Capitalizing Next Gen Sequencing to make cancer genome testing accessible, affordable
By Hariesh Ramanathan, Manager-Technology, Karkinos Healthcare
Next-Generation Sequencing (NGS) is a versatile DNA sequencing technology primarily applied in genetic testing, cancer research, and precision medicine. The significant advantage of NGS-based diagnostic tests is in their ability to detect very rare or subtle genomic mutations, which traditional methods might miss. By identifying specific genetic mutations causing cancers, NGS aids cancer physicians in choosing targeted therapies. Genomic testing also plays an important role in early cancer detection, especially hereditary cancers.
Karkinos Healthcare is the pioneer in accelerating the nationwide bench-to-bedside conversion of NGS services with its ‘Discovery through Delivery’ approach. It delivers cancer care via partnerships with hospitals, research institutes, and a network of advanced cancer diagnostic and research labs across India.
This care delivery method, via the Distributed Cancer Care Network (DCCN), is further enhanced by developing tailored cancer genome tests and solutions through industry-academia collaborations with premier institutes such as the Indian Institute of Technology (IIT). Working with these collaborators, Karkinos Healthcare’s diagnosticians, pathologists, and onco-physicians, combine their expertise at a state-of-the-art diagnostic facility with over 30% of India’s private sequencing capacity to offer molecular tests as the standard of diagnosis for oncology and advance cancer research in the country.
This blog will explore how NGS is deployed at Karkinos Healthcare to transform the cancer diagnostic landscape in the country and beyond.
Expertise in Genomic Sequencing
Our presence is bolstered through our existing network of Advanced Cancer Centers for Diagnostics and Research Labs in four cities—Mumbai, Kochi, Guwahati, and Chennai—and a fifth one coming up soon at Lucknow. These state-of-the-art cancer diagnostics and research centres drive unparalleled innovation in NGS in India.
It is worth mentioning that Karkinos Healthcare has grown to be a market-leading expert in expanding access to NGS services in the country. The company’s innovative D2C and B2B models have enabled us to quickly serve over 1.9 million citizens, leveraging a network of more than 800 physicians.
Karkinos’ Core Technological Capabilities and Service Excellence
Karkinos Healthcare leverages its widespread hospital partnerships to source and evaluate cancer-related ‘clinical insights’ (i.e., real-world observations of individuals and patients). This opens up a vast opportunity for applying NGS to further cancer research.
Karkinos Healthcare is in a constant endeavor to empower researchers and accelerate cancer research with Real World Evidence (RWE) from the Distributed Cancer Care Network (DCCN), which is standardized and curated by Karkinos Technology Platform and the capacity of the NGS Infrastructure powered by cloud-based scalable in-house developed pipelines in its ACCDR’s are distributed to in-house teams and institutional collaborators like IIT Madras, IIT Bombay, IIT Kanpur, and IIT Guwahati. This enables leading researchers in the country with the best technology in Karkinos ACCDR to integrate clinical insights with academic research catalyzed through Karkinos NGS tech infrastructure.
The real-world data from patients, which are used to further NGS research capabilities, refers to important observations, understandings, or conclusions derived from analysing patient data and using the information to expand medical knowledge and for posterity.
Karkinos Healthcare leverages every partnership to access patient insights, including the types of cancer diseases patients are presenting with, how patients respond to different treatments, and any identified genetic mutations or abnormalities. This collated data is shared securely (keeping the patient’s ID anonymous) with Karkinos’ in-house cancer research team and partnered research institutions, who then research to develop customised treatments for patients.
These clinical insights are then treated as requirements for their internal NGS research teams. This means the research aims to address these real-world needs identified through patient data.
By collaborating with prestigious institutions, such as IIT Madras, IIT Bombay, IIT Kanpur, and IIT Guwahati, Karkinos Healthcare can combine these clinical insights with academic expertise. This allows us to develop NGS-based solutions relevant to specific patient needs.
Karkinos Healthcare’s NGS infrastructure includes three Illumina NovaSeq X Plus, five Illumina NovaSeq 6000 units, PacBio long-read sequencers, Thermofisher Genexus sequencers, and Sanger Sequencers. These capabilities extend across four advanced diagnostics labs, where we conduct extensive research in (WGS, WES, Panels that are organ and hereditary-specific, single gene tests, guideline-based gene panels, KFlex to develop custom gene panels), Thermo Fisher somatic panels (KP500, K50), Illumina somatic panels (WES Somatic, K500, K75), PacBio long reads (structural variation, fusion, methylation, long read transcriptomics, RNA Sequencing (WTS) at Karkinos’ NABL accredited ACCDR Labs in Kochi & Mumbai along with our Advanced Cancer Research Labs in Guwahati and our upcoming lab in Lucknow.
In addition, Karkinos’ in-house bioinformatics portfolio, running on K-Cloud (Karkinos Cloud), significantly boosts our wet lab NGS capabilities. K-Cloud utilizes cutting-edge serverless technology for rapid data processing, which shortens turnaround times (TAT) for reports and allows for more comprehensive reporting. Combining clinical, research, and academic expertise accelerates the translation of research findings into optimum patient care (bench-to-bedside).
In addition to all the expertise mentioned above, Karkinos Healthcare’s genome testing capabilities are accentuated by the partnership with SOPHiA GENETICS, a cloud-native software company and a leader in data-driven medicine. Karkinos leverages SOPHiA’s sophisticated genomic data analysis solutions, significantly enhancing the company’s genomic research capabilities.
The SOPHiA DDM™ Platform is designed to compute a wide array of genomic variants and continually hone machine learning algorithms to detect rare and challenging cases. Karkinos Healthcare uses SOPHiA GENETICS’ technology to expand its offerings, advance research, and streamline workflow for various blood cancers, including Myeloid cancer and Lymphoma. In addition, the company analyses solid tumours for a variety of cancer types, including ovarian, prostate, breast, pancreas, lung, colorectal, skin, and brain cancers.
Karkinos Healthcare has also spearheaded research programmes to understand the genomic landscape of cancers in India with key collaborations spanning premier research institutions including the AIIMS, IITs, CNCI and Tata Memorial Hospital, apart from other tertiary care institutions. The research capabilities span genomics, proteomics, clinical and bioinformatics, data sciences, AI/ML, and multi-omics of cancer and have contributed to several key insights, publications, clinical tests, and products in these areas.
Strategic Partnerships and Future Outlook
By democratizing genome testing, Karkinos Healthcare is set out to redefine cancer diagnostics by applying advanced Next-Generation Sequencing (NGS) technology to make precision medicine in oncology more affordable and accessible. As said, through partnerships with numerous hospitals and research institutions nationwide, we leverage real-world clinical insights to develop impactful and targeted genomic tests.
Our unique “discovery through delivery” model, combined with the rapid addition of new test panels, positions Karkinos Healthcare to transform cancer care. Thus, the company is realising its vision of a future where NGS is the gold standard for precise diagnoses and personalised treatments that can be delivered globally.
