Comprehensive analysis of osteosarcoma genomes and transcriptomes using long-read sequencing technologies

Long-read sequencing (LRS) technologies permit to continuously read individual DNA/RNA molecules over long stretches of DNA (>10kb), thus providing unparalleled information to resolve complex structural variants (SVs), the repertoire of RNA isoforms and gene fusions at single-haplotype resolution, and infer methylation profiles. Despite these advantages, LRS has not been applied to analyse sarcoma genomes yet, in which complex SVs undetectable by Illumina sequencing and mediating gene fusion formation and oncogene amplification abound, as we have recently shown (Cortes-Ciriano et al., Nature Genetics, In press).
In this project, we will perform long-read whole-genome and transcriptome sequencing, as well as methylation profiling, to reconstruct the genomic architecture and identify aberrant gene fusions in 12 osteosarcomas, a sarcoma type for which survival and therapeutic options have not improved much over the last decades. We will firstly reconstruct the genomic architecture of complex rearrangements, including extrachromosomal elements mediating oncogene amplification and neochromosomes. Secondly, we will explore the impact of SVs on gene expression and their potential as a source of neoantigens by performing matched long-read RNA sequencing. Thirdly, will link methylation data with genomic and transcriptomic alterations to assess the functional impact of non-coding SVs, and epigenomic changes. Through the integration of long-read whole-genome, transcriptome, and methylation data this project will contribute to, for the first time, fully resolve the landscape of complex SVs and their functional impact in osteosarcomas, all of which will provide novel insights into the unique biology and genomic architecture of these tumours and uncover new vulnerabilities that could be potentially exploited for the development of novel therapeutics.