Reliable genetic diagnosis of NCF1 (p47phox)-deficient chronic granulomatous disease using high-throughput sequencing

Amy P Hsu^1*Eric Karlins²Justin Lack³T. Joseph Pepper⁴Karen Lau⁵Kimberly R. Marshall-Batty⁵Debra Long Priel⁵Joie Davis⁶Danielle L Fink⁵Christa Zerbe⁶John I Gallin⁷Harry L Malech⁷Steven M Holland⁶Douglas B. Kuhns⁵

• ¹National Institute of Allergy and Infectious Diseases Laboratory of Clinical Immunology and Microbiology, Bethesda, United States
• ²Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, United States
• ³NIAID Collaborative Bioinformatics Resource, NIH, Bethesda, United States
• ⁴Department of Mathematics, University of Maryland College Park, College Park, United States
• ⁵Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, United States
• ⁶National Institute of Allergy and Infectious Diseases Immunopathogenesis Section, Bethesda, United States
• ⁷National Institutes of Health National Institute of Allergy and Infectious Diseases, Bethesda, United States

Chronic granulomatous disease is caused by mutations in any of the 6 components of the phagocytic NADPH oxidase complex including gp91 phox , p47 phox , p22 phox , p40 phox , p67 phox , or EROS. Functional assays include reactive oxygen species (ROS) production, flow cytometry, and immunoblotting for NADPH proteins. The advent of high-throughput sequencing allows genetic diagnosis for all components except NCF1 (p47 phox ) due to two, nearly identical, pseudogenes (NCF1B, NCF1C). The majority of NCF1-CGD patients carry a 2-base deletion caused by crossover between NCF1 and NCF1B or NCF1C. Currently, NCF1 deficiency is diagnosed functionally: a characteristic DHR with low levels of residual ROS, loss of p47 phox on immunoblot, or digital droplet PCR or Gene-scan to enumerate intact (GTGT) or deleted (DGT). While this provides patients a clinical CGD diagnosis, for the 20% of NCF1-CGD patients with a non-DGT mutation a definitive genetic diagnosis is still lacking. We developed a bioinformatic method using existing short or long-read sequencing data from 48 NCF1-CGD patients or carriers to identify both DGT and non-DGT NCF1 gene mutations. Additionally, we confirm that the presence of DGT in NCF1 is due to pseudogene copy into the NCF1 locus. We compare NCF1 sequence from NCF1-CGD patients to cohorts of non-NCF1-CGD and healthy controls (1000Genomes), demonstrating pseudogene replacement of NCF1 in NCF1-CGD as well as the reciprocal replacement of NCF1B or NCF1C by NCF1 in some healthy controls. With this method, reanalysis of existing sequence data may provide genetic diagnosis to NCF1-CGD patients. This technique may be modified for other diagnostically relevant pseudogenes.