Dr Partha Pratim Majumder is a well-known genetic scientist with a Ph D in statistics and a long experience in human anthropology and genetic studies. He was the Founder Director with National Institute of Biomedical Genomics in Kalyani, near Kolkata, from March 2010 to September 2016 and currently serves as a Distinguished Professor at the Institute. He is also an adjunct professor with Translational Health Science in Faridabad and has been the HOD of Human Genetics Unit of the Indian Statistical Institute, Kolkata. Dr Majumder, a lead author of the Genome Asia 100K pilot paper, and his co-researchers, have described the whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups from 64 countries across Asia. In this interview with Dr Sumit Ghoshal, he gives a fresh update on Genome Asia 100K, the first large-scale human genome sequencing project for Asia, a region that is underrepresented in genomic datasets worldwide, as well as the clinical relevance and possible applications of the project.
The pilot study covers around 1,700 individuals and many unique population groups from across 64 countries. According to you, how diverse is this part of the study for a sample representation?
To understand this, you must first consider the genetic origin of much of the human population in this part of the world. The modern human being has its origins in Africa, while the centrepiece of evolution was in India. But it was far from homogenous – there was a lot of diversity on account of mating patterns and other changes taking place over long periods of time. Thus, multiple populations acquired a large number of genetic variants (mutations) that had different configurations. Hence, it is necessary to study a wide range of population groups to get a comprehensive picture. Of this, I believe, this dataset has a reasonably diverse sampling.
The introduction of your study mentions that non-Europeans have limited representation in genomic studies conducted in western countries. To what extent does your effort correct this anomaly?
We have only studied a miniscule bit of the total, mainly because of a crunch of funds. The expense involved is approximately Rs 2 lakh per individual genome. Hence if GenomeAsia100k has an ultimate objective of studying one hundred thousand genomes, the costs at present prices would be well beyond our capacity. Of course, the costs are coming down but that would take time. The costs in the Western countries are relatively less, and that is the main reason why most genomic studies in the West tend to cover their own populations. As we go along, our own studies could perhaps help to correct the tilt by about 20 percent.
What are your plans and timelines for taking the GenomeAsia100k project forward?
It is very difficult to predict the timelines that we might follow, but in the past two-three years, we have doubled the number of individuals covered, and we hope to progress as rapidly as we can manage.
In a global environment where large databases like BioBank Japan and China’s Kadoorie already exist, to what extent does your pilot project add to this information?
It may not be possible to compare our work with the biobanks that you mention, because their nature is different. The biobanks are repositories of tissue samples and other biological materials, which we have no plans to do. Besides, the Chinese population is a lot more homogenous, while ours is extremely diverse. Japan is a bit more diverse but a lot less than South Asia, which means that our work has a value of its own.
The ultimate objective of these genomic studies is to accelerate the discovery of disease associations across East Asia. This raises the question: To what extent does ethnicity make a difference in the genetic factors of disease?
We have a few examples of ethnicity having a definite association with particular diseases, but not too many. Thus, sickle cell anaemia and thalassemia are seen in some populations only within South Asia, and not in others. But very often the phenotypic expressions of the same genetic variant differ from one population to another, and this can change the clinical picture.
As you may be aware, there is a panel of genes that operate together to influence the progress and development of diabetes and determine who exactly will suffer serious complications. With what accuracy can this be predicted through a study of genetic mutations?
We have quite some way to go before we can reach there. But as the GenomeAsia100k project is now set, we would need a series of sub-projects in which the genomic patterns of normal persons would be compared with those afflicted with specific disorders. This would lead to a broader understanding of the role of genetics in disease.
It is believed that genetic patterns and their expression are also influenced by lifestyle factors, environment, etc. There are whole new fields springing up including Epigenetics and Nutrigenomics. How do you take these into account while interpreting genomic studies?
Our research is not advanced enough to analyse the impact of these factors.
MedGenome is listed as one of the founding partners of the GenomeAsia100k Project. What are the specific contributions that MedGenome and SciGenom Research Foundation have made to this Project?
One major role of the other partners in the project is to bring together an organization, so that appropriate resources are made available. Besides, activities such as generating data and providing direction and leadership to the project are also crucial contributions from their side.