Personalized Genomics Databases Show Racial Bias

Two of the top genomic databases, which are in wide use today by clinical geneticists, reflect a measurable bias toward genetic data based on European ancestry over that of African ancestry, a new study says.

Led by investigators at the University of Maryland School Of Medicine, a national group of researchers has confirmed for the first time what scientists have suspected. Estimates in 2011 were that more than 90 percent of research in genetics underlying disease, known as genome-wide association studies, has been done on people of European ancestry. A recent commentary in Nature by researchers from the University of Washington states that there has been a certain amount progress, but not enough.

The shortcoming in African ancestry genomic data was identified during an 18-month long study conducted under the auspices of the larger Consortium on Asthma among African-Ancestry Populations in the Americas (CAAPA). To create a benchmark for comparison to current database results, the researchers first created the largest, high-quality non-European genome data set ever assembled.

Genetic samples of 642 subjects from the African diaspora, including representatives from US, African, and Afro-Caribbean populations, were sequenced in order to produce this unique data set. Then, when compared with current clinical genomic databases, (Human Gene Mutation Database (HGMD) and ClinVar) researchers found a clearer preference in those databases for European genetic variants over non-European variants.

More Accurate Genetic Diagnoses

The research team was led by Principal Investigator Timothy O’Connor, PhD, assistant professor at the University of Maryland School of Medicine and a faculty member of the school’s Institute for Genomic Sciences. He is also a specialist in the areas of Human Evolutionary Genomics, Genotype/Phenotype Architecture, and Computational Biology.

“By better understanding the important role of African ancestry in clinical genetics, we can begin to actually identify a disease that has been forgotten or is not part of an individual’s self-identification,” says O’Connor.

“For example, if an African-American patient walks in the door, he might have 20 percent European ancestry, while another might have 20 percent African ancestry. That difference will dramatically change how many variants are found in their genome, and what disease risks they might encounter. That’s why we need to expand these databases to include a broader range of ancestries, in order to produce more accurate medical genetic diagnoses.”

O’Connor also points out that this shortfall in genomic data also comes at a financial cost.

“If you translate the review time it takes for each one of these variants to be sequenced in terms of cost in a clinical setting, you’re looking at a difference of about $1,000 more to analyze an African American’s genome than a European American’s genome—and you still receive less accurate results,” he notes.

African American Sequencing Panel For Genetic Research

In a related story, 23andMe, Inc. today announced a new grant from the National Institutes of Health (NIH), for the creation of a genetic resource for health research in African Americans that could improve the understanding of diseases in minority populations.

The $1.7 million grant, issued from the National Human Genome Research Institute, will go toward leveraging 23andMe’s data on more than one million customers who have consented to participate in research, creating an African American sequencing panel to be used as a reference dataset for health research. The de-identified genetic data will be made available to other health researchers at institutions around the world.

Most sequenced genomes available today are predominantly for people of European ancestry, limiting the accuracy of imputation for non-Europeans. But because of the large number of 23andMe customers who have consented to research — including tens of thousands of African Americans —scientists will be able to create a new panel of sequenced African American genomes.

Under this grant, 23andMe researchers will ask a subset of our African American customers who have consented to participate in research if they would be willing to participate and have their DNA sequenced to become part of this panel. Ultimately, the sequence panel data will be shared with the NIH, who will make it available to other researchers.

This in turn will expand scientists’ ability to make genetic discoveries for African Americans and help build a broader understanding of how genetics influence diseases and traits across multiple populations.

Michael D. Kessler, et al
Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry
Nature Communications 7, Article number: 12521 (2016) doi:10.1038/ncomms12521

Image: Brice Blondel for HDPTCAR/Flickr