Chronic Granulomatous Disease via the NCF2 Gene

Chronic granulomatous disease (CGD) is an inherited immunodeficiency characterized by repeated infections with bacterial and fungal pathogens and formation of granulomas. CGD immunodeficiency is due to an impairment of the NADPH oxidase complex resulting in an inability to generate superoxide in phagocytic cells to lyse pathogens (Song et al. 2011). Common pathogens include Staphylococcus aureus, Pseudomonas species, Candida albicans, Aspergillus species, and Nocardia species. Pneumonia, granuloma formation within gastrointestinal and genitourinary tracts, and failure to thrive are hallmark symptoms of the disorder. In severe cases, granulomas can lead to abscess formation and organ failure. Treatments include long courses of antimicrobials to ward off infections (Leiding and Holland 2012). Simultaneous administration of antimicrobials and corticosteroids may be used to resolve colitis associated with heightened inflammatory responses to infection (Leiding and Holland 2012; Song et al. 2011). Patients with CGD should avoid areas where fungal spores are common such as mulch, gardens, and yard waste. Approximately one in 200,000 newborns in the US is affected with CGD (Winkelstein et al 2000). Genetic testing can aid in differential diagnosis of CGD from other disorders associated with granuloma formation and hyperinflammation such as cystic fibrosis, hyper IgE syndrome, Crohn’s disease, allergic bronchopulmonary aspergillosis, and glucose 6-phosphate dehydrogenase deficiency (Song et al. 2011).

CGD is primarily inherited in an X-linked manner through mutations in the CYBB gene. Autosomal recessive forms of CGD also occur through mutations in the CYBA, NCF1, NCF2, and NCF4 genes (Roos and de Boer 2014). Pathogenic variants in the NCF2 gene account for about 17% of autosomal recessive cases and 6% of all CGDs. The majority of causative variants to date are truncating with deletion, nonsense, splice site, and insertion variants accounting for 18%, 21%, 22%, and 5% of cases. Gross deletions and missense variants account for 10% and 24% of cases (Roos et al. 2010; Gentsch et al. 2009; Köker et al. 2009). Pathogenic variants occur throughout the coding region with the majority being present within the TRP1-4 domain at the N-terminus (Roos et al. 2010). The NCF2 gene encodes the p67phox protein which is a subunit of the NADPH oxidase enzyme. This complex is essential for the production of superoxide which is central for intracellular killing of pathogens in phagocytes (Song et al. 2011).

In a series of 40 autosomal recessive CGD families with known reductions in dihydrorhodamine oxidation in neutrophils, mutations in the NCF2 gene were found in 15% of cases (Köker et al. 2009). Analytical sensitivity is ~90% for detection of causative mutation in the NCF2 gene with gross deletions being found in about 10% of cases (Roos et al. 2010).

This test provides full coverage of all coding exons of the NCF2 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).