Looking beyond the exons

There are several blood group genes, including ABO, RHD, FY and ICAM4 [4-7], which have had allele-specific promoter and intronic variants identified. These findings may prove useful for distinguishing which non-coding variants are associated with common blood group phenotypes. The significance of intronic regions is highlighted in recent publications reporting the genetic basis of blood groups phenotypes based on variation in gene regulatory mechanisms [8-10]. The identification of allele-specific non-coding variants is valuable to future gene regulatory studies as it provides candidates with a potential to disrupt a regulatory motif or a gain-of-function variant to introduce new motifs [11].

NGS, and more recently long-range sequencing have an increasing role in the characterisation of our blood group genes. The information generated demands sophisticated bioinformatics skills and provides an opportunity for exploration by the growing group of young professionals in the field, as seen in recent publications [3, 12-14]. In line with the increasing use of big sequencing data, a reference whole gene sequence representing major blood group alleles is needed more than ever. Moreover, shifting the comparison between alleles and variants established on these references from manual to computer facilitated retrieval is essential and accommodated for in the newly developed RCIBGT database.

Regarding having a reference build for each blood group major alleles, it is important to keep in mind that one would face the differences between various ethnic groups. Take the example of CR1 Helgeson phenotype, where the variant associate with the DACY/YCAD phenotype has tight linkage among the Caucasians but not Africans [9]. It is not feasible to fit all population under one reference build, therefore, a population-specific consensus has been proposed to resolve the issue [11]. The add-on value of the population consensus reference for each major blood group allele would allow identification of evolutionarily conserved regions. Although a conserved region does not necessarily translate to functional DNA elements in itself, it should be evaluated with biochemical signatures (e.g histone markers and expression data)[15]. However, when dealing with aberrant blood group phenotypes, it would be wise to start investigating variations within the conserved regions than other positions allowing random variations.

To conclude, while reference sequences are updated by NCBI, developments in long read/long-range techniques are enabling further improvements to blood group reference sequences by characterising allele-specific variants. We can now transverse in either direction between genotype and phenotype. This will prove valuable in the future discovery of new blood group alleles and in also in our understanding of blood group gene regulation.