The role of structural variation in promotion, evolution and treatment of various tumor types

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

Several collaborations within this project are currently ongoing. First, we are now finalizing the analysis of long-read sequencing of approximately 50 cancer cell lines, such as cervical, breast, lung and others. We have established a Nextflow pipeline to call small, structural and copy-number variants, and aiming to profile the landscape of oncogene amplification mechanisms on this dataset. The data and variant calls will be made publicly available, and we expect an initial preprint to become available in 2025. Second, we are continuing to work with Children's Mercy on using long-read sequencing as a genomic diagnostic test. We have now validated our long-read workflow on a cohort of pediatric blood cancer, where long-read approach showed high specificity and importantly improved sensitivity to cryptic, clinically-relevant fusions. Initial results are described in the preprint, we we are currently expanding the validation (https://www.medrxiv.org/content/10.1101/2024.11.05.24316078v1).