NCM 2023 Singapore: Investigating structural variations and complex cancer genomes using Oxford Nanopore sequencing

Widespread genomic aberrations are a hallmark of many cancer types. Despite their contribution to oncogenesis, the identification of complex driver events such as structural variants (SV) in cancer remains challenging. Short-read whole-genome sequencing (WGS) technologies have limited ability to handle SVs and complex genomes. Here we performed Oxford Nanopore WGS on tumour samples from childhood cancers and oesophageal adenocarcinoma. We developed an in-house consensus analysis workflow to identify consensus and somatic structural variations. Additionally, we utilized de novo assembly to delve deeper into cancer genome structure and misassembled regions associated with the identified consensus SV calls. The de novo assembly approach effectively covered up to 84% of the genome fraction based on the hg38 reference genome. By comparing our findings with available Illumina short-read WGS data, we discovered novel or improved genomic events using Oxford Nanopore sequencing. The long-read sequencing analysis uncovered multiple complex genomic events, providing higher-resolution insights into cancer-driver genes such as ERBB4, MAP2, IDH1, CASP8, BMPR2 and GATA3. Furthermore, we identified actionable variants such as KIAA1549-BRAF fusion genes with therapeutic implications. This investigation showcases the utility of Oxford Nanopore sequencing for comprehensive analysis of structural variations and complex cancer genomes. Our results contribute valuable insights into the field of nanopore sequencing analysis and shed light on the identification of novel driver events, thereby enhancing our understanding of tumorigenesis and offering potential avenues for therapeutic intervention.