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Clinical Sequencing Starts to Take Hold in India, but Cost, Lack of Education Remain Hurdles


NEW YORK (GenomeWeb) – Lower costs, increased education, and more population-specific genomic research are key for clinical sequencing to take hold in India, according to early adopters of the technology.

Several companies in India have recently begun offering clinical sequencing services and each has developed its own strategy and approach to delve into the nascent market.

For instance, New Delhi-based Lifecode Technologies is offering a diagnostic exome test for undiagnosed diseases with other NGS-based panels in its pipeline, While Mumbai's Positive Bioscience announced earlier this month that it would partner with Medanta, one of India's largest hospitals, to develop a genomics clinic that offers next-generation sequencing-based disease risk prediction.

And, as Clinical Sequencing News reported last week, Supratech Micropath, based in the state of Gujarat, has launched a number of research-based tests that it plans to validate for clinical use in preimplantation genetic screening and diagnosis, newborn diagnosis, and cancer.

Lifecode launched in 2013 with the goal of developing genomics-based diagnostics, Jameel Khan, the firm's managing director, told Clinical Sequencing News.

Lifecode has a somewhat unique business model. Not only is the firm working on developing its own sequencing-based assays, but a portion of its business is based on technology transfer to clients such as pathology laboratories or other companies looking to move into the genomics space. "We develop a pipeline, run it for a limited period, and then transfer it to the client," Khan said.

In addition, Lifecode will act as a service provider, running assays in its own lab that have been developed by other companies.

Currently, Lifecode offers a $2,000 diagnostic exome test for undiagnosed genetic disorders and is running around four to five tests per month, Khan said. He declined to disclose what NGS system Lifecode is using.

Lifecode also offers single-gene tests for various pharmacogenomics markers, and is also working on candidate gene tests within different disease areas, such as cardiology, using Sanger sequencing and allele-specific PCR.

Khan said that there are two major challenges in developing NGS-based diagnostics for the Indian market. One major challenge is cost. Health insurance in India is essentially "non-existent," Khan said, with the exception of some government employees, so patients pay for everything out of pocket.

Even though prices are coming down, a $2,000 price tag is still "not something everybody can afford," Khan said. "So the marketing has to be done intelligently." The second hurdle is physician awareness. "It is a major challenge to educate physicians that this is possible," he said.

Nevertheless, Khan said he anticipates that clinical NGS will continue to be adopted in India. For instance, he anticipates that Lifecode will move its pharmacogenomics tests onto an NGS platform and said that he thinks that the disease-specific tests will also eventually migrate to NGS, especially as test volumes increase and it makes more economic sense. "There is also the possibility that everything will go to exome sequencing," he said.

Lifecode currently focuses on diagnostics, rather than disease risk prediction, and Khan said that using next-gen sequencing to predict disease risk in otherwise healthy individuals is particularly challenging in the Indian market because there have not yet been enough population genomics-based studies of Indian individuals.

The majority of variants associated with an increased disease risk have not been validated in the Indian population, he said, so it is difficult to make accurate risk predictions. While there are currently ongoing efforts to do such studies, those projects are still in their infancy, he said.

Nonetheless, Medanta, a major hospital in India, is investing in such an idea. In partnership with Positive Bioscience, it is developing a personal genomics clinic where individuals will be able to get their exome sequenced to understand what diseases they may be at risk for developing.

Exome sequencing will be done on the Illumina HiSeq 2500 and will include genetic counseling along with the sequencing and analysis. The test will cost $1,600 and will be paid for out of pocket, Samarth Jain, co-founder and CEO of Positive Bioscience, told CSN.

In addition, Jain said, Positive Bioscience will develop several disease-specific array-based tests at significantly lower prices, including a test for the 10 most common cancers in India that will cost in $400 to $500 range and a test for the top 25 most common diseases in India for $650.

These tests will be marketed to healthy individuals with the aim of disease prevention, Jain said. Medanta will appoint a doctor in various disease specialty areas, such as cardiology, neurology, and oncology, to be trained in genomics and how to use the genomic data from the testing.

Jain said that Positive Bioscience is also looking to form similar partnerships with other hospitals in India that are looking to offer genomic-based testing for disease risk prediction.

In addition and separate from its hospital collaborations, Positive Bioscience offers exome sequencing for healthy individuals, as well as sequencing for cancer patients to identify targeted treatments, and has been receiving around 50 to 100 patient samples per month for its tests. Jain said that by the end of the year, he expects about 200 to 300 patient samples each month.

Positive Bioscience's expertise is in data analysis, Jain said, and it outsources all of the sequencing to a partner lab in London. In addition, the company is certified by India's National Accreditation Board for Testing and Calibration, which is equivalent to CLIA certification in the US, Jain added.

He echoed Khan's sentiments that costs and awareness of the technology were the two main barriers to adoption of clinical sequencing. "Right now it's more for the affluent that can afford to pay for it," he said.

However, he thinks that over the long term as costs decline, clinical sequencing will become more widely adopted. He said that using sequencing to predict disease risk could play an important role in preventative medicine in India, he said, where patients often do not go to the doctor unless they are sick because they pay for everything out of pocket.

However, he also acknowledged the criticisms of doing next-gen sequencing in otherwise healthy individuals. "This is new technology," he said. "And we try to make people understand that we don't know everything." As such, Positive Bioscience will store and update its patients' genomic files as new information is uncovered.

In addition, he said that the company is conservative in its disease risk predictions, does not report out variants of unknown significance, and confirms its genomic findings with other tests when possible. For instance, he said, in one case genomic testing found that a woman was at risk for hyperthyroidism, and it was recommended that she get a blood test. The blood test confirmed the result and the patient was able to receive appropriate treatment.

Disease risk prediction is also personal for Jain who said whole-genome sequencing of his own genome uncovered a risk variant for non-small cell lung cancer. "In India, this type of cancer is typically caught very late and the odds of surviving are low," he said. But because he knows he is at risk, he said his doctor regularly does a lung function test to increase the chances of early diagnosis.