Fig. 1

Study design and bioinformatics workflow for SV detection and integration. a Schematic overview of the study design. Two well-characterized reference cell lines (HCC1395 and HCC1395BL) were used to generate whole-genome sequencing data across five platforms (Illumina short reads, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and Dovetail Hi-C proximity ligation). Initial SV call sets were identified from each platform and combined together to identify high-confidence call sets. The SVs from high-confidence call sets were selected for PCR-based validation for deletion, insertion, intra-chromosomal inversion and inter-chromosomal translocation; copy number changes were validated by Affymetrix array. Large SVs (≥20kb) were validated using Bionano optical mapping. RNA-seq was used to validate the fusion gene and translocation events. b Schematic overview of the bioinformatics analysis workflow. Each platform’s data was processed by the aligner and SV caller specific to that platform. The tumor-only or somatic SV calls were selected by Survivor. The final call sets from each platform were integrated together using the Survivor software tool based a window-size approach and SV types