Pilot study of Asian genomes finds novel gene variants, highlights diversity

(Reuters Health) – An effort to map genomes across Asia has the potential to find novel gene variants affecting disease and responses to drugs, and to reveal the complex origins of Asian populations, early results suggest.

In a pilot study, researchers looked at more than 1,200 whole-genome sequences from individuals representing hundreds of population groups across Asia, and compared them with existing sequence data from almost 600 African, European and American samples, according to the report in Nature.

Asians, who make up about half the global population, have been severely underrepresented in human genetic studies, which limits the applicability of existing results for a large part of the world, the authors note.

The GenomeAsia 100K project seeks to address this disparity. A non-profit international consortium established in 2016, its members include Singapore’s Nanyang Technological University and industry partners such as South Korean biotech firm Macrogen and California-based MedGenome Inc.

The consortium’s initial goal is to sequence the genomes of 100,000 Asians and make the data available through a public database for use by researchers and pharmaceutical companies.

“At the beginning of the project, people were under the assumption the Asian variation is more or less a subset of what’s already been deciphered in the European population. That turns out to be not true,” Stephan Schuster of Nanyang Technological University, co-leader of the study, told Reuters Health by phone.

For the pilot study, the consortium team examined genome sequences representing people living in dozens of countries including China, India, Indonesia, Japan, the Philippines, Malaysia, Mongolia, Pakistan, Papua New Guinea and Russia, as well as samples representing minorities living in remote and isolated communities or belonging to various caste and language groups.

The team found that nearly a quarter of the protein-altering gene variants in their Asian dataset were not present in currently available public databases such as the 1000 Genomes Project and the Exome Aggregation Consortium. Most of the new variants were rare, yet more than 140,000 variants occurred in more than 1% of people in specific populations.

In rare disease genetics, the authors write, common variants are usually eliminated as suspects in searches for genes potentially involved in a disease, so these new examples can aid in such studies among Asian populations.

Awareness of genetic variants that affect an individual’s response to certain drugs is also important in tailoring treatment and conducting clinical trials, the researchers note. For example, they found that a known gene variant that increases risk for a severe disorder in reaction to carbamazepine, a drug used to treat nerve pain and seizures, is significantly more common in people from Austronesian-language groups.

“There are roughly 400 million individuals who belong to Austronesian groups that are at increased risk for carbamazepine sensitivity, including the vast majority of the people from Indonesia, Malaysia and the Philippines,” the study team writes.

The researchers also found wide variation between Asian groups in the presence of variants that increase risk for adverse reactions to the anti-clotting medications clopidogrel and warfarin.

Asians have been cut off from advances in genetics and genomics that have taken place especially over the last 10 years, Andrew Peterson, study co-author and chief scientific officer at MedGenome, told Reuters Health.

“(This is) a first step, to rectify that and to provide the tools so that Asians also have access to genetic information about disease and disease risk that is available now in Caucasian populations,” he said in a phone interview.

“The disparity that we’re talking about is huge between the information that’s available for Caucasians versus Asians. One study doesn’t restore balance,” Peterson said, but it’s a start in the right direction.

SOURCE: go.nature.com/2E82CGM Nature, online December 4, 2019.

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