Cytogenetically visible inversions are formed by multiple molecular mechanisms.

Cytogenetically detected inversions are generally assumed to be copy number and phenotypically neutral events. While non-allelic homologous recombination (NAHR) is thought to play a major role, recent data suggest the involvement of other molecular mechanisms in inversion formation. Using a combination of short-read whole genome sequencing (WGS), 10X Genomics Chromium WGS, droplet digital PCR and array comparative genomic hybridization we investigated the genomic structure of 18 large unique cytogenetically detected chromosomal inversions and achieved nucleotide resolution of at least one chromosomal inversion junction for 13/18 (72%). Surprisingly, we observed that seemingly copy number neutral inversions can be accompanied by copy-number gain of up to 350 kb and local genomic complexities (3/18, 17%). In the remaining resolved inversions, the mutational signatures are consistent with non-homologous end-joining (NHEJ) (8/13, 62%) and microhomology-mediated break-induced replication (MMBIR) (5/13, 38%). Our study indicates that short-read 30x coverage WGS can detect a substantial fraction of chromosomal inversions. Moreover, replication-based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy-number variation potentially contributing to the overall phenotypic presentation of those patients. This article is protected by copyright. All rights reserved.