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Among the numerous startups that have been working alongside the government in the fight against the COVID-19 pandemic has been HaystackAnalytics. The Mumbai-based healthtech startup is using genomics to trace the transmission of coronavirus in India and understand the transmission patterns of the virus to help the government plan a better strategy to fight the pandemic.

The applicability of genomics

Genome is the data centre for every living being. Sequencing this genome opens up these data points to be processed for understanding the diseases anyone is facing or will face. Sequencing the genome helps researchers to get five million data points for a pathogen to three billion data points for a human sample.

“Unlike the RTPCR (Reverse transcription polymerase chain reaction) tests which look at a very small piece of the information, genome sequencing provides a near complete information of the biological system stored in the DNA/RNA of a pathogen or a human. Sequencing is almost a gold standard of comprehensive information,” shares HaystackAnalytics’s co-founder and CEO, Dr Anirvan Chatterjee.

HaystackAnalytics is envisioning a world where several million diagnostic tests would be done daily based on genome sequencing technology and is building the technology for data handling, and data interpretation at that scale. HaystackAnalytics’ genomic SaaS solution replaces the current time-consuming processes of genomic data analysis (bioinformatics) and reduces the analysis time from several days to a mere a few minutes, explains the co-founder.

Dr Anirvan points out that while genomics is not a new interdisciplinary field of biology, its usage hasn’t percolated much outside academics into mainstream diagnostics. “While everyone in the healthcare industry understands the impact of genomics – right from enabling faster and accurate diagnosis to inferring the right medication to creation of new biomolecules and even new medicines – the adoption of genomics has been slow,” he says.

But, other factors make it difficult to accept this technology. The time required to analyse the genomic data is long and requires a high level of expertise. Further, the tremendous advances in modern computing are only beginning to be imbibed into genomics, necessitating a rapid churn in the analytical processes. The lack of such agile applications, combined with general inertia to onboard a new tech severely limits legacy healthcare providers to scale and adapt rapidly. And, in cases where sequencing platforms have been developed, the deployment of such technology at a mass scale has been limited especially in cases of resource-limited settings,” shares Dr Anirvan.

A ‘SaaSy’ way to accelerate adoption of genomics

Today, HaystackAnalytics is addressing these challenges to scale this technology and make it mainstream by bringing automation to genomics with the HaystackAnalytics genomic SaaS solution. A comprehensive one-test solution, HaystackAnalytics’ Ω-series is a genomic analysis software that analyses genomic data and can be deployed through the hardware that has been co-developed with Intel as a plug-and-play solution for diagnostic labs and hospitals. This will get genomics, which was otherwise mainly used for research, as a scalable solution for mass deployment for patients. This will also remove the need for current molecular diagnostic labs to update infrastructure or reskill. “HaystackAnalytics is an enabler of genomics-driven comprehensive diagnostics that reduces uncertainty for doctors and encourages better decision-making leading to better patient outcomes,” explains Dr Anirvan.

Having worked for a decade in genomics, Dr Anirvan’s expertise lies in the deployment of Next Generation Sequencing (NGS)-based analysis in healthcare at the University of Oxford and DTU Denmark. At HaystackAnalytics, Dr Anirvan is joined by the startup’s two co-founders – Prof Kiran Kondabagil and Gaurav Srivastava. While Kiran is at the Indian Institute of Technology, with significant expertise in molecular biology, infectious disease, genomics and evolutionary biology, Gaurav is an alumnus of IIT, Kharagpur with expertise in navigating operations of tech startups across Singapore and India.

The three co-founders and the team spent the first six months in stealth building the genomic analytic platform for rapid tuberculosis antibiotic test. In early 2021, the platform was being tested in private and government healthcare setup. The startup received a government grant to build the capability for COVID-19 genome analysis. “Because of the platform’s default software capabilities, we were able to quickly migrate the application to suit the needs of COVID-19 genome sequencing,” says Dr Anirvan. In June 2021, the startup launched the rapid tuberculosis antibiotic test. The solutions were deployed in JJ Hospital in Mumbai and were also leveraged in the National TB Elimination Programme. Now HaystackAnalytics is gearing up for the launch of their next clinical application on their platform, internally dubbed “ΩID” which has been validated for detecting several 100 pathogens in a single test.

“The back-end AI-Machine Learning driven inferencing engine enables us to rapidly empanel new use cases for genomic diagnostics, and also enable drug-discovery. Today, we are creating several applications wherein each application is focused on one disease or one scenario outcome,” he says.

Intel Startup Program bridges the last mile gap

A key factor that has enabled HaystackAnalytics to accelerate its product development journey in the early days has been its association with Intel. “Intel has been a key player in developing computing technology for genomics with globally leading universities such as MIT and Harvard. Intel chips have been game changers in the field. Intel India also has deep expertise in core memory and computing optimisation specifically for handling genomic data processing algorithms enabling us to take the analysis on-site for the client more easily and build scale at a greater level,” shares Dr Anirvan. In 2020, getting selected for the Intel Startup Program brought the opportunity to leverage this expertise and co-develop a computing device to enable last mile access to the Haystack genome analytic platform. He says, “The EDGE computing device has been built taking advantage of numerous consumer products already available in the market. By customising the computing device, we have been able to bridge the last mile gap in building scale by enabling direct deployment of the software by the diagnostics or hospitals.”

A multi-level impact

In a span of a year since the launch of genomic SaaS solutions, the impact that HaystackAnalytics has been able to drive speaks for the need and effectiveness of its platform. Today, the startup’s plug-and-play genome sequencing solution allows diagnostic labs and providers to move to a technology-centric approach of diagnosis for general patient consumption, which promises better accuracy, faster turnaround time, all at a significantly lower cost.

“By bringing automation to genomics, we are able to drastically reduce the test turnaround time by anywhere between 33 to 85 percent depending on the disease/infection,” Dr Anirvan says. For instance, introducing a single test for 18 antibiotics for tuberculosis, HaystackAnalytics reduces the turnaround time to four days instead of four-six weeks incurred by the traditional testing methodologies. This also means there is elimination of the need for multiple diagnostic tests and the end-user, which can be the patient, the clinician or the doctor, can get the required information on day one of the test results. The other advantage that a platform like HaystackAnalytics brings especially when used in a public health setting is that, unlike current diagnostic tests which help to diagnose disease outbreaks, the platform will be able to use the genomic data to preempt disease outbreaks.

The software also has a versatile use case application depending on who the end user is. While in the case of clinicians or healthcare practitioners, they are able to derive answers to questions such as which drug will work better, public healthcare policymakers or decision-makers are able to use the data to find intelligent ways of applying public health interventions where they are most required.

Why genomic diagnostics is the future

The startup believes that the shift from the current day diagnostic protocols towards molecular and genomic diagnostics has only just begun. “We expect in the next five to seven years, 30 percent of the current day pathological diagnostic tests that are being done, will actually transition into genomic test on the clinical side,” says the CEO.

Scaling at breakneck speed

From the first test launched by HaystackAnalytics, they have scaled rapidly and multiple partners have come on board to utilise the whole genome sequencing solution provided. “We have launched the TB WGS test as our first test and we have grown the total market 20x in the last four months and now own 90 percent market share. Just in this product, we expect the market to increase 25x in the next 12 months working with our partners and expect a similar growth trajectory for all our products that we are rolling out,” quotes Gaurav Srivastava.

Almost all of the top 10 diagnostic labs of the country today are partnering with HaystackAnalytics. “Metropolis, Dr. Lal Path Labs, Anderson, Thyrocare to name a few top players and now have all of the major hospitals as our partners with Hospitals like AIIMS, CMC Vellore all sending us their samples,” shares Dr Anirvan.

HaystackAnalytics is following the model of partnership with diagnostic labs and hospitals, enabling them to get started with their Genomic product offerings. With multiple partners coming on board in the last five months, there is a display of intent and desire of the industry to upgrade with the cutting edge solutions provided by HaystackAnalytics. There are several products in the pipeline catering to chronic and infectious diseases diagnostics and some of them are being developed in collaboration with partners.

“Even though Genomics as a market itself is nascent and set to grow 100x in the next 3-5 years. For the industry to handle as much data and volume, technology and automation is the only way forward. Us being an innovator in this technology opens up a tremendous market ahead of us to scale but what drives us is the opportunity to make a lasting change in the way healthcare is perceived by all stakeholders ” concludes Kiran.

How the Intel Startup Program is empowering startups to unlock their potential

The Intel Startup Program is Intel India’s flagship program to engage with technology startups who have an IP or innovative solutions that have the potential to create impact on customers and align with Intel’s focus areas. The program is at the forefront of engaging with India’s startup ecosystem through high impact collaborations with the industry, academia and government and runs multiple initiatives that are either vertically aligned or focused on emerging technologies.

It engages with startups that have a unique global or local value proposition to solve genuine customer problems, enabling them with domain and business expertise from the industry and the best mentorship from Intel.

For more details visit: https://www.intel.in/startup-program