Targeted Genomic Sequencing in Large Human Genes to Detect Induced Structural Variants

Partial inhibition of DNA replication leads to de novo copy number variant (CNV) formation throughout the genome, especially at common fragile sites (CFSs). We previously showed that these hotspots for genome instability reside in late-replicating domains associated with large, transcribed genes. In this study, we performed targeted, error-corrected genomic sequencing of multiple large genes in several human cell lines. The svCapture pipeline was used to call novel structural variant junctions in co-analyzed samples. Multiple samples were analyzed from cell populations under different replication stresses, with suppression of DNA repair pathways, and in different cell cycle stages, to determine the mechanisms underlying CNV formation at these loci. Data are provided as raw genome sequencing reads and processed multi-sample VCF files with sequenced junctions encoded as breakends.]]>