High-throughput complement component 4 genomic sequence analysis with C4Investigator
Wesley M Marin1, Danillo G Augusto1,2,3, Kristen J Wade1
1Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, California, USA.
Insights
Complement component 4 (C4) gene variation impacts immune function. A new bioinformatics tool, C4Investigator, enables high-throughput analysis of C4A and C4B sequences, revealing extensive genetic diversity and potential disease associations.
Area of Science:
- Genetics and Genomics
- Immunology
- Bioinformatics
Background:
- The complement component 4 (C4) genes (C4A and C4B) are critical for immune system pathways.
- C4 genes exhibit complex variations including copy number, size (long/short forms), and linkage to blood group antigens (Rodgers/Chido).
- Previous high-throughput genomic analysis of C4 variants was challenging due to high sequence similarity and genetic complexity.
Purpose of the Study:
- To develop a novel bioinformatics pipeline, C4Investigator, for comprehensive, high-throughput characterization of human C4A and C4B sequences.
- To enable detailed analysis of C4 gene copy number, size variants, and nucleotide-level sequence variations from short-read sequencing data.
- To investigate the extent of C4A and C4B genetic variation in human populations.
Main Methods:
- Development of a bioinformatics pipeline named C4Investigator.
- Input processing of paired-end targeted or whole genome sequencing data.
- Analysis of C4 gene copy numbers, C4A/C4B variants, Rodgers/Chido epitopes, and long/short forms (C4(L)/C4(S)).
- Generation of full aligned C4A and C4B sequences for nucleotide-level analysis.
Main Results:
- C4Investigator successfully characterizes comprehensive C4A and C4B sequence variation from short-read data.
- Analysis of the 1000 Genomes Project dataset revealed that C4 genes are highly poly-allelic.
- Numerous identified variants have the potential to significantly impact C4 protein function and immune response.
Conclusions:
- C4Investigator provides a robust solution for high-throughput genomic analysis of complex C4 gene variations.
- The high degree of C4 poly-allelism underscores its importance in immune system regulation and disease susceptibility.
- Further research into C4 variants can elucidate their roles in autoimmune and pathogenic diseases.
Abstract:
The complement component 4 gene loci, composed of the C4A and C4B genes and located on chromosome 6, encodes for complement component 4 (C4) proteins, a key intermediate in the classical and lectin pathways of the complement system. The complement system is an important modulator of immune system activity and is also involved in the clearance of immune complexes and cellular debris. C4A and C4B gene loci exhibit copy number variation, with each composite gene varying between 0 and 5 copies per haplotype. C4A and C4B genes also vary in size depending on the presence of the human endogenous retrovirus (HERV) in intron 9, denoted by C4(L) for long-form and C4(S) for short-form, which affects expression and is found in both C4A and C4B. Additionally, human blood group antigens Rodgers and Chido are located on the C4 protein, with the Rodger epitope generally found on C4A protein, and the Chido epitope generally found on C4B protein. C4A and C4B copy number variation has been implicated in numerous autoimmune and pathogenic diseases. Despite the central role of C4 in immune function and regulation, high-throughput genomic sequence analysis of C4A and C4B variants has been impeded by the high degree of sequence similarity and complex genetic variation exhibited by these genes. To investigate C4 variation using genomic sequencing data, we have developed a novel bioinformatic pipeline for comprehensive, high-throughput characterization of human C4A and C4B sequences from short-read sequencing data, named C4Investigator. Using paired-end targeted or whole genome sequence data as input, C4Investigator determines the overall gene copy numbers, as well as C4A, C4B, C4(Rodger), C4(Ch), C4(L), and C4(S). Additionally, C4Ivestigator reports the full overall C4A and C4B aligned sequence, enabling nucleotide level analysis. To demonstrate the utility of this workflow we have analyzed C4A and C4B variation in the 1000 Genomes Project Data set, showing that these genes are highly poly-allelic with many variants that have the potential to impact C4 protein function.
