Bengaluru: When Deepshikha Satish’s mother was diagnosed with heart disease, the bioinformatician from Delhi jumped right into an urgent, high-stakes area of clinical medicine related to cardiovascular diseases. Now she plans to fill in an important gap in India’s gene database related to heart disease.
The crisis made her see a harsh reality: Doctors don’t know for sure what medicines work for their patients. It’s a method of trial and error.
“Today, or for ages, doctors (have been) treating humans as guinea pigs… (a doctor) just checks how your body is reacting to that particular drug. We need specific knowledge about specific drugs, whether this drug is going to be beneficial for my body or not. (a doctor) must be certain about it before prescribing any medicine,” said Satish.
Satish, who holds a PhD in Translational Bioinformatics from ICGEB JNU-Delhi and a certification in Healthcare Entrepreneurship from IIT Delhi, set up Dr. Omics in July 2023, a molecular diagnostic lab. Its ambitious first project is to create a large-scale, India-specific genomic database for coronary artery disease (CAD) through whole exome sequencing.
“We are trying to incorporate each and every ethnicity of the Indian population, and we will incorporate at least 10,000 people into this project,” said Satish, who leads more than 40 employees.
But their ambitious project is still stuck due to a lack of funds. Satish is hopeful as they recently got virtually incubated at the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad.
Worldwide, the field of genomics is giving a boost to the field of medicine. Countries like the UK and the US have put billions of dollars into genome projects to create vast data sets that fuel drug discovery and personalised medicine. But the global advances fall short when it comes to treating people of diverse genetic makeup, like in India.
“What we are following as a treatment is based on the other countries’ gene database. We see that India has many epigenetic changes which have already happened many years back during big droughts, famines. This needs to be studied further,” said Kriti Chandel, a preventive cardiologist working in Bengaluru.
Earlier this year, the Ministry of Science and Technology launched the Genome India project. It has sourced genetic blueprints from 10,000 individuals across 83 ethnic groups, which makes it the country’s largest genomic sequencing exercise.
However, both Chandel and Satish say the government’s project lacks specificities and is yet to mature to use it for specific diseases.
“In this clinical trial, we are doing a case-control study, and that’s why we are not ina position to utilise the existing publicly available data. Second, the data that’s available is not particularly regarding coronary artery disease, and we need that (data) from scratch,” said Satish.
A case-control study is a type of study where different groups are formed and observed for a specific outcome.
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The funding paradox
Satish frequently travels from Delhi to the Centre for DNA Fingerprinting and Diagnostics (CDFD) in Hyderabad, where Dr. Omics is virtually incubated to find more funders.
The project which started in 2024 has now secured its first round of funding of around Rs 10 lakh from the Department of Science and Technology (DST), Amazon Web Services (AWS), and Illumina, an American biotech company.
This round of funding only covers 200 samples, and for robustness, the team needs money to carry out sequencing for 500 samples. That would cost Rs 50 lakh more. The irony is that venture capitalists (VCs) told Satish that the amount is too low for them to fund.
“(VCs) are asking us to go to the government for funds. But the process is (so) lengthy that we (have been) waiting for one year or so for Rs 50 lakh,” said Satish. She aims to clear the funding gap very soon with the help of CDFD, Hyderabad and start on phase 1 trials.
“This will be the biggest and most accurate data regarding cardiovascular diseases or coronary artery disease. We want to include each and every ethnicity present in India so that no one is left behind,” said Saitsh.
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What is whole exome sequencing
If DNA is a book which has precise instructions to sustain life, then each chapter can be considered a gene.
Inside each chapter, one can find paragraphs pertinent to how life runs. The paragraphs are called exons. There are gaps in between these paragraphs where an editor can write their notes, or leave them as it is.
Whole Exome Sequencing (WES) meticulously highlights the informative paragraphs, while skipping the editor’s notes in between paragraphs. Technically put, WES looks for a small portion of the genome that codes for protein and is unlike Whole Genome Sequencing (WGS), which reads the entire DNA sequence, including the filler notes and gaps in between the paragraphs.
The first step is to cut the DNA into tiny pieces and use a special type of “DNA magnet” to pick only the exons. The selected pieces are read by a machine to determine the exact order of their genetic letters. Finally, an expert compares the sequence with a reference to look for a variation in the paragraph that could possibly explain a health condition in a selected DNA sample.
Although WES is inexpensive compared to WGS, it can overlook some mutations. It misses out on large structural changes that can be spotted by WGS.
“WES is like opening a bag of worms,” said a preventive cardiologist who doesn’t want to be identified. The criticism is that WES can create more tangled questions than answers and can also compromise patients’ privacy if there is negligence in data analysis and storage.
Satish confirmed that the data collected during the process will only remain with Dr. Omics and not with any of the funders.
That said, the cardiologist quoted earlier finds the project more aspirational than practical.
Preventive cardiologist Chandel finds it important to have an India-specific database in the case of Coronary Artery Diseases (CAD) and said the Dr.Omics project might help experts like her.
“We will come to know if a person has a risk factor of developing heart disease in future. It will help in precision medicine,” said Chandel.
Satish is still moving forward, trying to find funders. She said that if she fails to find more funds, she is prepared to move ahead to sequence 200 samples.
“We will provide you with firsthand information about whether you are going to develop this disease. And if you have developed it, we can tell you whether the medication that you are utilising is suitable for you or not,” said Satitsh.
(Edited by Theres Sudeep)