The complex variation of the complement component 4 (C4) genes has prevented their effective inclusion in genome-wide studies based on SNP arrays and exome sequencing. Here we provide resources to facilitate the analysis of C4 in both C4-focused and genome-wide studies.
We describe a combination of molecular assays and downstream inferential strategies that utilize droplet digital PCR (ddPCR) to infer the C4 gene contents of each genome analyzed – including the combination of C4AL, C4AS, C4BL, and C4BS genes present. This method has high (64/64) concordance with results obtained using Southern blotting. Common C4 alleles can also be imputed from flanking SNPs. Though recurring mutation at C4 makes imputation less effective than it is for simpler variants, we found that the common C4 alleles can generally be imputed with 0.7 < r2 < 1, making this approach useful for large cohort studies. We provide the reference panel for imputation that we created from the HapMap samples.
Check back for updates: we are creating advanced reference panels from whole-genome sequencing of much larger numbers of people, which we hope will enable the imputation of lower-frequency C4 alleles.