Impact and characterization of serial structural variations across humans and great apes

Modern sequencing technology enables the detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through series of mutations, a phenomenon we term serial SV (sSV), remain understudied since their complexity poses a challenge for SV discovery. Here, we present NAHRwhals (https://github.com/WHops/NAHRwhals), a method to infer repeat-mediated series of SVs in long-read genomic assemblies. Applying NAHRwhals to 58 haplotype-resolved human genomes reveals 37 sSV loci of various length and complexity. These sSVs explain otherwise cryptic variation in medically relevant regions such as the TPSAB1 gene, 8p23.1 and the DiGeorge and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently and involved non-repeat-mediated processes. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and revealing broader implications for disease than prior studies suggested.