Is whole exome sequencing (WES) sufficient for genetic testing in C3 glomerulopathy?

Genetic Testing for C3 Glomerulopathy: Whole Exome Sequencing Is Not Sufficient

Whole exome sequencing alone is not sufficient for genetic testing in C3 glomerulopathy and should be complemented with additional specialized testing for comprehensive evaluation of complement dysregulation. 1

Recommended Genetic Testing Approach for C3 Glomerulopathy

• Next-generation sequencing (NGS) techniques such as panel sequencing and whole-exome sequencing (WES) are recommended as initial genetic testing methods for C3 glomerulopathy 2
• WES can identify mutations in complement-related genes but has significant limitations in detecting all relevant genetic variants in C3 glomerulopathy 2, 3
• Additional specialized genetic testing is necessary to identify:
  • Copy number variants (CNVs) in complement genes 4
  • Deep intronic mutations that may be missed by exome-only sequencing 2
  • Regulatory region variants that affect complement gene expression 2

Limitations of Whole Exome Sequencing in C3 Glomerulopathy

• WES is limited to protein-coding exons and cannot identify genetic variants in deep intronic regions and regulatory regions 2
• Some stretches of DNA, even if included in the sequenced region, can be difficult to read with standard WES 2
• Recent research has shown that rare complement gene variants are not significantly enriched in C3 glomerulopathy cases compared to controls (6.8% vs 5.9%), suggesting that WES focusing only on these genes may miss important genetic factors 4
• A significant common variant locus at 6p21.32 (HLA region) has been identified in C3 glomerulopathy, which may not be adequately captured by standard WES analysis 4

Comprehensive Evaluation Approach for C3 Glomerulopathy

• For patients with C3 glomerulopathy, a comprehensive complement analysis is necessary, including 1:

  • Serum complement levels (C3, C4, CH50)
  • Specialized complement regulatory protein testing
  • Genetic testing
  • Autoantibody evaluation

• Specific genetic testing should include screening for mutations and allele variants in 2, 1:

  • C3
  • Complement factors H, I, B
  • CD46 (membrane cofactor protein)
  • Complement factor H-related proteins (CFHR) 1-5

• Evaluation for acquired factors is equally important, as most cases of C3 glomerulopathy are driven by acquired factors rather than genetic mutations 3:

  • Antibody to C3 convertase (C3 nephritic factor [C3Nef])
  • Anti-factor H antibody
  • Evaluation for monoclonal gammopathy (especially in patients ≥50 years) 1

Clinical Implications and Best Practices

• When WES analysis does not identify mutations likely responsible for the phenotype, whole-genome sequencing (WGS) should be considered 2
• Data from genetic testing should be re-analyzed at least every 3 years to check for newly discovered variants in patients who did not receive a diagnosis after the first round of testing 2
• Many specialized complement tests are not routinely available in commercial laboratories and may require sending samples to specialized reference laboratories 1
• Genetic counseling must precede genetic testing, and handling of incidental findings should be discussed in advance 2

Diagnostic Algorithm for C3 Glomerulopathy

1. Perform renal biopsy with immunofluorescence to confirm C3-dominant glomerular deposits 2, 1
2. Conduct comprehensive complement analysis including serum C3, C4, and CH50 levels 1
3. Perform initial genetic testing with NGS panel or WES targeting complement-related genes 2
4. Test for autoantibodies (C3Nef, anti-factor H) 2, 1
5. In adults ≥50 years, evaluate for monoclonal gammopathy 1
6. If initial genetic testing is negative but clinical suspicion remains high, consider:
   • Whole genome sequencing 2
   • Specialized testing for copy number variants 4
   • Analysis of regulatory regions 2
7. Consult with institutions with greater experience with these diseases for specialized testing 2