[Application of copy number variation analysis based on raw data of next-generation sequencing in the molecular...

Objective: To study the application of copy number variation (CNV) analysis based on the raw data of next-generation sequencing (NGS) in diagnosing primary immunodeficiency disease (PID). Methods: One hundred sixty-five patients with suspicious PID were tested by NGS in the Department of Rheumatology and Immunology, Shenzhen Children's Hospital during September 2014 and Mary 2017. The raw data of the patients who got negative result were further analyzed for the CNV with CNVkit software. The pathogenic CNV were identified in the databases including Resource of Asian Primary Immunodeficiency Diseases (RAPID), Human Gene Mutation Database (HGMD) and ClinVar with the known 344 pathogenic genes of PID. The associated literature from January 2010 to May 2019 were searched in Pubmed, Weip, Wanfang and CNKI database with key words as "primary immunodeficiency disease" "copy number variation" and "next generation sequencing" . Results: Ninety-five out of 165 patients (57.6%) had negative result of the NGS test, among whom the patients with immune dysregulation had the highest negative rate (68.6%, 24/35). CNV analysis found large fragment deletion in 12 patients, within which 7 was X-linked inheritance, 3 was autosomal recessive inheritance, 2 was autosomal dominant inheritance. Partial exon deletion was found in 4 patients while whole gene deletion in 8 patients. According to the review of literature, CNV was reported in 51 pathogenic genes of PID (14.8%, 51/344) , mainly intern deletion (70.6%, 36/51), while autosomal recessive inheritance (56.9%, 29/51) was the most common pattern. Conclusions: CNV is not rare in PID. When the phenotype is clear in the patients who have negative NGS test, CNV should be considered.