Analysis of Loose Ends in Cancer Genome Structure

Short-read sequencing (SRS) forms the basis of our understanding of cancer genome evolution, yet it is widely thought to be inadequate for detecting structural variants (SVs). To understand the nature of cancer SVs missed by SRS, we introduce the concept of "loose ends" - sites of missing rearrangements revealed by balancing copy number (CN) across the genomic intervals and adjacencies of a genome graph.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001011047	Short read whole genome and long read Oxford Nanopore sequencing of matched tumor/normal material from 10 Melanoma and 1 case of TNBC.	Illumina NovaSeq 6000 PromethION	44

Publications	Citations
Most large structural variants in cancer genomes can be detected without long reads. Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, Imieliński M. Nat Genet 55: 2023 2139-2148	8