Nanopore-only telomere-to-telomere assembly of isochromosome 17q in childhood medulloblastoma | LC26

Abstract
Childhood cancer is characterised by chromosomal abnormalities, such as isochromosomes — chromosomes possessing two regions of centromeric sequence — which are frequent in childhood cancer. Genetic and functional consequences of isochromosomes remain poorly understood due to their complex and highly repetitive genetic landscapes. Here, we demonstrate that nanopore-only sequencing of cancer patient samples enables the telomere-to-telomere (T2T) assembly of complex chromosomal abnormalities, achieving base-level resolution of isochromosome architecture for the first time. We performed whole-genome sequencing of five retrospective tumour tissue and paired blood from individuals diagnosed with medulloblastoma. Libraries were prepared using the Ultra-Long DNA Sequencing Kit V14 (SQK-ULK114) or Ligation Sequencing Kit V14 (SQK-LSK114) and sequenced on a single PromethION Flow Cell. For a tumour harbouring an isochromosome 17q (i17q), an N50 of 31,696 kb and mean coverage of 59x was achieved, compared to 37,477 kb and 68x for the germline blood. Using hifiasm (ONT), we generated haplotype-resolved de novo assemblies of the i17q and the corresponding germline chromosome 17 (chr17) from which it arose. The resulting assemblies were comparable in completeness to existing T2T chr17 reference assemblies. Reconstruction of i17q breakpoints provided novel insights into the potential mechanism of formation. T2T assembly of complete centromeres for 47 chromosomes enabled the discovery of somatic epi/genetic features in highly repetitive regions for the first time. This revealed previously uncharacterised centromeric variation in the germline chr17 that preceded i17q formation. Together, these results establish a foundation for the investigation of isochromosomes and other complex chromosomal abnormalities in cancer from both solid tumour tissue and blood samples.

Biography
Eleanor Woodward is a PhD student at the Wolfson Childhood Cancer Centre, Newcastle University. Her research focuses on the genomics of childhood cancer, which often possess complex chromosomal rearrangements. Using nanopore sequencing and genome assembly techniques, Eleanor is able to elucidate the mechanism by which recurrent chromosomal aberrations arise and understand their consequence in childhood cancer.