The largest genetic study of an Asian population reaches its first milestone

Joel P. Joseph

The Genome Asia 100K Project, launched in 2016, aims to sequence the genomes of 100,000 Asian individuals to address the underrepresentation of non-European populations in most published genomics studies. The first pilot phase of the project was completed recently, with the publication of 1739 genome sequences from samples spread across 64 different Asian countries. 

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The genes of a population tell the story of its members – their ancestry, their health, and their chances of getting a disease. Scientists have now studied the complete set of genes of 1739 people from different ethnic populations in Asia. The study is the largest of its kind conducted in an Asian population and was carried out by a group of scientists from several Asian countries and the USA – the GenomeAsia100K consortium.

Eight Indian institutions were involved in the study viz., National Institute of Biomedical Genetics (NIBMG), Kalyani; SciGenom Research Foundation (SGRF), Chennai; MedGenome Labs, Bangalore; Indian Statistical Institute (ISI), Kolkata; SRM Institute of Science & Technology (SRMIST), Chennai; Narayana Nethralaya Foundation, Bangalore; Madras Diabetes Research Foundation (MDRF), Chennai; and Dr Mohan’s Diabetes Specialities Centre, Chennai.

Despite being the most populous continent, Asian populations are often under-represented in global genomic studies. Recognizing this gap, the consortium embarked on a project to study the genomes of 100,000 people residing in Asia – GenomeAsia100K project.

A point on the DNA (gene locus) that is informative in one population, or even in all populations of a geographical region, may not be informative in other populations,” Partha P Majumder, Founder and Distinguished Professor at NIBMG says, This is because of different population ancestries and demographic histories of populations.” 

The project is aimed to generate high-quality DNA sequences of 100,000 people and thereby characterize the variations at gene loci, understand genomic ancestries, and get medically relevant information for Asian populations. 

The pilot phase of the project, which is now published, marked the milestone of reaching about one-fifth of the target. This phase included sequencing and analysis of the genomes of 1739 people from 219 populations of Asia spread across 64 countries. Of these, 598 were from India – the largest number of people from a single country. Majumder collected the DNA samples of people from many tribal and non-tribal populations from different regions of India over a period of 30 years. 

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Sample Distribution - Genome Asia
Sample sizes, location, language and social hierarchy associated with samples from south Asia (Source: Wall et al, Nature 576, 106 – 111 (2019) — CC BY 4.0 (http://​cre​ativecom​mons​.org/​l​i​c​e​n​s​e​s​/​b​y​/4.0/)

Other groups from India were also instrumental in collecting samples from unique ethnic populations. We sequenced the genomes of people from the Irula tribe of Tamil Nadu,” Parani M, Professor and Head, Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, says. The Irula tribe is an ethnic group that has not interbred with other groups and its people are adept at finding and catching venomous snakes by hand. 

The study found some interesting data that was missing in the earlier databases. Comparing our data of Asians with those available in the public databases, we found about 200,000 informative points on the DNA – DNA markers – in the Asian individuals that were unreported in the existing databases. These are novel DNA variants in Asians,” Majumder says,We found that 23% of protein-altering DNA variants were unreported in existing databases.”

The study revealed some medically important details – that a certain change in the DNA sequence of a gene called NEUROD1 could cause a specific kind of diabetes in Asians, a specific variation found exclusively in South Indians in the DNA sequence of the Haemoglobin gene could make them more prone to beta-thalassemia, and that certain DNA variations found specifically in Asians in BRCA1 and BRCA2 genes could make them susceptible to breast cancer. 

It is critical to study genomes. Today, through Genome [studies], we are relearning how language, culture, food, environment, behaviour have shaped humans,” Moinak Banerjee, Scientist G, Rajiv Gandhi Centre for Biotechnology, who was not involved in the study, says. 

Banerjee underscores the importance of collaborations from different quarters in such studies. He explains that different expert communities working in isolation with individual biases will result in a lot of noise. Genomics can dissect and help understand the noise in the data generated by anthropologists and public health experts. So, collaborations are a must,” Banerjee says. 

The published results form only a small part of the story. Once the project is complete, the genomes of 100,000 Asians will portray a detailed picture of the Asian population. India, on its own, is headed in this direction with the launch of Genome India – an initiative to catalogue the genome data of 10,000 Indians. 

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Joel is a graduate student and science writer.