Reference Genomes Should Reflect Population Diversity: An Interview with Valerie Schneider
Thursday, November 3, 2016
In a recent Mendelspod interview, host Theral Timpson talked with Valerie Schneider of the National Center for Biotechnology Information about the work of the Genome Reference Consortium (GRC) to bring more ethnic diversity to the latest human reference assembly (GRCh38).
Describing the reference genome as something like a Rosetta Stone for scientists working with genomic data, Schneider says it is “really the central piece of data upon which most genomics-based analyses are done, [serving as] the coordinate system for annotations ranging from genes to repeats to epigenomic markers.”
As the importance of increasing the representation of population diversity in this reference has become more appreciated, the GRC team has worked to bring many more ethnic populations into the reference. Currently this is being addressed by patches and the use of alternate loci scaffolds, Schneider says. Scientists working with population graphs are among the early adopters of these new alternate loci scaffolds.
The new ethnic genomes “are also intended to stand on their own as complements to the reference so users can examine variation for their own samples in the context of these different backgrounds, or they can try to get genome-wide views of different populations,” Schneider says.
She and her colleagues are looking forward to seeing the ways in which this information will be used by both the basic and the clinical research communities. One effort she is particularly excited about is underway at the McDonnell Genome Institute at Washington University, where scientists are generating a set of high-quality, de novo whole genomes from a wide variety of populations.
At the ASHG annual meeting earlier this month, the GRC hosted a workshop entitled “Getting the Most from the Reference Assembly and Reference Materials: Updates and Developments from the Genome Reference Consortium (GRC) and Genome in a Bottle (GIAB).”