Genome-wide reconstruction of complex structural variants using read clouds

Microfluidic partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, retains long-range information in short sequencing reads. Such read cloud approaches represent a powerful and cost-effective alternative to single-molecule long-read sequencing. We developed GROC-SVs, which uses read clouds for structural variant detection and assembly, and apply it to Illumina-sequenced 10× Genomics sarcoma and breast cancer data sets. Validation demonstrates substantial improvement in specificity of breakpoint detection compared to short-fragment sequencing, at comparable sensitivity, and vice versa. The long-range information also facilitates sequence assembly of breakpoints; importantly, consecutive breakpoints closer than the average length of the input DNA molecules can be assembled, with some events exhibiting remarkable complexity. We show that chromothriptic rearrangements occurred before copy number amplifications and that single-nucleotide and structural variants are not correlated. We predict significant advances in structural variant science using 10×/GROC-SVs and other read cloud-specific methods.