Consensus-based allele detection

A method for genotyping alleles in at least one homologous genetic set, comprising:

• (i) providing a DNA-containing sample from a subject that includes at least one homologous genetic loci set, wherein said homologous genetic loci set comprises red cell antigen-encoding RHD gene and RHCE gene;
• (ii) performing PCR amplification of regions of said homologous genetic loci set using consensus sequence-specific primers, wherein said consensus sequence-specific primers bind to consensus sequences that are common to the RHD gene and RHCE gene and wherein the consensus sequence-specific primers comprise at least one forward consensus sequence-specific primer and one reverse consensus sequence-specific primer, thereby generating a pool of RHD and RHCE amplification products;
• (iii) sequencing a plurality of said RHD and RHCE amplification products in order to determine the relative proportion of each nucleotide at each position;
• (iv) performing a sequence alignment between the sequencing read results of (iii) and at least one reference sequence, with said reference sequence corresponding to one of the genes in said RHD and RHCE homologous genetic loci set;
• and
• (v) performing genotype calling of the allele or alleles in said sample based on the relative proportion of each nucleotide at each of a plurality of discriminant positions in said alignment.