Anirvan & Co do pioneering gene sequencing work

Genomics played a vital role in freeing us from the scourge of Covid, says data scientist Anirvan Chatterjee. “The RT-PCR test emerged because of genome sequencing of SARS-CoV. The test being able to tell whether the variant is Delta or Omicron, that again came from sequencing. So, the entire biology is sitting in the sequence,” explains Anirvan, founder & CEO of HaystackAnalytics, an IIT Bombay-incubated company with a vision to scale genomics through the use of big data.

Haystack, founded four years ago, has created impact through its Omega TB (ωTB) application, a one-time comprehensive drug-resistance test for tuberculosis that aims to eliminate the infection from India. In this, Anirvan took his learnings from being part of the NHS, UK, team that developed genome sequencing as a method for detecting TB, the world’s first such rollout for any disease. Usually, a standard TB diagnosis would take around 40 days and cost about Rs 12,000, but without the guarantee of accuracy. In comparison, ?TB offers complete diagnosis within 10 days and at 60% of the cost – enabled by genome sequencing. This can also then help determine which drug would be best for treatment.

Anirvan did his MSc in biotechnology from the Institute of Science, Mumbai, and a PhD in applied biology from the University of Mumbai. After completing his post-doc at the University of Oxford, he returned home to join IIT Bombay, where he began researching on viral genomics. Anirvan and his co-founders – Gaurav Srivastava and fellow scientist, Prof Kiran Kondabagil – realised that while genome sequencing was workable in India (since sequencer devices were available), very little genomic analysis was being done because of the huge investment requirements.

The greater challenge, however, lay in lack of awareness. “A government generally takes on new technologies that are doing well. But the people who are supposed to take up genome sequencing are waiting for the government to pay for it. We told ourselves, ‘It will take time but let’s work on it,’” Anirvan says.

Progress has been rapid. Anirvan was told it would not be achievable in less than five years, but in one-and-a-half years, their work was already being talked about among clinicians.
Health check
Genome sequencing is the process of determining the order of nucleotides in DNA, which ultimately determines body traits. Sequencing is hugely complex. “Imagine taking today’s paper and passing it through a shredder, then taking all those shreds and putting the paper back together. The DNA data that is gathered is like those shreds of paper. The challenge is, it is not 10 or 20 pages; this runs into millions and millions of letters for one sample, and if we try to put this together like a jigsaw puzzle, it’s not going to happen. That is where the entire technology – data mining, handling of big-data, and AI, etc. – comes in,” says Anirvan. The idea, he says, is to faithfully put the sequence back together, to quality-control, automate and validate the process.

Another “mammoth” task involves reconstructing the DNA of a disease so that a clinician can use the resultant raw data to determine what a sample contains. This is done through a cloud-based software application that clinicians can affordably access from any lab. “We had to write the entire architecture, the code, and the basic information of the different conditions we are looking at, and then automate it for clinical significance,” Anirvan says.

Haystack has also designed a genome sequencing-based test that can replace RT-PCRs to better detect new variants and pathogens. “The next time a new strain comes, it won’t take us two months to sequence it because it will be detected by our software – it will already be sequenced,” says Anirvan.

Haystack’s initial research was funded by the Biotechnology Industry Research Assistance Council. The company also received angel funding from veterans in healthcare