Distinct sequence features underlie microdeletions and gross deletions in the human genome

Microdeletions and gross deletions are important causes (~20%) of human inherited disease. Their genomic locations are strongly influenced by the local DNA sequence environment. Yet no systematic study has examined the generative mechanisms. Here, we obtained 42,098 pathogenic microdeletions and gross deletions from the Human Gene Mutation Database (HGMD) that together form a continuum of germline deletions ranging in size from 1 bp to 28,394,429 bp. We analyzed the sequence within 1-kb of the breakpoint junctions and found the frequencies of non-B DNA-forming repeats, GC content, and the presence of seven of 78 specific sequence motifs in the vicinity of pathogenic deletions correlated with deletion length for deletions of length ≤30 bp. Furthermore, we found the repeats of DR, GQ, and STR appear to be important for the formation of longer deletions (>30 bp) but not for the formation of shorter deletions (≤30 bp) and significantly (Chi-square test P-value < 2E-16) more microhomologies were identified in flanking short deletions than long deletions (length >30 bp). We provide evidence to support a functional distinction between microdeletions and gross deletions. A deletion length cut-off of 25-30 bp may serve as an objective means to functionally distinguish microdeletions from gross deletions.