Asia-wide Genome Mapping Project Reveals Insights Into Asian Ancestry, Genetic Diversity

By Bio-IT World News Staff

December 6, 2019 | After a global genetic comparison, a team of international scientists has discovered that Asia has at least ten ancestral lineages, whereas northern Europe has a single ancestral lineage.

In their first study reported in Nature (DOI: https://doi.org/10.1038/s41586-019-1793-z) this week, the GenomeAsia 100K consortium analyzed the genomes of 1,739 people, which represents the widest coverage of genetic diversity in Asia to date.

The study covers 64 different countries and provides what the authors call "the first comprehensive genetic map for Asia" that will guide scientists in studying diseases unique to Asians, improve precision medicine and identify drugs that may carry higher risk of adverse reactions for certain ethnic groups.

Despite forming over 40% of the world's population, Asian people have previously accounted for only 6% of the world's recorded genome sequences.

The goal of GenomeAsia 100K—which launched in 2016—is to better understand the genome diversity of Asian ethnicities by sequencing 100,000 genomes of people living in Asia. It is a non-profit consortium hosted by Nanyang Technological University, Singapore (NTU Singapore), the only academic member. Its three other members are Macrogen based in South Korea, Genentech, a member of the Roche Group in United States, and MedGenome from India/US.

NTU Professor Stephan C. Schuster, the consortium's scientific chairman and a co-leader of the study, explained the significance of GenomeAsia 100K's initial findings on the vast genomic diversity in Asia in an official statement: "To put it into context, imagine we looked at all people of European and based on the level of their genetic diversity, observed that they could all be grouped into just one ancestral lineage or population. Now, if we took that same approach with our new data from people of Asian, then based on the much higher levels of genetic diversity observed we would say that there are 10 different ancestral groups or lineages in Asia."

How the database of Asian genomes was formed

Over the course of the last three decades prior to the pilot project, thousands of blood and saliva samples have already been collected by scientists and anthropologists from donors across Asia in hopes that one day, a deeper analysis to gain insights into the Asian community can be done.

Of particular interest were participants from remote and isolated communities, who have long been the subjects of study by anthropologists but have not yet undergone genomic analysis, until the GenomeAsia 100K project was kickstarted.

The pilot study included 598 genomes from India, 156 from Malaysia, 152 from South Korea, 113 from Pakistan, 100 from Mongolia, 70 from China, 70 from Papua New Guinea, 68 from Indonesia, 52 from the Philippines, 35 from Japan, and 32 from Russia.

Genomic DNA extracted from the blood and saliva samples was then sequenced in laboratories of the four consortium members in the US, India, South Korea and Singapore. The digital sequencing data were subsequently sent to Singapore for processing and storage.

Singapore was selected by the consortium as the host, as the country offered good travel connections for collaborating scientists, strong supercomputing facilities to crunch the data, and the required cybersecurity standards in its data center for handling sensitive genetic data.

The combined data was compiled and analyzed by NTU scientists, including Asst. Prof Hie Lim Kim, a population genomics expert at the Asian School of The Environment, with the help of the National Supercomputing Centre Singapore (NSCC) and international collaborators.

Different Asian ethnic groups respond differently to mainstream drugs

Every person has approximately 3.2 billion different nucleotides, or building blocks, in their genome, which form their DNA "code".

It's estimated that for the genomes of any two people, 99.9% of this code is the same and on average, 0.1% or three million nucleotides, are different between them.

This genetic variance help humankind colonize the most diverse environments on the planet and make it resilient to disease, but it also results in a differential response to many medicines.

"Genetic variance is the reason we are distinctively different from each other including differences in the diseases that each of us suffer from during our lifetimes. Understanding these differences is the most important source of clues that we have for driving the discovery of innovative new medicines," Andrew Peterson, an author of the paper and an expert in the use of genetics to drive drug discovery, said in a press release.

The frequencies of known genetic variants related to adverse drug response were analyzed for the genomes collected in this study.

For example, Warfarin, a common anticoagulant drug prescribed to treat cardiovascular diseases, likely has a higher than usual risk of adverse drug response for people carrying a certain genetic variant. This particular genetic variant has a higher frequency to appear in those with North Asian ancestry, such as Japanese, Korean, Mongolian or Chinese.

Using data analysis, scientists can now screen populations to identify groups that are more likely to have a negative predisposition to a specific drug.

Moving forward, the GenomeAsia 100K will continue to collect and analyze up to 100,000 genomes from all of Asia's geographic regions, in order to fill in the gaps on the world's genetic map and to account for Asia's unexpected genetic diversity.