CSIR completes first ever human genome decoding in India news

[ppgj]

CSIR completes first ever human genome decoding in India news

08 December 2009

Scientists at the Institute of Genomics and Integrative Biology (IGIB), Delhi, a unit of the Council of Scientific and Industrial Research (CSIR), have achieved the first-ever human genome sequencing in India.

The CSIR scientist have sequenced the genome of an anonymous healthy Indian citizen, an official release said, without naming the individual.

This feat has been achieved by a team of very young scientists, said union minister of state for science and technology Prithviraj Chavan while addressing a press conference in New Delhi.

The completion of the first human genome sequence puts India in the league of select few countries such as the United States, China, Canada, United Kingdom and Korea, which have demonstrated the capability to sequence and assemble complete human genomes.


CSIR could achieve this by adopting new technologies and by effectively integrating complex computational tools with high throughput analytical capabilities, the release said.

The human genome has 3.1 billion base pairs. The team at IGIB generated over 51 gigabases of data using next generation sequencing technology, resulting in over 13x coverage of the human genome.

This next-generation sequencing technology enables massively parallel sequencing of millions of genomic fragments of 76 base pairs, which are then mapped back to the reference genome. This humongous exercise was made possible with the CSIR supercomputing facility at IGIB, said S K Brahmchari, DG, CSIR.

The sequencing of the first human genome in India in conjunction with Indian genome variation programme opens newer vistas for low-cost affordable healthcare and predictive medicine in future for the masses. This also opens up newer possibilities in disease diagnostics, treatment and sustaining low-cost drugs in the market, the release added.

While the first human genome sequence effort took more than a decade spending over a billion US dollars, CSIR scientists at IGIB finished the complete sequencing and assembly in much shorter time comparable with similar recent effort the world over. By using next generation technologies and skills, they successfully bridged the technological gap that existed a decade ago.

CSIR has been endeavoring to nucleate such teams in different niche technological areas and the initiative seems to be paying off now.

The first human genome sequence in the world was a result of the International Human Genome Project comprising scientists from United States, United Kingdom, France, Germany, Japan and China. The project formally started in 1990 and the sequencing was completed in 2003. India could not be a part of this large initiative as in the early nineties it lacked the necessary resources.

domain-b.com : CSIR completes first ever human genome decoding in India

 

[ppgj]

India maps first Human Genome Sequence
Posted: Wednesday, Dec 09, 2009 at 0849 hrs

'The human genome sequence is like a map of the human body.'

New Delhi: Using as little as 10 millilitres of blood from a “healthy 52-year-old-man”, scientists at the Institute of Genomics and Integrative Biology (IGIB) in Delhi have successfully mapped the Human Genome Sequence for the first time in India.

The breakthrough paves the way for predictive healthcare and the possibility of identifying why certain people (with particular gene sequences) do not respond to certain medications, and what diseases a particular gene carrier, or a population, is likely to develop.

While the actual genome sequencing was completed in 45 days, the project took two years of background work — setting up a supercomputer facility, procuring software and standardizing protocols. The team that achieved the feat was led by Dr S Sridhar and IGIB PhD student Vinod Scaria, both in their mid-thirties.

The world’s first Human Genome Sequence was a result of the International Human Genome Project comprising scientists from the US, UK, France, Germany, Japan and China. The Project began in 1990, and the sequencing was completed in 2003.

“The human genome sequence is like a map of the human body. Through this map, we can tell what leads to what. We can use this map to predict mutations in the gene, like predicting how a certain person may get a certain disease. We can predict for instance, who will get the common bipolar disease or single nuclear polymorphism,” IGIB director Dr Rajesh Gokhale said.

“Through the same tool, we can predict the chances of a particular disease affecting a population. We can also explore aspects like why certain drugs don’t affect certain people,” he added.

Despite the high cost of sequencing, scientists at IGIB predict that it may soon become a fairly popular procedure.

“While genome sequencing is certainly expensive now, in about five years, we can look forward to making it a common diagnostic tool. A cancer patient for instance should be able to avail this facility, and the sequencing can predict what drugs will be useful for him,” Dr Gokhale said.

The 52-year-old man was chosen from among several people profiled because he was at the “onset” age for certain diseases, but was healthy in terms of biochemical parameters like blood and cholesterol count. Ninety-nine per cent of the sequencing is complete, and the full human map will be ready over the next two weeks, the researchers said.

In its official statement today, the Ministry of Science and Technology lauded the “unique” achievement “by a team of very young scientists”. The Council of Scientic and Industrial Research (CSIR), the country’s premier industrial research and development organization, stressed that Indian scientists had taken very little time to complete the mapping compared to other countries.

India maps first Human Genome Sequence

 

[Rage]

Interesting....

Does this represent a major technological achievement ? I think so.

Intriguingly, the test subject whose genome was used for decoding - some 55 year old mamzer from Jharkhand - had his genetic sequencing show that he was susceptible to bipolar disorder, collateral cancers, five variations of ulcer and three types of coronary disease

This sets the stage for predictive medicine, diagnostics and early disease management for millions to come, and given the preeminence of medical tourism in India, lends itself to our cause in a purely commercial aspect.

With the large diversity of ethnicities and tribes we have in this country, mapping the genetic sequences for various castes or gothras will help to identify the various diseases they are naturally susceptible to, and streamline public policy in healthcare and medical decision making - before the fact. If I recall correctly, a project to this effect's already on the cards.

I wonder what sequencing method they used: i.e. whether they used Emulsion PCR isolates or a DNA ligase or polymerase or electrophoresis. Anyone with information to this cruxial question, please feel free to share.

Here's a base guide to human genome-mapping for those who want the know:

http://www.youtube.com/watch?v=gngsL9FRpqc

 

[ppgj]

'Genome sequencing can be applied in clinical setting'
Prashanth G N, TNN 10 December 2009, 03:13am IST

BANGALORE: The man behind India's genome sequencing of a 52-year-old Jharkhand resident is understandably elated. It is the first time ever that Indian scientists have mapped the entire gene structure of an Indian. But Sridhar
Sivasubbu of IGIB, New Delhi, the primary guide in gene sequencing project, is not one to take sole credit for it. He spoke to TOI on how the project was a participative venture and what implications it has for future research in medicine, biology and genetics. Excerpts:

You are the man behind India's first-ever mapping of the entire gene structure of an Indian. You must be on the top of the world.

Definitely. It is first gene mapping ever in India. But India's first genome mapping has been a collaborative exercise. The project was first conceived of by Samir K Brahmachari, now DG of CSIR, and leadership was later provided by Rajesh S Gokhale, now director of IGIB. I and Vinod Scaria, and six students of IGIB were the team that did the sequencing. While I and Scaria happen to be the primary guides of the team, we have worked under leadership of Gokhale. Regardless of who has been involved, it is a beautiful high that Indian scientists have been able to do a complete genome sequencing. We hadn't done it before. We are among the very few in the world with this expertise.

Would you describe the genome sequencing as a breakthrough in Indian science? What would its significance be?

Undoubtedly a breakthrough in Indian computational biology, genetics and bio-informatics. The gene mapping has two significances. One, it is a technological achievement — India did not have and was not aware of the technology that went into genome sequencing. We can now say we have this technological expertise. We've bridged a major technological gap in Indian science. Secondly, geno-me sequencing can be applied in clinical settings. We can develop tools for clinical applications.

Can genome sequencing help address serious ailments?

Let's say genome sequencing will have great value in predictive medicine. It is also a good starting point to understand some of the most complex disorders. Our institute looks into complex disorders and we plan to use the genome sequencing technology to understand them.

Can it be said that a typical North Indian 'Indian' has been mapped?

We really can't say that. We would have to do genome sequencing of number of people more to be able to note any similarities in gene structures, if any, among Indians. We can't generalise that the Indian gene structure is so and so with just one sequencing. I would say we've started the process.

'Genome sequencing can be applied in clinical setting' - India - The Times of India

 

[ppgj]

After human genome sequence, scientist duo looks ahead
Posted: Manoj C G, Thursday , Dec 10, 2009 at 0149 hrs

New Delhi: They have taken India to the elite club of countries that have successfully sequenced the human genome. But for Vinod Scaria and Sridhar Sivasubbu — the two young scientists from the Council of Scientific and Industrial Research (CSIR), who have achieved the historic feat — work has just begun.

They believe sequencing of one human genome is only the first step — the challenge is to look at varied genomes and apply the knowledge for clinical application of various complex diseases. So, while congratulatory messages kept pouring in, it was business as usual for the two masterminds.

Success is not new to Scaria and Sivasubbu — one a 28-year-old doctor-turned-scientist, the other a molecular biologist in his late 30s. Together, they decoded the genome of a zebrafish in April this year. The positive result, they say, prompted them to go for a similar experiment with human genome.

“The genome of a zebrafish is approximately half the size of a human genome but it was a very good model,” Sivasubbu told Newsline, “and that gave us the confidence. But it was a high-risk game and not many at the Institute of Genomics and Integrative Biology (or IGIB, where the two work) knew about the project. We deliberately kept a low profile.”

Working together for nearly two years now, the two say they have a penchant for taking up high-risk projects and believe CSIR allows them to do so by ensuring a large amount of funding and providing the right scientific ambience. Scaria was also part of the IGIB team that had, in 2005, discovered that microRNA, the tiny segments of genetic material found in humans, have an anti-viral effect on HIV.

While they belong to different fields — Sivasubbu is an experimental molecular biologist, while Scaria’s expertise in bio-informatics — they complement each other well. Both come from small towns and consider Craig Venter, the pioneer in human-genome sequencing, their idol. Scaria comes from Kozhikode, Kerala, and Sivasubbu is from Tirunalveli, a small town in Tamil Nadu, where he completed his Masters and a PhD in Genetics.

An MBBS, Scaria finds the world of genetics challenging and interesting. “After completing MBBS from Calicut Medical College, I joined CSIR for PhD,” he says. “I realised during my MBBS days that doctors have no clue about DNA or genomes.

After human genome sequence, scientist duo looks ahead