Improving diagnosis in Li-Fraumeni syndrome using long-read whole-genome and integrated multiomic sequencing | LC26

Abstract
Li-Fraumeni syndrome (LFS) is a rare but highly penetrant hereditary cancer predisposition disorder classically caused by germline pathogenic variants in the TP53 tumour suppressor gene. Individuals with LFS face markedly elevated lifetime cancer risks and often develop early onset or multiple primary tumours across a wide spectrum. Despite this strong genotype–phenotype association, a substantial proportion of clinically suspected LFS cases remain unresolved following short-read sequencing due to TP53 variants that may be mosaic, deep intronic, structural, or otherwise cryptic to conventional methods. Here, we describe an ongoing study evaluating the potential of Oxford Nanopore Technologies long-read whole-genome sequencing (WGS) to increase diagnostic yield in this unresolved subset. We are performing long-read WGS on blood samples from a cohort of 290 individuals from the International Sarcoma Kindred Study with strong clinical suspicion of LFS but negative prior short-read testing. Long-read sequencing enables comprehensive detection of structural variation, complex rearrangements, repeat expansions, and difficult to resolve genomic regions that may harbour previously undetectable alterations or pathogenic mechanisms relevant to an LFS like phenotype. In parallel, a subset of 50 matched samples from this cohort will undergo true multiomic analysis. By sequencing genomic DNA and cDNA on a single nanopore flow cell, this integrated approach allows simultaneous interrogation of genomic sequence, transcript structure, and epigenetic signatures from the same sample. This design aims to determine whether transcriptomic or epigenomic signals, such as allele specific expression, aberrant splicing, or dysregulated p53 related pathways, can provide diagnostic insight in cases where genome-level analysis remains inconclusive. Together, this work will evaluate the utility of long-read WGS and integrated multiomic sequencing for improving diagnostic yield in hereditary cancer syndromes, with the goal of resolving currently unexplained LFS-like presentations that lack identifiable TP53 mutations using standard testing.

Biography
David Thomas is the inaugural Director of the Centre for Molecular Oncology at the University of New South Wales and Chief Strategy and Science Officer at Omico. As a clinician-scientist, his focus is on the application of genomic technologies to the understanding and management of cancer, particularly sarcoma. He established the not-for-profit company, Australian Genomic Cancer Medicine Centre, trading as Omico, to lead a national precision medicine program for patients with rare and early onset cancers. He has over 200 research publications, including lead or senior author papers in Science, Cancer Cell, Journal of Clinical Investigation, and The Lancet Oncology.