Abstract
Chromosomal microdeletions represent a complex class of genetic disorders. Recently, 16p13.3 microdeletions encompassing TBC1D24and 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. Repetitive sequences and non-canonical secondary structures potentially predisposing to the microdeletions were analyzed. Microdeletion breakpoints were successfully mapped in all patients using TLA, split read analysis, PCR/Sanger sequencing, or nanopore sequencing. Other technologies identified only approximate breakpoints. Alu sequences and non-B DNA motifs were detected in most patients. Noteworthy, two unrelated individuals were carriers of the same deletion. Mechanistically, non-allelic homologous recombination, through a 639 bp sequence with 96.2% homology, appears to underlie a recurrent 16p13.3 microdeletion. 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 syndromes. This research contributes to a deeper understanding of microdeletion-associated disorder pathophysiology in medical genetics.