Optical Genome Mapping Improves Genetic Diagnosis in Chronic Granulomatous Diseases

Abstract Purpose: Chronic granulomatous disease(CGD) is mainly caused by defects in genes encoding subunits of NADPH oxidase complex (CYBB, CYBA, NCF1, NCF2, NCF4), and its chaperone (CYBC1). Next generation sequencing has successfully identified pathogenic variants in 131 clinically confirmed CGD patients in the single center, left 4 cases negative. This study sought to explore new technology to resolve these diagnostic dilemmas at whole genome level. Methods: The clinical data were collected. Optical genome mapping (OGM) was performed to investigate clinically-relevant structural variants greater than 500 bp in size. Targeted long-range PCR followed by next generation sequencing and Sanger sequencing were utilized for confirming breakpoints junctions.Results: OGM find a novel pathogenic copy number variant in NCF2 (1506 bp ~ 1526 bp in length) in P3. The exact downstream breakpoints of this deletion located in a thymine (T) rich region (18 T in reference and 58 T in P3), which remain difficult to detect with current short-read and long-read sequencing. Together with a second pathogenic variant in NCF2 in trans (c.1130_1135del) detected by exome sequencing, P3 was genetically diagnosed. Conclusion: OGM improves genetic diagnostic yield (1/3) in challenging CGD patients. Structural variants in NCF2 and other genes should be considered in undiagnosed CGD disease. Further research in undiagnosed population with OGM is warranted.