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HindustanTimes Sat,02 Aug 2014
Genomic prediction: test that spots disease risk
Aasheesh Sharma, Hindustan Times
December 06, 2013
First Published: 16:01 IST(6/12/2013)
Last Updated: 12:24 IST(9/12/2013)

Every evening, after he returns home from work, Vivek Bhargava, 40, managing director of a digital advertising firm based in Mumbai, joins his 10-year-old daughter to play mind games on his smartphone to prevent the onset of premature memory loss.

Subhashini Chandran, 39, an entrepreneur based in Port Blair, has become ‘mindful’ of what she eats, and runs 10km every morning, apart from practising mudra therapy. Ever since Chandran underwent a simple saliva-based test to predict her health, she has transformed her lifestyle from hyperactive to stable.

“I keep in fairly decent shape. But the genomics test from Map My Genome exposed some weak links. I realised I was prone to certain stress-related health vulnerabilities. It even measured my tolerance to a few drugs,” she says.

In a country where curiosity about their future has kept astrologers and soothsayers in business, the emerging science of genomic prediction – which decodes a person’s genetic composition to help him or her identify diseases they might suffer from in the future –  is finding many takers.

Apart from curiosity, the possibility of scientifically confirming the likelihood to get life-threatening conditions such as breast cancer, diabetes, or coronary diseases, providing them an opportunity to modify lifestyles, is driving the popularity of such tests.  In Hollywood, the discovery of the mutated gene, BRCA 1 (BReast CAncer causing gene-1) prompted actor Angelina Jolie to undergo a double mastectomy, bringing down her chances of developing breast cancer from 87 per cent to five per cent.

http://www.hindustantimes.com/Images/popup/2013/12/genes-brunch.jpg

Closer home, getting their genes analysed has helped a few hundred Indians discover conditions previously unknown to them. Take the case of B Srinivasan. The 60-year-old Chennai pre-school manager realised he had a marginal propensity towards sudden cardiac arrest. “After the initial shock, I dealt with it calmly. Although I did not tell my family, after detailed counselling, I have regulated my food timings to a large extent.”

A spit-second decision
Once a client gets in touch with a genomics testing company, they courier a testing kit to the customer. The client then spits into a highly-sterile test tube that keeps the saliva stable for more than 30 days. After the DNA is extracted at a laboratory, detailed reports are sent, explaining the likelihood of people acquiring specific diseases, in comparison to the average Indian.

“The structure of the person’s DNA is extracted from the saliva and is analysed. After this, customers are called for counselling sessions in which experts help them understand what the report means, and how they could change their lifestyles to reduce the likelihood of diseases they need to watch out for,” says Anu Acharya, co-founder of Map My Genome, the Hyderabad-based laboratory which generates a ‘GenomePatri’ for clients. “The extracted DNA is used to identify potential hazardous markers in the DNA, which have links to more than 100 health conditions,” adds Acharya.

Many disorders, says Acharya, can be traced back to minor genetic differences. “Although the genome for all humans is the same, minor differences do exist. This variation is responsible for the unique phenotype (appearance, colour of skin/eyes, texture of hair etc) and differences in the health of each individual. In most of the cases, this variation is passed on to the next generation.”

But a genetic predisposition doesn’t necessarily mean the ailment is unavoidable, says R Narayanan, co-founder of Chennai-based XCode Life Sciences, that began offering gene-based predictions in 2012. “You might be genetically predisposed, but you can lead such a healthy lifestyle that the gene itself is not allowed to misbehave,” he explains.

Acharya’s own GenomePatri, for instance, showed a substantially greater lifetime risk of getting Type-2 diabetes than the average Indian. She was predisposed to it by 41 per cent, much higher than the Indian average (20 per cent). So, in the last few months, Acharya has cut out carbs from her diet and is trying to stay stress-free. “Many people become nervous. But if you take the findings positively, you can change your lifestyle and minimise their impact,” she adds.

Mumbai-based entrepreneur Bhargava, for instance, decided to be proactive. His report said he had four times higher the risk of developing Alzheimer’s and dementia than an average Indian. “The counsellor said I could delay and even avert the disease provided I began exercising my brain on a regular basis. But in case I retired early and slid into inactivity, its onset could be quicker,” he recalls. Now, for at least an hour every day, Bhargava and his daughter solve puzzles on Lumosity, a site that hosts workouts designed by neuroscientists to improve core cognitive functions.

See them coming

A few of the diseases for which a prognosis can be made through genetic testing:

* Lifestyle ailments such as obesity, stroke and cardiovascular diseases

* Life-threatening diseases such as diabetes and only certain types of cancer

* Neural conditions such as bipolar disease, Alzheimer’s and multiple sclerosis

Analyse this
At times when the tests predict that a person is predisposed to a potentially life-threatening disorder, genomic counsellors, many of them trained doctors, step in to guide clients on diet and lifestyle. Genetic counsellor Dr Shilpa Reddy of Map My Genome recalls the case of a 32-year-old software engineer based in Hyderabad (name withheld) who returned to India from the United States and took a saliva test. “High consumption of red meat and alcohol had triggered intestinal inflammation. His reports said he had a high risk of colorectal cancer (40 per cent compared to 13.6 per cent for the average Indian). So we advised him to take control of his diet, go slow on the alcohol and resume exercise,” says Dr Reddy.

Similarly, R Bharath Kumar, 40, a Chennai-based apps developer, was advised by counsellors from X-Code to attempt mindful eating after realising he was predisposed towards diabetes. “I had developed a sweet tooth in my 30s and led a desk- bound life. So I suspected I could have been a potential diabetic. But a scientific confirmation and diet counselling kicked me out of inactivity and towards better fitness.”

The caveats
These are early days for the few companies engaged in predictive genomics in India. Experts say there is a concern because the framework for these tests is based on Caucasian genes. “We are not aware of any large private genomic studies taking place in India with an Indian population,” says Dr Sridhar Shivasubbu, a scientist at the Institute of Genomics and Integrative Biology in Delhi’s Council for Scientific and Industrial Research – India’s largest chain of research labs. “This means that many of these predictions are going to be on the basis of a Caucasian gene pool. The prediction value of an Indian person getting a disease will be completely different from what is going to be applicable to a person of Caucasian or African descent.”

Overall, for a large amount of people in the Caucasian population (mostly in Europe and North America), the DNA makeup is similar. “But in India there is a huge diversity in genetic makeup. The lack of data on the basis of Indian population could skew the findings,” points out Shivasubbu.

Direct to consumer genetic predictions can be tricky terrain, says Dr Vinod Scaria of the Institute of Genomics and Integrative Biology, unless it is done on the advice of a doctor. “If a person is predisposed to a life-threatening condition (a sudden cardiac arrest or a certain cancer), the first thing to do is to visit a doctor who is trained to handle such situations and kept in direct contact with patients, rather than somebody who is just involved with theoretical or laboratory studies. It is only then that they should make changes in lifestyle,” says Dr Scaria.

Also, priced between `10,000 and `25,000, the package of tests aren’t exactly cheap. Number   crunchers also question the numerical values used in genomic prediction. “All this data comes out in terms of predictions values. And the predictions are only as good or bad as the denominator value. As the number of controlled cases goes up, you end up making better predictions. Clearly in India, that is not the case, yet,” says Dr Shivasubbu.
Acharya admits that the Indian gene pool at the moment isn’t large enough for certain diseases. “But the data we use does take global population numbers and validates it against Indian studies,” she adds.

How private is your DNA?
 
As they gain in popularity, genome tests could bring in serious privacy concerns. Who has the ownership of the DNA? What’ll it be utilised for? What sort of research will be done? In the long run, can it be sold out to international research agencies? “A DNA sample is a common heritage of the people who have donated it. No one is allowed to send sample DNA samples outside national boundaries. International privacy norms should be followed here too,” adds Dr Shivasubbu.

Map My Genome’s Acharya says they take their privacy seriously. “We ensure strict confidentiality. No data is sold to any third party.” Adds Narayanan of XCode Life Sciences, “The data we have is assigned with a barcode so identity of the individual remains unknown.”

In 2008, Time magazine anointed the genome test kit devised by the California-based 23 and Me, the world’s leading company in the direct-to-consumer genomics space, its Invention of the Year. But recently, the company attracted a lot of criticism after a mix-up in samples.

The science itself is work in progress, says Narayanan. “By 2025, conventional medicine would make way for customised medicine, that’s when genomics will realise its true potential,” he says. 


How it works
Genomic prediction - that decodes genetic composition to help a person identify diseases he or she might suffer from in the future – works on the basis of a saliva sample. Here is how the tests are carried out

Once a client gets in touch with a genomics testing company, they courier a testing kit to the customer. The person then spits into a highly-sterile test tube that keeps the saliva stable for more than 30 days. Priced between Rs. 10,000 and Rs. 25,000, the package of tests aren’t cheap.

The DNA is used to identify single nucleotide polymorphisms, (potential hazardous markers), which could have links to health conditions like diabetes, cancer and stroke. Relative risk is calculated as likelihood of developing a disease in the experimental group compared to the reference group.

After the DNA is extracted at a laboratory, detailed reports are sent, explaining the likelihood of people acquiring specific diseases, in comparison to the average Indian.

Then, customers are called for counselling sessions in which experts help them understand what the report means, and how they could change their lifestyles to reduce the likelihood of diseases they need to watch out for. An interesting application of genomic-based prediction is pharmacogenomics, which tells you whether specific drugs agree with your genes or not.



From HT Brunch, December 8

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