Are you genetically predisposed to some diseases? Do you carry genetic mutations that can impact the health of your child? A debit card-sized IndiGenome card, recently unveiled by the government, will help you find the answers if your genetic information is captured in a database that India's umbrella research organisation - the Council of Scientific and Industrial Research (CSIR) - is building. Once your genome is sequenced from your blood sample and added to this database, the card can be used to read the information embedded in your genes, just as your debit card is used to generate a financial transaction statement from your bank's database.
Well, the card is not the key. Genome sequencing - or mapping the pattern of the basic building block of every living cell - is. A genome contains all of a living being's genetic material (simply put, the genome is divided into chromosomes, chromosomes contain genes, and genes are made of DNA). Each genome has approximately 3.2 billion DNA base pairs, and the way they are arranged, or variations and mutations in their pattern, can provide clues about the individual's health or ill health, inherited or acquired. Already, 1,008 individuals, chosen to represent India's social, ethnic and geographic diversity, have been issued such cards. Over 280 doctors in 70 institutions have been trained to make sense of such data. A CSIR institute, the Institute of Genomics and Integrative Biology (IGIB) - which is spearheading the Genomics for Public Health in India, also called IndiGen project - is planning to enrol 20,000 Indians for whole genome sequencing in the next couple of years to build a larger database. The data will be important for building the knowhow, baseline data and indigenous capacity in the emerging
area of precision medicine. IndiGen will have applications in a number of areas, including faster and more efficient diagnosis of rare diseases. The other benefits are cost-effective genetic tests, carrier screening applications for expectant couples, enabling efficient diagnosis of heritable cancers and pharmacogenetic tests to prevent adverse drug reactions.
In fact, IGIB leads two other programmes - Genomics for Understanding Rare Diseases India Alliance (GUaRDIAN) Network and Genomics and other Omics tools for Enabling Medical Decision (GOMED), led by Dr Mohammed Faruq, to see that the genome database and genetic screening leads to development of cost effective diagnostic tools and tests that are licensed out to private and public medical institutions.
The world over, fall in cost for genome sequencing (a reason for which is increase in computing power) is leading to path-breaking applications spanning the entire spectrum of healthcare - diagnosis to treatment and drug development to prevention and wellness - and unrelated fields such as agriculture, animal productivity, environment, sports and many more. Consider this: CSIR took six months to sequence the genomes of 1,008 Indians. Seventeen years ago, a global initiative led by the US National Academy of Sciences, had taken 12 years, and spent $3 billion, to complete the sequencing of the first human genome. Today, sequencing a person's genome does not cost more than $1,000. In fact, Sam Santosh, Chairman of MedGenome Labs, a private venture, says he can sequence a complete human genome in his Bengaluru lab for $500-600.
The Industry
The catalyst for the IndiGen project was advent of Next Generation Sequencing (NGS) in the last decade or so. (NGS helps an entire human genome to be sequenced in a day. The previous Sanger sequencing technology used to take over a decade.) The technology is being used by both IGIB and MedGenome for high-throughput sequencing, i.e. sequencing hundreds of thousands of genes in one go.
IndiGen is a good start but there are countries that are much ahead. Genomics England, a public-private partnership between the UK government and world's biggest NGS sequencing machine maker, Illumina, has completed sequencing of 1,00,000 genomes of British citizens comprising a mix of cancer patients, rare disorder patients and healthy people. A new agreement for sequencing of 3,00,000 genomes, with an option to increase it to 5,00,000 over the next five years, was signed by the two partners on January 13. "Countries such as Estonia and Iceland are attempting to sequence every single citizen and link the data with their health schemes. The US has decided to do it for every single rare disorder patient," says Praveen Gupta, Managing Director & Founder, Premas Life Sciences - the authorised partner of US-based Illumina in India.
"The global high-throughput genomics industry will be in the range of $10-12 billion. With an estimated 25-30 per cent annual growth, it is expected to become a $25-30 billion market in the next three-four years," he says. Premas sells tools (reagents, platforms, software, training) to labs that do genetic testing in India. With 90 per cent market share, it drives NGS technology in India, too. "The high-throughput genomics market in India, including reagents, instruments and services, will be about Rs 500 crore. Approximately 50,000 samples must be reaching India's clinical (service) market on an annual basis," says Gupta.
Dr Sridhar Sivasubbu and Dr Vinod Scaria, IGIB scientists at the forefront of the IndiGen programme, say genome sequencing is just one piece of the initiative. IGIB has two other programmes - Genomics for Understanding Rare Diseases India Alliance (GUaRDIAN) Network and Genomics and Other Omics Tools for Enabling Medical Decision (GOMED) - to ensure their genome database and genetic screening lead to development of cost-effective diagnostic tools and tests that can be licensed out to private and public healthcare institutions. "GUaRDIAN focuses on rare diseases. Given that we are a billion-plus people, even the rarest of the rare diseases is found in a few lakh people. So, this programme caters to 70 million people living with some genetic disease. We find technological solutions for these 7,000-odd diseases and partner with a network of 280 clinicians across 70-odd institutions to offer our solutions," says Sivasubbu.
"Patients and their families connect with us through the GUaRDIAN network. We sequence their genes to find the mutation, and once we find it, we go back to their communities with a cost-effective test to identify that mutation. You just have to look for that single mutation in others, and that's cost-effective," says Scaria. Instead of whole genome sequencing, which costs between Rs 50,000 and Rs 1,00,000, a single assay developed by IGIB through these programmes costs Rs 2,000. The team led by Sivasubbu and Scaria has developed 180 tests for 180 genes and transferred the technology to private diagnostic labs. The institute itself has catered to about 10,000 patients and carried about 25,000 tests in the last two years. "We have entered into partnerships with about a dozen companies. The format of the collaboration depends on the business models they follow," says Sivasubbu.
Premas Life Sciences
The authorised partner of US-based Illumina in India provides tools (reagents, platforms, software, training and troubleshooting) to labs engaged in genetic testing in India. With 90 per cent market share, it drives the New Generation Sequencing technology in India
It works in areas other than healthcare, too. For example, Tagtaste, an online platform for food professionals, uses the company's services to understand the genomics of taste. It has customers and partners such as Pepsico, Coca Cola, Nestle and ITC
Dr Lal PathLabs
The company has licensed diagnostic tests for 27 conditions from Institute of Genomics and Integrative Biology (IGIB)
Has a portfolio of more than 200 different types of tests
It is active in fields like rep- roductive health, cancer di- agnosis, pharmacogenomics
Medgenome Labs
The Bengaluru-based player considers itself as the private sector avatar of IGIB. It offers not just genetic tests but also carries out research. It has collaborated with Singapore's Nanyang Technological University to sequence 1,00,000 whole genomes from Asia. The Genome Asia project has already completed sequencing 10,000 whole genomes, of which about 8,000 are from India
MedGenomes research associates recently sequenced and analysed the genome of the Cobra snake. The findings, published in Nature, suggest the possibility of developing a new method of producing anti-venom completely in the lab.
Lifecell International
The company is in the genetic testing space. It has tied up with IGIB and offers tests ranging from basic screening (prenatal screening, newborn screening, etc) to high-end ones based on NGS. It tests more than 50,000 patient samples every month
Mahajan Imaging
The company has set up a new R&D wing to focus on cutting-edge scientific and clinical research and help radiology and genomics companies develop world-class clinically relevant products. The idea is to integrate imaging and genomic data
Trivitron Healthcare
The Chennai-based chain wants to develop tools using genomic data that can work on conventional platforms. It is talking to IGIB and trying to get its knowhow for manufacture of products for sale to pathology labs
The Private Hand
Dr Lal PathLabs, a pathology lab chain with big plans in the genetic testing space, has an entire department for such tests. "We offer tests of all levels - Karyotyping, which looks at the macro level, Microarrays, which offer intermediate resolution, and NGS, used to elucidate the DNA sequence at the micro level. The fields we are active in include prenatal reproductive health, cancer diagnosis and pharmacogenomics (study of how genes affect a person's response to drugs). We have more than 200 tests and conduct around 300 tests per day," says Dr Vandana Lal, Executive Director, Dr Lal PathLabs. The company has licensed tests for 27 conditions from IGIB. "The imported technology is expensive. The idea to partner with CSIR labs is to bring these cutting-edge technologies to Indian masses at a reasonable cost," says Dr Lal.
Lifecell International is another player in the genetic testing space that has tied up IGIB. "We offer tests ranging from basic screening (prenatal screening, newborn screening, etc.) to high-end ones based on NGS. We test more than 50,000 samples a month. PCR-based tests range from Rs 2,000-5,000 whereas tests based on NGS and those involving sequencing of large parts of the genome can cost upwards of Rs 20,000," says Ishaan Khanna, CEO, Biobank & Diagnostics, Lifecell. He believes the IndiGen database will help in development of better analysis and interpretation tools. "Our focus is on developing rapid genome testing for children in NICU (Neonatal ICU) and similar other scenarios where doctors need clear actionable results in the shortest possible time. IndiGen provides the right mix of Indian genome database," he says.
But not every partnership is for access to cost-effective tests. Mahajan Imaging, a medical imaging chain, has set up a Centre for Advanced Research in Imaging, Neuroscience and Genomics to focus on research and helping radiology and genomics companies develop clinically relevant products. The idea is to integrate imaging and genomic data. "We started the project six months ago and are among the first imaging companies to get into genomics. In the next three-five years, it will be possible for an AI algorithm to look at the radiology image and give genomic readings on it," says Vidur Mahajan, Associate Director, Mahajan Imaging.
Chennai-based Trivitron Healthcare sees in IndiGene data an opportunity to develop multiple testing platforms. It wants to develop tools using genomic data that can work on conventional platforms. "There are almost 1,00,000 pathology labs in India. Hardly 500-1,000 must be doing genetic testing. Companies like ours are talking to IGIB and trying to get the knowhow to manufacture products for a larger population," says Jameel Ahmad Khan, Head, R&D, Trivitron. "IGIB will develop the knowhow, provide proof of concept, and we will convert it into a product which pathology labs without highly trained manpower can also run," he says.
Bengaluru-based Medgenome Labs considers itself a private sector avatar of IGIB, perhaps even a couple of years ahead in research and development. The company not only does genetic tests but also carries out research. It has collaborated with Singapore's Nanyang Technological University to sequence 1,00,000 whole genomes from Asia. The Genome Asia project has already completed sequencing of 10,000 whole genomes, of which about 8,000 are from India. On December 4, international journal Nature published the initial findings from the project - genetic variation, population structure, disease associations, etc., from a whole-genome sequencing reference dataset of 1,739 individuals of 219 population groups and 64 countries across Asia. "We sequence a person's genes and other relevant parts of the genome for specific mutations to understand what is causing the disease and specific drugs and dosage the person will respond to. We also help pharmaceutical companies understand genomes and discover new drug targets and biomarkers," says Sam Santosh, Chairman, MedGenome. With about 120 sales people, the company claims it is generating samples from around 10,000 clinicians across the country. "We were the first to enter the market. In that sense, we created the market, and would be having 60-65 per cent market share. The sequencing market must be in the range of $70-75 million," says Santosh. The company expects its diagnostic business to touch $100 million in four years. Interestingly, MedGenome's research associates recently sequenced and analysed the genome of Cobra snake. The findings, published in Nature, suggest the possibility of developing a new method of producing anti-venom completely in the lab.
Other Sectors
Illumina's India partner Premas Life Sciences is not selling its next generation sequencers only to healthcare firms. Gupta says it has more than 200 installations in India alone. "Anything which is living has a DNA nucleic acid and can be sequenced. We have a mass research market and practically every institute has the sequencer. Somebody will be working on cow, somebody on rice, a third institute on some bacteria," says Gupta.
IGIB researchers Dr Sridhar Sivasubbu and Dr Vinod Scaria vouch for this. The institute is getting requests, including partnership offers, from non-medical players. Tagtaste, an online platform for food professionals, wants to understand the genomics of taste. "In a lighter vein, you could say that the efficiency of a professional wine taster depends on his genes," says Scaria. With customers and partners such as Pepsico, Coca Cola, Nestle and ITC, and a clientele that includes chefs of global hotel chains, taste is serious business. "The point is, if a person is paying Rs 3,000 for a curry or Rs 5,000 for a soup, you better get the taste right," says Scaria. IGIB also works with Adam's Genetics for R&D and product development in the area of fitness. "One of the companies works in the cricket industry. Each player can be genetically tested for performance and food intake because not all muscles have the same size and some people gain weight, some don't gain muscle mass, while some may be more prone to injury. Genetic tests can find out who is prone to injury, or whether weightlifting is the right exercise for a player or not," says Sivasubbu.
The Future
Indians are 17 per cent of the world's population. But only 0.2 per cent genomic data is from the Indian population. This is one area where India can lead. We have so many diseases, and if we can provide the genetic design, the world can develop diagnostics and therapies. "We can create ideas. We didn't invent computers but we created the IT industry. In the same way, we didn't invent genomic sequences but tomorrow we can create a genome informatics economy," says Premas' Gupta.
There are other possibilities, too. "A lot of pundits say that in the next five-six years, 15 per cent of the world's population will be whole genome sequenced. If I require 100 GB data for a genome sequence, for 1.5 billion people, 25-30 exabytes of data will be needed. The entire data content on YouTube, globally, is 0.8 exabytes. Imagine the kind of data generation and analytics possibilities we are talking about," says Gupta. "We need people to analyse this data. If we can take the lead and train our manpower, we can move the world, we can create a new industry which can lead for the next 20 years just the way the IT industry did," he adds. Incidentally, Gupta claims that TCS has already bought Illumina's sequencing platform. So has WIPRO. It seems IT companies are already sensing an opportunity.
Sivasubbu says it took India 10 years to scale up from sequencing one genome to 1,000 genomes. "In the next decade, it may be a million."
@joecmathew
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