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A new socially responsible approach to grouping gene variation in populations

In genetic research and medicine, scientists examining how common or rare a DNA variant is in a set of individuals often want to group people in a particular way — by geography, ancestry group, or some clinical characteristic — groupings that are referred to as stratified allele frequencies.

But some common methods used to stratify groups can be problematic and a team of genomic researchers has proposed a new approach to calculating and presenting stratified allele frequencies that is both scientifically useful and socially responsible. The approach is outlined in a paper that appears in the most recent American Journal of Human Genetics.

Headshots of Sarah Nelson and Stephanie Gogarten
Sarah Nelson          Stephanie Gogarten

“Some common ways to group individuals to calculate stratified frequencies rely on either social constructs of race or ethnicity, or the idea of predominant genetic ancestry. These approaches can have negative consequences of reinforcing the harmful idea that race and ethnicity are defined by genetics, which has undergirded scientific racism and eugenics,” said lead author Sarah Nelson, a senior research scientist with the Genetics Analysis Center (GAC), housed in the Department of Biostatistics at the University of Washington School of Public Health.

“In this paper, we recommend an approach that uses statistical methods to measure ancestry segments across the genome versus assigning an individual to an ancestry group, and reporting allele frequencies for segments with similar ancestry. This approach better reflects the underlying structure of the genome, and mitigates the harms of grouping individuals.”

Researchers recognize that this may not be a perfect solution; it’s unclear how this way of reporting allele frequencies would be used in clinical settings. Also, depending on how it’s implemented, the approach may rely on some of the same continental categorizations that make the predominant ancestry approach problematic.

“But overall, we think this approach is better as it attempts to mitigate social harms of grouping approaches and leverages what we know about the genome as a collection or mosaic of different ancestries and histories versus a singular identity,” said Nelson.

Stephanie Gogarten, a GAC research scientist, co-authored the study along with former GAC researcher Tamar Sofer, now at Harvard University.