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Genome sequencing: A solution to India's problem of rare genetic diseases

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Some months ago, a woman — three months pregnant — came to see a paediatrician at Government Medical College in Kozhikode carrying an unusual request.

She wanted to know if there was a way to find out if her unborn child could develop a rare immune disease her firstborn was suffering from. The white blood cells in her six year-old girl’s body behaved abnormally, leading to organ infections and retarded growth. Doctors, so far, had been unable to cure the girl, she said.

It appears the worried mother had come to the right doctor. Dr Geeta Govindaraj took up her case and reached out to the Institute of Genomics and Integrative Biology (IGIB) in Delhi, run by the Council of Scientific and Industrial Research (CSIR).

First, using genome sequencing, the scientists at IGIB found out the exact genetic abnormality in the first child. This information was to be used to find out if the foetus too carried the same abnormality.

Time was short. The woman underwent an antenatal procedure in Kozhikode and her samples were sent to the Centre for Cellular & Molecular Biology (CCMB) in Hyderabad. Tests were done using primers sent by IGIB and the results showed the foetus did not have the genetic abnormality.

“The mother’s joy knew no bounds. She delivered a healthy baby a few weeks ago,” Dr Govindaraj tells ET Magazine. “We are able to make a difference in the lives of common people, thanks to genome sequencing.”

New Beginnings
A disease is seen as rare if it affects one in 2,500 individuals, according to the Indian Council of Medical Research. And going by this definition, the girl’s genetic abnormality was not rare.

Nearly seven crore Indians suffer from rare genetic disorders, making it a massive medical and economic burden, says CSIR director general Shekhar C Mande.

Also, most of those suffering from these disorders do not know they have the disease and even if they knew about it, they are unaware of the treatment options, he says. Then there is the problem with lack of genetic data. “No reliable genetic information of Indians is available and for research, our scientists have to rely on gene data banks from the US and the UK — or of Caucasians,” he says.

That struggle with genetic data is about to end. India has just concluded a six-month pilot project of sequencing genomes of Indians for healthcare and biomedical use. The project, named IndiGen, mapped genomes of 1,008 people across major Indian ethnicities to help researchers develop measure to prevent cancer and rare genetic diseases.

“The mapping can help parents undergo carrier screening [to identify inheritable disease risks] and help us know why certain people do not react to certain drugs or have adverse reactions to some drugs,” says IndiGen project head Sridhar Sivasubbu.

Another aim of the project is to know a person’s ancestry for biomedical reasons.

Know Your Genome
A genome is a person’s complete set of deoxyribonucleic acids or DNA, including all genes with more than 3 billion DNA base pairs. By sequencing the genome, researchers can discover the functions of genes and identify mutations responsible for cancer and rare genetic diseases.

“With specific information on the Indian gene pool, genome sequencing can go a long way as a prognostic and diagnostic tool and bring down treatment expenses of individuals,” says Sivasubbu, a scientist at IGIB.

Genome sequencing will also lead to precision medication, instead of clinicians giving drugs based on collective knowledge. Diagnostic companies such as Dr Lal Path-Labs and Lifecell have already partnered with IndiGen, offering genetic testing.

About 800 individuals who took part in the genome sequencing project, will get an Indi-Gen card. They can download the IndiGen app and receive the reports on phone. “The in-depth reports, however, can be accessed only through consultation with the clinician,” says Sivasubbu.

He says the gene data will be stored in highly-secured supercomputers and the IndiGen cards will be made anonymous. Thus, even if one loses the card, the person’s genetic information will not be compromised.

With IndiGen, India has joined the list of countries that have ongoing genome mapping programmes, except for the fact that participants in China and the US number over a million while the UK is gene mapping 100,000 people. Thus, the next target for India will be to scale up the project to add more participants and bring down the project cost.

“We will undertake 20,000 human genome sequencing in less than two years. Costs are likely to drop drastically as chemicals are now readily available and major capital expenditure has already been undertaken,” says CSIR’s Mande.

For IndiGen, the cost per sample came to Rs 1 lakh while 10 years ago, the cost of the first genome that was sequenced in India was Rs 50 lakh. Sivasubbu is optimistic that in two to three years, the cost will drop to below Rs 50,000. In the US, a genome can be sequenced for as low as $200 (Rs 14,000).

Dealing with Data
While sequencing is a simpler part of the process with a NovaSeq genome sequencing machine taking around three days to sequence 48 samples, analysing the data will be the next big challenge since a single sequenced genome has 120 gigabytes of data, say scientists.

“IndiGen is a move in the right direction. But we lack sufficient number of clinical geneticists and counsellors to handle that kind of information for the benefit of the common people,” says Girisha M Katta, head of the medical genetics department at Kasturba Medical College in Manipal.

To be sure, CSIR is planning to train more clinicians for gene data interpretation and rope in more labs for sequencing. “Apart from IGIB and CCMB, National Institute of Biomedical Genomics in Kolkata and Indian Institute of Science in Bengaluru will also be part of the IndiGen project. We are also training more physicians to study medical genetics for speedier analysis,” says Mande.
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