Impact and Characterization of Serial Structural Variations Across Humans and Great Apes

Authors

Wolfram Höps
Tobias Rausch
Michael Jendrusch
Jan O Korbel
Fritz J Sedlazeck

Publication Date

9-13-2024

Journal

Nature Communications

DOI

10.1038/s41467-024-52027-9

PMID

39266513

PMCID

PMC11393467

PubMedCentral® Posted Date

9-13-2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Humans, Animals, Hominidae, Genome, Human, Genomic Structural Variation, Genomics, Haplotypes, Genomic instability, Genomic instability

Abstract

Modern sequencing technology enables the systematic detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through a series of mutations, a phenomenon we refer to as serial SV (sSV), remain underexplored, posing 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 haplotype-resolved human genomes from 28 individuals 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, 22q11 and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently, after the human-ape split, and involved non-repeat-mediated processes in addition to non-allelic homologous recombination. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and suggesting broader implications for disease.

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