34x, and BC-associated methylation signatures remained detectable at lower depths (2–5x) using multiplex sequencing. We observed global hypomethylation alongside cancer-specific promoter hypermethylation patterns in urine from BC patients, as well as copy number alterations in ucpDNA from BC patients. Although the study is limited by the small sample size, the detection of cancer-specific molecular features demonstrates the general feasibility of obtaining informative cancer (epi-)genomes out of urine using Oxford Nanopore technology. Future work will focus on developing predictive models for early bladder cancer detection.

Biography
Bioinformatician by training, Roland completed his PhD in Munich, followed by post-doctoral positions in Toronto, and then as senior bioinformatician at the Wellcome Trust Centre for Human Genetics, Oxford. Since 2017, Roland has been a Research Fellow/Group Leader at the Institute for Cancer and Genomic Sciences, University of Birmingham, and is the Bioinformatics and Genomics Theme Lead for the Bladder Cancer Centre, Birmingham.