Sunday, October 16, 2016

The Hindu - Oct 12, 2016

Sam’s world of science

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Entrepreneur Sam Santhosh is leading genetic research with his laboratories across the country. Genomics is the next big thing for humanity, he says

gene manSam Santhosh, CEO SciGenome, loves reading and archaeologyphoto: H.vibhu
gene man Sam Santhosh, CEO SciGenome, loves reading and archaeology photo: H.vibhu
Asecond innings is almost always about new beginnings and not always about cricket. For Sam Santhosh, Silicon Valley entrepreneur from the State, it is about embarking on a completely new path of genetic research, different from his earlier preoccupation with the software industry. It is also about his fascination for the prehistoric and related travels to remote archaeological digs.
His first success story was marked by several business acquisitions in the US and in the founding of an IT company Calsoft, a product re-engineering firm, in 1992, which grew to global proportions. He sold it handsomely in 2009 and began his second innings.
This time round he is a far more “relaxed” entrepreneur, a man who now wishes to wield his experience in ways to help societies, monetise new opportunities and indulge in his varied interests - history, mathematics and reading to name a few.
When most entrepreneurs still looked at genetic research with unease Sam pre-empted the next big thing that will be the vehicle of change for humanity as was the computer 30 years ago. He switched to genetic research founding SciGenom Inc.- a genomics R&D organisation, in 2010.
“The entire genetics research has been a long struggle. It took three billion dollars, 12 years of work and 15 countries to arrive at the first human genome sequence but genomics is the future, the next big thing, a much bigger revolution than computers. This may take another 25 years to play out but its impact on humanity will be bigger. This is the best chance, specifically for India, to use this moment for related research that will be useful to the people and country,” he says sitting in the boardroom of Hotel Le Meridien, on the sidelines of a global convention on genetic research hosted by his foundation. The first such mega event was held in Thiruvanthapuram in 2011 followed by, next year, in Chennai.
Hailing from Thrissur, and after his MBA from IIM Kolkata, Sam worked on his own in Kochi for three years, computerising businesses before he left for California in 1991. The eco-system there nurtured an out-of-the-box thinking, a trait that he wishes to ingrain into young mindsets here.
“If Steve Jobs was in India, he would have definitely done well but he could not have founded Apple - though he did come to India and drew his philosophy from here,” he says implying that scientific thinking needs to be stoked among students and start ups here and that India has the philosophical edge to back that. In payback mode Sam organised a reading initiative in 2014 along with Kairali channel to inculcate reading habits among MBA students. His gene research lab in Kochi and the spin-off companies MedGenome, soon to become in Silicon Valley parlance, a unicorn, Agri-Genome in Hyderabad are satellite labs into research, DNA Sequencing and Analysis and promote scientific thinking. “DNA sequencing is the powerhouse. It is a technology that will help other industries find solutions. In fact, we incubate solutions,” he says.
Currently Sam is savouring the moment with top scientists who are working on important discoveries, debunking myths, finding answers and exploring the unknown. “It’s an exciting field,” he says, adding that the capacity and funding for scientific research in India is low.
In his new scheme of things his other passions - reading and travelling - play an important part. He travels often guided by his keen interest to archaeological digs where he diligently follows unearthing the dead past, the latest being to the dig in Anuradhapura in Sri Lanka, where the Chola empire excavations dating back to 950AD are underway.
“The biggest story unsaid in South Indian history is about the second Chola Empire, from 950AD-1300 AD. In this part of the world not only was it the biggest empire but its influence in South and South East Asia is under appreciated,” he says revealing his deep interest in history of South India, something that he wishes to collate in detail.
With altruistic diversions has business taken a back-seat in his second innings? His work model is new and is about off shoots and spin-offs from a core concept. “People have not done this before, but wealth will be generated through spin-offs,” he says adding sequencing services will incubate other services. “This is the goal. It made sense to invest.” With a clear roadmap for scientific development in the future and buzzing with novel ideas Sam wishes that the scientist in India would be more appreciated. For his business is all about the power of the scientist and of monetising the power of science for humanity.

Saturday, May 7, 2016

The Public Intellectual in India by Romila Thapar - Book Review

"To Question or Not to Question? - that is the Question"

Romila Thapar is a renowned Indian historian with a number of excellent history and philosophy books to her credit. However, this book is different – it tries to examine the current status of the public intellectual in India. The origin of the book is a talk that she gave at the third Nikhil Chakravarty Memorial  Lecture (yes, I had also not heard of him but checked up on Wikipedia -  Nikhil was a respected journalist in India who founded the journal Mainstream) in Oct 2014. The lecture was titled “To Question or Not to Question, That is the Question”. That lecture has been revised and expanded in this book and five more essays added from other well known intellectuals – Sundar Sarukkai, Dhruv Raina, Peter deSouza, Neeladri Bhattacharya and Javed Naqvi, which were in response to Romila’s essay. The book concludes with a brief summary by Romila Thapar with her comments on the other responses.

In Romila Thapar’s lecture she laments the state of the current Indian affairs, the declining role of the Public Intellectual in India, the increasing communal polarization by religion, the rising Hinduvta extremism and trend towards increasing authoritarian behavior by the Indian Government. Surprisingly she downplays the economic development since the liberalization of 1992, and strangely believes that it has not made much impact. (I guess you have to be really living in an intellectual cocoon not to see how the last twenty years of development has brought millions of Indians out of poverty!). Other than that her essay is great and it brings out a large number of issues and points that all Indians need to think about, with her principal concern being about the legacy of colonialism that still leaves a significant mark on all major Indian policies.

Sundar Sarukkai’s essay focuses on nature of questioning and whether Thapar’s call to question needs to take into account certain fundamental characteristics of the act of questioning such as scientific rationality, knowledge/ignorance level, intellectual honesty, and ethics. Dhruv Raina’s essay focuses on Science and Democracy and argues that the institutional transformation of science over the last couple of years (a transformation in which the scope of criticism and skepticism is limited) has altered the relation between science and the public as well as the critical discourse on science and society.  According to him the world of ‘Big Science’ and dependence on large funding has reduced the independence of scientific thinking and thus reducing the effort to work for the good of society. Peter deSouza in his essay focuses on the definition of the public intellectual and his or hers different personas to examine the logic at work in the public intellectual. His essay is in three parts, with the first part covering the stories of three individuals (Priya Pillai in India, Yeshayahu Leibowitz in Israel and Avijit Roy in Bangladesh) which are tragic examples of what public intellectuals can face in today’s world. The second part examines the factors that prevent public intellectuals being more active and third part looks at how these factors work in Indian politics today.
The fourth essay is by Neeladiri Bhattacharya and it questions the framework of Thapar’s question and the type of public individual that she is referring to. He is more optimistic than Thapar on the state of Indian affairs and feels that the role of the public intellectual in India has not diminished much. I found the final essay by Jawed Naqvi, the best of the lot. Starting with a couple of examples where the Public Intellectuals have played an important role in recent developments in India, he still highlights the major challenges faced by questioning voices in the supposedly democratic fabric of Indian society. Urging us to look beyond the much-hyped Hindu-Muslim divide in India, he brings to open the caste consciousness still highly relevant in India.

All the essays are of very high quality and I salute Romila Thapar for this endeavor to bring them out in a single book format. This is a must read for all Indians who are concerned with the future of our country.

Tuesday, April 19, 2016

Sequencing 100,000 Asian genomes for tailor-made healthcare - Straits Times, Singapore

NTU to host project database; aim is to reduce bias of medicine towards Westerners - Lin Yangchen

Not too far in the future, you may be able to receive tailor-made medical treatment for your body, increasing your chances of survival and recovery from serious illnesses.
This is one of the aims of an initiative to sequence the genomes of 100,000 Asians over the next three to four years. The move will try to reduce the bias of modern medicine towards Western populations.
An earlier project in 2009 stimulated interest in Asian genetics when it surveyed specific genetic variations across 1,928 people in South-east and East Asia.

Now, Singapore's Nanyang Technological University (NTU) will host the database for the ambitious new project, which was announced by the non-profit multinational consortium, GenomeAsia 100K, in February.
NTU president Bertil Andersson noted that almost all current personal genomics efforts focus on Western populations. He said: "The new consortium will benefit the Asian population as it sheds light on the genetic fabric of Asians."
Singapore has very high standards in finance and corporate law.
NTU'S PROFESSOR STEPHAN SCHUSTER, on the partners of GenomeAsia 100K choosing NTU to host their database because of Singapore's reputation for accountability.
Asia has more than four billion people, making up more than half of the world's population.
The project aims to cover at least 40 countries across Asia, and all major ethnic groups on the continent.
Combined with data such as people's living environment and health status, the exercise will make it possible to better understand and treat diseases in Asians, said venture capital firm Emerge Ventures. The Singapore firm supports the consortium's meetings, and helps it find potential partners and philanthropic donors.
The consortium's scientific chairman, NTU's Professor Stephan Schuster, said: "There is a massive bias in medical research; Europeans have been developing drugs for Europeans without asking how compatible these pharmaceuticals are for the rest of the world."
He explained the benefits of customising medical treatment to individual patients, an approach known as precision medicine.
For example, he said, the debilitating effect of chemotherapy on cancer patients makes it important to administer the right drug to minimise suffering and maximise the chances of recovery.
GenomeAsia 100K comes after a similar initiative - the 100,000 Genomes Project - was launched in 2012 by the British government-owned company Genomics England.
The partners of GenomeAsia 100K chose NTU to host their database because of Singapore's reputation for accountability, said Prof Schuster. He said: "Singapore has very high standards in finance and corporate law. We were given the trust and confidence from the other Asian countries." He stressed that the consortium will abide by the United States' Genetic Information Nondiscrimination Act of 2008, which prohibits the use of genetic data in health insurance and employment.
When data enters the database, it will be accessible only to the consortium members for an initial period of 18 to 36 months for analysis, after which it will be made available in anonymised form to the scientific community at large, he added.
To date, 50,000 DNA samples have been collected through blood or saliva samples from a network of clinics across Asia with the help of two of the consortium's founding members, genomics companies Macrogen in South Korea and MedGenome in India.
Macrogen's chairman, Professor Jeong Sun Seo, said: "As the consortium is envisioned to be independent of any government's interest, there is greater scope for comprehensive coverage of the peoples of Asia."
Mr Mahesh Pratapneni, chief executive of Emerge Ventures and exective chairman of GenomeAsia 100K, added: "The consortium is expected to contribute towards better global healthcare outcomes by channelling the collective capabilities of the leading industry players in the region."
The consortium is in talks with potential academic and industry partners in Singapore, Malaysia and Thailand, and is looking for more partners and philanthropic sources to make up the US$150 million (S$200 million) total funding it says it needs.
Prof Schuster pointed out that any concerns about ethnicity issues are unfounded. He said: "Some people are apprehensive that if you unravel differences in ethnicity, you make some people a lesser man and others a better man.
"But it's not true. It gives people pride in their identity, and also it gives them their history."

Thursday, November 12, 2015

The Brain: The Story of You by David Eagleman - A book review

From Incognito to Singularity!

In his earlier illuminating book ‘Incognito’, David Eagleman showed us our hidden selves and challenged us to think about ourselves differently. He continues in that direction in his new book ‘The Brain: The Story of you’ and visualizes the possibilities of the future of the brain  and in fact the future of our species.  The Singularity is a concept popularized by the well known futurist scientist Ray Kurzweil (refer his book ‘The Singularity is Near’ in 2005) where he envisioned a future where we will be able to leave our bodies and live in a digital world by uploading our brains into a computer system. Kurzweil was pretty much vague on the details  but Eagleman in this book shows us how challenging that can be.

With over 100 billion neurons and many trillions of connections among them, the complexity of the brain is unquestionable but understandable. However the fact that  ‘consciousness’ emerges from this is the amazing outcome that leaves us in awe. Kurzweil had argued that ‘consciousness’ is a rather natural outcome of a complex interconnected system, and in books like the ‘The Age of Spiritual machines’ it was assumed that soon computers and robots (and may be the Internet) would develop a consciousness.

But as we understand more about the biological nature of the brain and its learning system, we will start doubting whether an artificial system will ever develop  consciousness on its own. I don’t doubt that when technology is advanced enough we would be able to create a human like (or a human better) intelligence but I don’t  think a machine or AI system can naturally develop  consciousness if its creator (that is us) did not train it to. 

The best parts of David Eagleman’s book are where he explains (a) how the plasticity of the brain and its self learning ability to understand patterns can be leveraged in the future to provide different inputs to the brain (than the normal sensory inputs that we are born with) (b) how many other inputs that we don’t normally recognize influence our brain – a beautiful example is on how our emotions are influenced by the input  to our brain from our facial muscles when we witness an event (c) what will be our future – I leave this for you to read and find out!  

Thursday, August 6, 2015

Interview with ET HealthWorld


INTERVIEW: MedGenome raises Series B to advance the practice of precision medicine in India

MedGenome, a leading provider of genomics research services globally announced $20 million Series B investment from Sequoia Capital on June 22nd 2015.

MedGenome, a leading provider of genomics research services globally announced $20 million Series B investment from Sequoia Capital on June 22nd 2015. Sam Santhosh, CEO MedGenome, speaks to Shahid Akhter on the path that MedGenome is treading now and what lies ahead.

1. What prompted you to genomics and how has been the journey so far?

The completion of the first draft of the human genome by the International Human Genome Project in 2001 originally attracted me to this field. I was intrigued by the opportunity produced through understanding and leveraging the genomic source code which is the language of life for all living beings. I spent few years in reading and learning about the subject during which period, the DNA sequencing technology went through a revolution by exponentially reducing sequencing cost while increasing processing speed. For example, sequencing the first human genome took 10 years and cost about $3 billion, while now we are at a stage talking about a $1000 genome in two weeks.

With the advent of these new technologies called Next Generation Sequencing (NGS), I saw the opportunity of creating a company for genome sequencing and data analysis. Genomics can create dramatic changes in healthcare, agriculture, animal sciences, environmental protection, bio-fuel, and so on. Using the same technologies vertical solutions in these domains could be developed. So I created a services company called SciGenom and MedGenome was incubated as an entity for medical genetics. And we spun it off as a separate company in 2013. So far the growth has been encouraging.
We have a leading position in clinical genomics in India and has set the benchmark for clinical genomics in emerging markets. We have also pioneered genomics-based research in India through our network of collaborators to enhance our understanding of the diseases at the genetic and molecular level. These were possible because of our extreme focus on bringing the latest advancements in technology in the Indian market - be it the advanced NGS lab in Bangalore or the launch of the non-invasive prenatal test for the first time in a facility in India - and success in developing world class bioinformatics pipelines.
2. What was your initial vision for the company? Where do you think you are with the vision?

Initial vision was to create a company in India applying genomics to improve personalized medicine in India and reduce the burden of inherited diseases. Subsequently the vision got enhanced to provide genomic research solutions to pharma once we understood the potential of Indian population to provide better understanding of complex diseases. And this has been very exciting and rewarding experience.

We have the most advanced technologies in our lab, for example the latest Illumina HiSeq 4000 machine addition to our lab; the first in India. We have developed intellectual property through proprietary platforms such as OncoMD, our cancer mutation platform and OncoPept, our immunotherapy solutions supported by our unique bioinformatics pipelines and proprietary databases. We are also the leading clinical genomics company in the country. We have our presence in the US as well through our R&D lab in San Francisco and office in Boston. And the recent Series B funding will allow us to expand our offerings and reach further.
3. How do you find the concept of 'genetic testing' gaining currency in India today? How does this compare with global market?

We have seen good progress on the acceptance of genetic testing. It is a function of awareness and the affordability, both of which have been focus actions for MedGenome as the leader in the market.
What has been very encouraging is the consistency of the prescribers once they see the value of genetic testing in their practice. We work with thousands of doctors every month across hundreds of institutions and the collaborations have been very enlightening.

It is also important to not stop at delivering a report but also support the patient in learning about the specific nature of the genetic condition. Which is where counselling plays an important role.

Globally, genetic testing has gained considerable traction in clinical setting for diagnosis, prevention, treatment and management of a wide variety of diseases with an underlying genetic reason, in light of the recent advances and celebrity endorsements. It is a rapidly expanding segment of the molecular diagnostics market worldwide given the increasing awareness about the value that these tests bring to the healthcare providers.

4. How would you summarize the trends in the molecular diagnostics sector over the past five years?

Genomics has seen rapid advances in the technology of decoding the DNA, triggering a revolution in our ability to understand the genetic and molecular basis of health and disease.

Genomic biomarkers as companion diagnostics are helping the pharma majors to provide more targeted therapies. Oncology has taken a lead in this so far but applications in other disease areas have been looked into. Genomics to enable differential diagnosis in neurological disorders is a good example of this.

Translation of large scale sequencing data into information of clinical utility is gaining importance globally. In the US, many companies have leveraged this opportunity - Foundation medicine is offering comprehensive genomic profiling for tumors, Invitae provides genetic testing across multiple disease areas and Natera has grown on its proprietary non-invasive prenatal tests. Over a million tests in NIPT have been prescribed in the US so far. So an understanding of the need and the acceptance for genetic testing have been encouraging so far.

Predictive medicine, using advances in accurate technologies in medicine, genomics, proteomics, cell biology, imaging etc. and allowing us to predict how, when, and in whom a disease will develop has gained traction in the recent years. This could be a new revolution in human health care where genetic information contained in an individual's genome is interpreted to predict future predisposition to diseases. Many companies have been built and are experiencing growth leveraging this trend, in the US especially.

Lot of work went into advancing the use of genomics in exploratory research and drug discovery in the recent years.
5. Your opinion about the genetic testing market and where does MedGenome stand?

 Genetic testing has clinical applications for diagnostic, predictive, carrier, prenatal & pre-implantation testing, and newborn screening, also playing a vital role in pharmacogenetic testing. It offers distinct advantages because of its ability to facilitate early disease detection with simpler and cost effective treatment and stratification of patients into groups allowing selection of optimal therapy.

It is going to be the standard in the future. A genetic testing report will be an integral part of a physician's decision making process. As far as MedGenome, it is a leader in the clinical genomics market. MedGenome offers more than 100 tests currently across Oncology, cardiology, ophthalmology, neurology and nephrology. We have pioneered the launch of advanced genetic tests in the country - such as the non-invasive prenatal test launched this year. We will be the only company conducting this test in a facility in India.

Outside India, we are focused on providing diagnostic and research solutions only. Our OncoMD, cancer analytics platform, provides valuable clinical parameters to enhance the value of a diagnostic report through an API integration. Our OncoPept, cancer immunotherapy solution, allows identification and prioritization of peptides towards vaccine development by pharma and biotech.

6. What hurdles you have faced since inception?

 One of the first hurdles was on educating the prescribers and the patients on a larger scale about genetic test offerings and the impact it can have on patient's life. We had few who were aware and were early adopters, but to scale and customize the offerings, we needed to generate awareness. Cost of infrastructure was also important. We focused on having the latest technologies in sequencing for India and that required investment. It has allowed us to provide high quality reports with faster turn-around times which is essential for the stakeholders. We also had to develop our IP on population specific variants in Indian patients. Such information allowed us to refine our genomic data interpretation more accurately giving us an edge in the Indian market.
7. What are the challenges you feel the genomics and biotech industries are facing today? Do we need regulations or code of conduct?

 Rising R&D costs is a challenge that is experienced by the biotech companies globally. Regulatory barriers and reimbursement from insurance companies is also having a significant impact on the success of the industry. Genomics, as a discipline, is recently studied as a means to improve R&D efficiency by improved patient stratification for clinical trials, thereby reducing the time and cost required for the trial. Regulatory authorities are also encouraging this as the results from these trials are more targeted and in favour of the needy.
From genetic testing perspective as well, certain factors like regulatory body approval, and reimbursement from insurance companies are crucial. In the western world, insurers have started accepting genomic tests in their formulary as it is expected to reduce the cost of down-the-line treatment. Another challenge is on patient confidentiality and ownership of genomic data. Requirement is to have policies and committees to enforce a check on this as genetic testing grows in the clinical practice.
In India, these tests are yet to be offered at affordable prices. There is also a great need for clinicians who have a good understanding of genomics and its clinical significance. Genetics, as far as I understand, is not widely adopted as part of the medical college curriculum in India.

The patient journey must be well managed so that if a particular condition is identified, the experts are brought in to handle the situation and help the individual. There is a dearth of genetic counsellors who can explain genomics findings to the affected individuals and their families. In addition to this, lack of baseline genomics data of Indian origin and unclear policies on intellectual property rights also pose hindrances to the industry.
8. Where do you see MedGenome 10 years from today?

 We want to be a global leader in genomics-based diagnostics and research. A company working on cutting-edge technologies and where core capabilities and Intellectual property are built.

We have an opportunity to look beyond generics in the Indian health care space and contribute towards drug discovery and exploratory research and gain a prominent role in the global healthcare industry.
9. Any advice you would like to give to budding entrepreneurs?
Science provides huge number of opportunities for budding entreprenuers. I would urge them to look beyond IT and Ecommerce and leverage the revolutionary advances in Genetics, Nanotechnology, Neuroscience and Robotics to develop products and solutions that can make a significant difference to humanity.