Chronic Granulomatous Disease Panel

Chronic granulomatous disease (CGD) 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. Simultaneous administration of antimicrobials and corticosteroids may be used to resolve colitis associated with heightened inflammatory responses to infection (Leiding et al. 2012). Patients with CGD should avoid areas where fungal spores are common such as mulch, gardens, and yard waste. Approximately one in 200,000 births 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 (Leiding and Holland 2012).

CGD is primarily inherited in an X-linked recessive manner through pathogenic variants 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 CYBB, CYBA, NCF1, NCF2, and NCF4 genes account for 70%, 5%, 20%, 5% and <1% of cases respectively (Leiding and Holland 2012; Roos et al. 2010; Roos et al. 2010). The NCF1 gene is currently not analyzed in this panel due to the presence of pseudogenes. Disease onset with individuals with X-linked CGD is ~3 years with mortality occurring in 20% compared to autosomal recessive forms with onset ~7 years and mortality occurring in 8% of cases. Together the CYBA, CYBB, NCF1, NCF2, and NCF4 genes encode the NADPH oxidase complex which is essential for superoxide production required for intracellular killing of pathogens in phagocytes (Song et al. 2011). See individual test descriptions for additional information on the molecular biology of each gene.

Pathogenic variants in the CYBB, CYBA, NCF1, NCF2, and NCF4 genes account for 70%, 5%, 20%, 5% and <1% of cases respectively (Leiding and Holland 2012). In autosomal recessive CGD families with known reductions in DHR oxidation in neutrophils, pathogenic variants in the NCF2 and CYBA gene were found in 15% and 25% of cases respectively (Roos et al. 2010). Without analysis for the NCF1 gene, clinical sensitivity for the panel is ~80% for detection of pathogenic variants in CGD patients. Analytical sensitivity is >90% for CYBB, CYBA, and NCF2 with gross deletions only being present in a few cases (Roos et al. 2010). Analytical sensitivity for NCF4 gene should also be high as all pathogenic variants to date are detectable by sequencing.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes 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 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).