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Background  High-resolution oligo-SNP array allowed the identification of extremely small pathogenic deletions at numerous clinically relevant regions. In our clinical practice, we found that small pathogenic deletions were frequently encountered at chromosome 9p and 9q terminal regions.    Results  A review of 531 cases with reportable copy number changes on chromosome 9 revealed142 pathogenic copy number variants (CNVs): 104 losses, 31 gains, 7 complex chromosomal rearrangements. Of 104 pathogenic losses, 57 were less than 1 Mb in size, enriched at 9p24.3 and 9q34.3 regions, involving the  DOCK8, KANK1, EHMT1  genes. The remaining 47 cases were due to interstitial or terminal deletions larger than 1 Mb or unbalanced translocations. The small pathogenic deletions of  DOCK8, KANK1  and  EHMT1  genes were more prevalent than small pathogenic deletions of  NRXN1, DMD, SHANK3  genes and were only second to the 16p11.2 deletion syndrome, 593-kb (OMIM #611913).    Conclusions  This study corroborated comprehensive genotype-phenotype large scale studies at 9p24.3 and 9q24.3 regions for a better understanding of the pathogenicity caused by haploinsufficiency of the  DOCK8, KANK1  and  EHMT1  genes.    Trial registration number  None; it is not a clinical trial, and the cases were retrospectively collected and analyzed.    Electronic supplementary material  The online version of this article (doi:10.1186/s13039-016-0291-3) contains supplementary material, which is available to authorized users.

molecular cytogenetics

Enrichment of small pathogenic deletions at chromosome 9p24.3 and 9q34.3 involving DOCK8, KANK1, EHMT1 genes identified by using high-resolution oligonucleotide-single nucleotide polymorphism array analysis