Development of Ethnicity-Specific Reference for Interpreting Genome Data

In a study appearing in PLoS Genetics, a Stanford University-led team described the “ethnicity-specific” reference genome approach it used to analyze whole genome sequences from four members of a single family.

By incorporating estimated allele frequency data from the 1000 Genomes Project into the existing human reference genome, the researchers came up with three synthetic human genome references containing the major alleles identified in European, African, or East Asian populations — a strategy that’s intended to more accurately represent the genetic variation present in each of the major HapMap populations.

“There has been a large focus, at least in the genome-wide association study space, on Caucasian populations,” first author Frederick Dewey, a researcher at Stanford University’s Center for Inherited Cardiovascular Disease, told GenomeWeb Daily News. “What we hope to show is that ethnicity certainly matters — it begins at the point of genome assembly and carries all the way through variant interpretation and annotation.”