Mechanistic insights into 16p13.3 microdeletions encompassing TBC1D24 and ATP6V0C through advanced sequencing approaches

Abstract

Chromosomal microdeletions represent a complex class of genetic disorders. Recently, 16p13.3 microdeletions encompassing TBC1D24 and ATP6V0C have gained prominence as structural variants associated with neurodevelopmental disorders, but their occurrence mechanisms remain unexplored. We used a comprehensive range of sequencing technologies (mate pair genome sequencing, linked-pair genome sequencing, nanopore sequencing, targeted locus amplification (TLA), long range and nested PCR followed by Sanger sequencing), to map the exact 16p13.3 microdeletion breakpoints in eight previously reported individuals. Microdeletion breakpoints were successfully mapped in all patients using TLA, split read analysis, PCR/Sanger sequencing, or nanopore sequencing. Alu sequences and/or non-B DNA motifs were detected in all patients. Mechanistic analysis identified distinct pathways underlying these rearrangements. Noteworthy, two unrelated individuals carried identical microdeletions that might have been mediated by an atypical form of non-allelic homologous recombination, given the presence of a 639 bp sequence with 96.2% homology. Microhomology-mediated end-joining and non-homologous end-joining emerged as other mechanisms driving these 16p13.3 microdeletions, which differs from other studied contiguous gene deletion syndromes. This research contributes to a deeper understanding of microdeletion-associated disorder pathophysiology in medical genetics.