It is hard to overstate the importance of the human reference genome. In our editorial we want to acknowledge the value of this resource and at the same time ask what it would take to improve it further towards a reference that better reflects human diversity.
First and foremost we think that the Genome reference consortium (GRC) needs assistance from the community to fill gaps in the current reference and provide alternative assemblies for highly divergent regions. Just to give an example, currently there are only three diverse regions incorporated in the genome, but there likely are hundreds more. One of them, one that the GRC is actively working on, is the repeat rich region in chromosome 1q21.1 that is implicated in several cognitive and developmental disorders. Unfortunately the GRC does not have the resources to focus on more than a handful.
Of course there are also things the GRC can do to improve the reference.
Some improvements have already been decided upon, for example a switch to common haplotypes. This decision brings its own challenges – determining what is a common versus a rare haplotype is not always easy. And some important information may be lost in the conversion, for example in cases where the common allele contains a stop codon whereas the rare allele reads through and produces the protein. The latter is likely to be medically relevant.
Another desirable feature would be an easier navigation system to make the reference more user friendly.
What are your experiences with the human reference genome? What are the areas you think need improvement? Do you think a reference that reflects human diversity is attainable or even desirable?