On May 10th 2016 I will be attending the BioConclave Conference in London, which aims to build closer relations and collaboration between Indian and European life sciences. This drive to build a greater link between the healthcare systems of India and Europe sparked my interest, and I started to wonder about the role of Indian genomics in all of this. So before I head off to the City Hall next week for the BioConclave I thought I would take a deeper look into the current status of the Indian genome data and what the future might hold for Indian genomic research.
But first here is a little more background on the aims and past successes of the BioConclave conference.
A bit more about BioConclave
BioConclave is an annual conference that looks to build relationships between both companies and academia to explore commercial, joint research, licensing and funding opportunities for India, the UK and Europe.
"Our mission is to showcase India’s diverse expertise in the life sciences and healthcare sectors with specific focus on research and development; biotech and pharma; new technologies and medical devices."
The 2015 BioConclave conference resulted in much networking and many business opportunities, alongside at least one high profile Indian-UK partnership. In this particular instance, the Indian company Advatech announced its intention to invest one-million pounds into a diagnostics centre in Leeds. Let's hope the 2016 conference results in similar fruitful relationships for Indian and UK health and biotech companies.
The need for Indian genomic data
The huge variation between members of the human population, due to centuries of migration and out-breeding, makes associating genetic variations with certain diseases very difficult. The best way to overcome these difficulties is to have a reference genome and control samples that are as similar to your samples as possible. This is why parents and siblings are the ideal control sequence when looking for rare disease mutations in children. And this is why it is fundamentally important to sequence as many different ethnic subpopulations as possible.
In 2009 a news story published in Nature discussed the results revealed about Indian ancestry by a study led by David Reich of the Broad Institute in Cambridge, Massachusetts, and Lalji Singh of the Centre for Cellular and Molecular Biology in Hyderabad, India (1). In this story the author stated that:
"India makes up around one-sixth of the world's population, yet the South Asian country has been sorely under-represented in genome-wide studies of human genetic variation."
The current status of Indian Genomics
To overcome India's under-representation in genome-wide studies, in 2003, the Indian Genome Variation Database (IGVdb) was established. The objectives of this study were to collect samples from 15,000 individuals from different Indian subpopulations, select 1000 genes relevant to common diseases and drug response and identify at least 5–10 informative markers per gene in the Indian subpopulations, which would be useful for candidate gene studies (2). The first whole Indian genome was announced in 2009, with the analysis and variant annotation being published in 2012 (3).
At least three initiatives alongside the IGVdb have been launched to sequence Asian subpopulations, including Indians. The Singapore genome variation project has looked at single nucleotide polymorphisms (SNPs) from DNA samples of Chinese, Malays and Indians. The Malaysian Node of the Human Variome Project has performed genome wide mapping of the ethnic Malaysian population, which includes Indians. Finally, GenomeAsia, an initiative launched earlier this year, intends to sequence 100,000 Asian individuals, including Indian subpopulations.
Furthermore, the Indian Government has recognised the need represent to its population and its research in the ever growing field of genomics; The National Institute of Biomedical Genomics in Kalyani, West Bengal, was set up by the Government of India in 2010 as the first institution in India specifically devoted to research in biomedical genomics.
Searching through Repositive, I found more than 10 studies that have specifically looked at the genomic or expression profiles of Indians populations. One particular study caught my eye, from Xpressomics, which took paired tumour and healthy samples from Malays, Chinese and Indians to study the transcriptomics changes in breast cancer. This clearly highlights that Indian populations are being studied, in and out of the context of disease, with regard to genomics and transcriptomics.
Awareness of Indian genomics projects
As I have detailed above, there are many projects underway that are sequencing the Indian population, and multiple studies have already been performed to look at how variants may affect this specific ethnicity in disease. However, the current awareness of the availability of this data is still low.
Recently I gave a presentation at a DNAdigest-Repositive workshop on the current status of genomics data sources and the diversity of sequenced ethnicities across the globe. After my talk, an attendee asked me if I knew of any projects that were involved in sequencing Indian genomes as he didn't know of any - highlighting the need to spread the word and increase the discoverability of this data. This is a need, alongside driving international partnerships, that both the BioConclave conference and Repositive aims to address.
The future of Indian genomics in Healthcare
Below I quote a Repositive user's opinion on why genomic study into Indian populations is fundamentally important:
"A large scale genome-wide association study is yet to be done on the Indian population to unveil disease-variant associations, which will allow us to understand the genomic structure of the Indian population and how it influences healthcare. Bearing in mind, that India is a very ethnically, culturally and food-habit-wise diverse country, it will always be a challenge to work on this diverse data."
With the BioConclave in sight, I wonder what collaborations and partnerships will be formed with Indian genomics in mind, and how these will go on to shape the future of Indian, and European, healthcare.
- Reich, D. et al. Nature 461, 489-494 (2009)
- Brahmachari, S. k. et al. Human Genetics 118, 1-11 (2005)
- Patowary, A. et al. Human Mutation 33, 1133-1140 (2012)