Next Generation Sequencing: an innovative approach to preventive medicine | Sunday Observer

Next Generation Sequencing: an innovative approach to preventive medicine

Acclaimed as cutting edge of diagnosing various diseases using the latest techniques of Next Generation Sequencing ( NGS) and the first of its kind in Sri Lanka, the Credence DNA facility has opened a new door and hope for patients, especially, those at risk of predictive diseases such as, cancer. The success rate so far in cases handled by the facility are encouraging.

The Sunday Observer spoke to the CEO & Founder Director of Credence Genomics Dr Vaz Gnanam to find out how the advanced techniques he is using has helped to raise the overall quality of human health.

Excerpts...

Q. The Credence DNA facility has been acclaimed as cutting edge of diagnosing various diseases using the latest techniques of Next Generation Sequencing ( NGS). It is also the first of its kind in Sri Lanka. As the CEO, and founder Director Credence which operates this facility, tell us what your work involves and how this innovative approach to preventive medicine was conceptualized?

A. In 2011 we aimed to build a genomics company which would leap frog conventional technology. We would be able to provide a unique product / service offering based on this cutting edge technology. The technology commercialized at that time was the next generation sequencing platform. There was at that time two major platforms available, one based on a semiconductor chip and the other optics. We choose the semiconductor based platform knowing that there would be a cost benefit in the future.

Q. As one of the latest medical advancements, many people are still unaware of what exactly Bio technology means and its link to human health. What is it? Explain in detail.

A. That is a question which really has no boundaries to an answer. Biotechnology as a field has been there for many years and has evolved with new technologies that are made available from other interdisciplinary fields. In itself, biotechnology would encompass the use of organisms to create new products or use of technology/engineering to modify organisms, processes in relation to organic functions or impact biological systems at a macro or micro level. In human health, biotechnology has played an important role in research, diagnostics and therapeutics. For example, the presence of biomarkers allows us to find the presence of a disease and this is a product of biotechnology. Next generation sequencing is also an area of biotechnology and overlaps fields of chemistry, nanotechnology, mathematics, and computational science. Molecular biology which has been there for a long time is also an area of biotechnology used in everyday healthcare. Pharmaceuticals also use biotechnology to synthesize various chemicals or enzymes in the drugs we take. Even the sensors used in your simple blood glucose monitoring is a contribution of biotechnology integrating electronics and engineering. So the spectrum is quite large.

These are only a few areas that contribute to healthcare but biotechnology even impacts other areas such as, the food we grow (biofertilizer) , food we eat (GMO), textiles we wear, detergents we use, plastics we use as disposable plates , disposable cutlery (biodegradable products), and even fuel in some instances (biodiesel). Hence, biotechnology and its encompassing fields have a lot of value to add to human life in general.

Q. What is a genome? What is it made of?

A. The genes and related genetic material that are seen in all living things. This includes DNA which is the instruction set for cell division and regeneration of tissue. DNA is composed of four building blocks – adenine, guanine, thymine and cytosine (A, G, C, T)

Q. What is meant by genomics??

A. Genomics is the study of the various functions, characterizations, and applications of the genome. Since the availability of high throughput sequencing also called next generation sequencing organizations like ours can build comprehensive research and diagnostic tools to further this field. New fields are also evolving in the research arena based on other inter related areas surrounding genomics such as, epigenomics, metagenomics etc,.

Q. Is there a link between genomics and genetics?

A. In my opinion they are inter related. Though genetics is a study of inheritable gene traits and genomics as explained earlier, in the genome and its characters we can definitely see overlapping areas in the work we do. Apart from being inter related they are constantly evolving, and with more information comes a better understanding about our makeup and the basis of disease, treatment etc,. These areas are not only applicable in medicine but also in agriculture, zoology and other fields of science.

Q. What are the benefits of this technology for human beings, especially, in terms of human health?

A. Next Generation Sequencing has many applications which span almost every life science field. In relation to humans the advent of this technology allows one to generate a large amount of data on the DNA with a least amount of error and at the highest quality. To explain the magnitude of data that DNA carries we are looking at 6.4 billion bases. So, considering how many combinations and permutations you can have when considering the altering of such sequences along with other inter related chemical changes you can imagine the magnitude of coverage this technology has the potential to offer. As we look at the vast expanse of outer space trying to make sense of stars, planets, etc we are now able to do this with our own “inner space” by using this technology. With this information inherited disease patterns can be studied, personalized medicine can be administered reducing side effects, fertility success rates can be increased, infection can be accurately detected and cured, tissue can be matched more accurately, to name a few. Future evolution of this technology will most probably impact most areas of our lives and lead to cures with minimal to no side effects.

Q. How does this technology help in improving the quality of health care?

A. When clinicians understand what is available and are able to adopt it into their clinical portfolio they will be able to treat patients accurately with less side effects. In the long run, the cost per patient will come down, thus reducing the burden on government expenditure and have positive patient outcomes. These would lead to a general improvement in the quality and delivery of health care, holistically.

Q. I understand that one of the significant tests Credence has created is to diagnose patients with predictive cancer tests for breast and colorectal cancer by allowing patients with inherited predisposition to these diseases, to screen their DNA . How do such tests benefit the patient? Can they prevent the risk of cancer by just getting their DNA tested?

A. Credence has two products which are catered around inherited risk, Credence Breast and Credence Colorectal. The products are catered to the Sri Lankan population and can predict with extreme accuracy the presence of inherited cancer. We have a product for precision medicine which looks at 50 genes and identifies the chemotheraupetic agents which the tumor will respond to. As a bleeding edge diagnostic company we are working on a non invasive version which could be of benefit to many patients and cover both, acquired and inherited types of cancer.

Q. It is said that Sri Lanka has a high percentage of cancer and other inherited diseases. Are they inherited patterns ? Can DNA testing help keep track of mutations that cause them?

A. Usually, acquired mutations (somatic mutations) are the higher percentage in cancer. Inherited disease would represent roughly 5 – 10% of patients presenting with cancer. As for other inherited diseases Thalassemia is also seen in a large population of Sri Lankans and Maldivians. Other non-communicable diseases also follow inherited patterns such as, heart disease, Alzheimer’s, cholesterol, diabetes, etc. Apart from our products which deal with the most common type of cancers we have Credence Inherited Disorder panel which covers approximately 325 genes and over 800 diseases in a single test.

Q. How do you extract DNA from a person? What are the instruments used? How many extractions do you need to arrive at a firm conclusion?

A. The process of extracting DNA is a chemical process which we can do on any sample or tissue for any organism. This is done in our central facility. We need a very small quantity of DNA to be able to diagnose and identify the particular condition or infection.

Q. Prenatal screening is said to be one of the greatest success stories of genomics research. Elaborate. Do we have this facility in Sri Lanka?

A. Yes, at this point we offer Non invasive pre natal screening and will be adding more products for fertility to increase the success of IVF.

Q. What is gene mapping? How does it help in identifying and preventing inherent diseases in a person?

A. In short, it’s a study of inheritable traits in families with known inherited diseases and mapping these differences. With the availability of the human genome project this area has advanced rapidly.

Q. What are the other uses of this technology?

A. As explained earlier NGS can be used across multiple fields and is not restricted to medicine. It can be used in all areas of life sciences. Agriculture, marine biology, zoology and many other areas have the benefit of such high throughput data.

Q. It has been said, the benefits of genome sequencing is still unclear in the case of healthy persons. Your comments?

A. That is not the case anymore. Now, with the information that we have we can find out how each individual reacts to specific types of food and exercise. As an organization we are now working to provide lifestyle genomic applications to help people make healthier decisions on their genetic makeup.

Q.The New Scientist refers to a gene variant that arose six generations ago in an Amish group which has made it possible for the group to outlive others not carrying the gene for ten years longer and protects them from diabetes. Does DNA also protect one from diseases, especially, chronic ones like diabetes?

A. Mutations can be both good and bad. When a group of humans live in a particular environment for a long period of time, or are faced with external stimuli that can modify their gene makeup the mutations could help them to adapt to their particular environment. For example, carriers of sickle cell anaemia are resistant to malaria, another example is a mutation of a gene Apolipoprotein AI which affects a small group in Italy and reduces their cholesterol, thus preventing blockages.

Q. Can it also cure persons of rare skin and other complications?

A. This would be specific to the DNA and the mutations present.

Q. Can gene technology be abused? Can people start altering their DNA with cheap easy gene editing technology?

A. Any technology can be abused. There are ethical issues when it comes to gene editing and manipulation. The same process that can cure cancer may also create a super human. We have already seen genetic modified organisms, especially, when it comes to food. Food that has a longer shelf life, and can be transported in different conditions. Bigger vegetables, more colourful fruit are just a few modifications we have seen.

Q. What is the link between enzymes and DNA?

A. DNA is the instruction set from which enzymes are created.

Q. Rapid DNA sequencing was developed in the 1970s. But, it has taken many years for it to be put into full use . Why?

A. Rapid DNA sequencing or Sanger sequencing has been around for a while. The reason it has taken a long time is due to time, cost and reliability as opposed to the latest methods. Though Sanger is an older method it was an important foundation for the newer technologies we use today.

The Human Genome Project was a singular project that finished ahead of schedule. Another important development that happened in parallel was the development of powerful computing infrastructure and applications which are needed in analyzing large amounts of data.

Q. Compared to the methods used in the past, how far have we progressed today?

A. Today, with NGS technology and advanced computation we are able to analyze larger quantities of genomic material than was previously possible. Our very own facility is equipped with both scientists and bio informaticians who work in tandem on delivering precision diagnostics to patients with validation and precision.

Q. Is genetic counselling part of your program? Elaborate.

A. Yes, in most tests that are predictive we offer pre test and post test counselling as a service. This would allow patients to review their family history and relevance to the test in the pre counselling stage.

Post counselling would help the patient understand the outcome of the test, to them and their future generations if applicable along with the necessary steps that need to be taken for a better quality of life

Q. Who is it given to? Do you have a genetic counselling team? Who comprises it? Are they specially trained in this field ?

A. Yes the team is led by Dr. Padmapani Padeniya and she is a qualified counsellor.

Q. What is its role in genetic therapy?

A. At the moment we are not offering gene therapy as a service but with NGS along with the data components we would be able to provide invaluable information to augment gene therapy.

Q. What are the latest developments in DNA sequencing?

A. The most important developments in DNA sequencing is cost and affordability. As with any new platform we have seen costs decline, allowing us to provide cheaper and affordable precision diagnostics to patients. The platform of NGS is now recognized as in both diagnostic and research with the ability to develop into other areas such as, gene editing for therapeutics, precision medicine, pharmacology discovery, liquid biopsy, lifestyle genomics, as well as information in overlapping fields of science, along with development of new areas of study. A lot of hardware suppliers are focusing on creating efficient desktop sequencers, point of care sequencers, etc.

Apart from the hardware - software development plays an important role mainly algorithms, clustering technologies, machine learning and artificial intelligence. In summary, in the past 2 decades the field of genomics and genetics has seen the fastest growing changes which can now be likened to the rapid changes seen in computer science and inter related fields. A significant contribution to such large changes is the presence of high throughput sequencing.

Q. Your plans for the future? At present you have confined yourself to preventing and identifying diseases. Will you be going in for treatment of diseases sometime in the future?

A. As an organization we will continue to develop along the line of clinical genomics which would also include therapeutics and advanced diagnostics. We do have a dynamic team at Credence and this is a team effort.

Our board and shareholders also believe in the vision of creating global products and the partnership with Apollo Healthcare India.

Q. If someone wants to contact you for more information or to access your health partners who should they contact?

A. Our contact details are on www.credencegenomics.com and we have a 24 hour hotline you can call on, 0710380011. 

With built-in quality control and validation, laboratory tests represent the future of medicine

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