Determination of the loss of function complement C4 exon 29 CT insertion using a novel paralog-specific assay in
1Division of Molecular Medicine and Genetics, Guy's Hospital, King's College London, London, United Kingdom.
Insights
Genetic variants in complement C4A and C4B genes, specifically a CT insertion causing non-expression, are linked to diseases like lupus. Our new assay accurately detects this common null allele, crucial for genetic association studies.
Area of Science:
- Immunogenetics
- Molecular Biology
- Human Genetics
Background:
- Genetic variants affecting complement C4A and C4B gene expression are prevalent in European populations.
- These variants, particularly C4 null alleles, are associated with autoimmune diseases, notably systemic lupus erythematosus.
- A common cause of C4 null alleles is a 2 bp CT insertion in exon 29, leading to a non-sense mutation.
Purpose of the Study:
- To develop a novel, high-throughput, paralog-specific assay for detecting the C4 CT insertion polymorphism and its copy number.
- To accurately genotype this specific C4 variant, overcoming limitations of previous methods.
- To assess the frequency of the C4 CT insertion in healthy European cohorts.
Main Methods:
- Development of a high-throughput, paralog-specific assay.
- Genotyping of healthy cohorts from the United Kingdom and Spain.
- Analysis of C4 gene copy number variation (CNV) and its impact on genotyping.
Main Results:
- The C4 CT insertion was found in 4.17% of the UK cohort and 1.78% of the Spanish cohort in the C4A gene.
- One individual in the Spanish cohort carried the CT insertion in the C4B gene.
- A weak correlation was observed between the C4 CT insertion and flanking MHC polymorphism.
Conclusions:
- The developed assay is effective for high-throughput, paralog-specific detection of the C4 CT insertion.
- The frequency of this null allele variant varies between European populations.
- Current SNP-based genome-wide association strategies may miss disease associations due to this C4 variant and CNV.
Abstract:
Genetic variants resulting in non-expression of complement C4A and C4B genes are common in healthy European populations and have shown association with a number of diseases, most notably the autoimmune disease, systemic lupus erythematosus. The most frequent cause of a C4 "null" allele, following that of C4 gene copy number variation (CNV), is a non-sense mutation arising from a 2 bp CT insertion into codon 1232 of exon 29. Previous attempts to accurately genotype this polymorphism have not been amenable to high-throughput typing, and have been confounded by failure to account for CNV at this locus, as well as by inability to distinguish between paralogs. We have developed a novel, high-throughput, paralog-specific assay to detect the presence and copy number of this polymorphism. We have genotyped healthy cohorts from the United Kingdom (UK) and Spain. Overall, 30/719 (4.17%) individuals from the UK cohort and 8/449 (1.78%) individuals from the Spanish cohort harboured the CT insertion in a C4A gene. A single Spanish individual possessed a C4B CT insertion. There is weak correlation between the C4 CT insertion and flanking MHC polymorphism. Therefore it is important to note that, as with C4 gene CNV, disease-association due to this variant will be missed by current SNP-based genome-wide association strategies.
