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Dramatic fall in DNA sequencing costs
Our Bureau, Mumbai | Thursday, October 14, 2010, 08:00 Hrs  [IST]

Owing to the competition in the sequencing field, the price of decoding a complete human genome or the cost of whole-genome sequencing is dropping and that's fuelling a "renaissance of activity" for scientific sleuths tracking down the genetic causes of disease, according to some experts.

The cost of the federal Human Genome Project, which issued its first draft in 2000 and a complete genome sequence in 2003, was estimated at $2.7 billion in 1991. But the prices have fallen considerably and today the rate for whole-genome sequencing is edging below $10,000 . The cost the chemical reagents required to do the tests — is merely $1,000, Harvard geneticist George Church had said recently

During the past decade, DNA sequencing costs have fallen dramatically fuelled in large part by tools, technologies and process improvements developed by the Human Genome Project. NHGRI subsequently launched programmes in 2004 to accelerate improvements in sequencing technologies and to further drive down the cost.

Last year, the programme surpassed the goal of producing high-quality genome sequences of 3 billion base pairs — the amount of DNA found in humans and other mammals — for $100,000. The cost to sequence a human genome has now dipped below $40,000. Ultimately, NHGRI's vision is to cut the cost of whole-genome sequencing of an individual's genome to $1,000 or less, which will enable sequencing to be a part of routine medical care.

The rapid price decline is reviving hopes that DNA tests can reveal which combinations of genes are linked to extreme or distinctive traits.

According to another expert,the cost of DNA sequencing might not matter in a few years. “People are saying they’ll be able to sequence the human genome for $100 or less. But it still could cost you $2,500 to store the data, so the cost of storage ultimately becomes the limiting factor, not the cost of sequencing.”

But these issues look relatively trivial compared to the challenge of mining a personal genome sequence for medically actionable benefit. He points out that not only is the cost of sequencing “essentially free,” but the computational cost of dealing with the data is also trivial. However the interpretation of the data will be keeping us busy for the next 50 years, he adds

Or as another expert puts it: “We are close to having a $1,000 genome sequence, but this may be accompanied by a $1,000,000 interpretation.”

The “$1,000 genome” is an arbitrary target that has nevertheless obtained a magical notoriety through repetition. The catchphrase was first coined in 2001, although by whom isn’t entirely clear.

One of those hopefuls was 454 Life Sciences, which in 2007 made Jim Watson the first personal genome using NGS, at a cost of about $1 million. Since then, the cost of sequencing has plummeted to less than $10,000 in 2010. Much of that has been fuelledd by the competition between Illumina and Applied Biosystems (ABI). When Illumina said its HiSeq 2000 could sequence a human genome for $10,000, ABI countered with a $6,000 genome dropping to $3,000 at 99.99% accuracy.

Earlier this year, Complete Genomics reported its first full human genomes in Science. One of those belonged to George Church, whose genome was sequenced for about $1,500.

Nearly all the second generation platforms have placed bets on third generation technologies. Illumina has partnered with Oxford Nanopore; Life Technologies has countered by acquiring Ion Torrent Systems; and Roche is teaming up with IBM. PacBio has talked about a “15-minute” genome by 2014, Halcyon Molecular promises a “$100 genome,” while a Harvard start-up called GnuBio has placed a bet on a mere $30 genome.

According to David Dooling of The Genome Center at Washington University, the widely debated cost of the Human Genome Project included everything—the instruments, personnel, overhead, consumables, and IT. But the $1,000 genome—or in 2010 numbers, the $10,000 genome—only refers to flow cells and reagents. Clearly, the true cost of a genome sequence is much higher . In fact, Dooling estimates the true cost of a “$10,000 genome” as closer to $30,000, by the time one has considered instrument depreciation and sample prep, personnel and IT, informatics and validation, management and overheads.

In the meanwhile according to a report,more than $18 million in grants to spur the development of a third generation of DNA sequencing technologies was announced recently by the National Human Genome Research Institute (NHGRI).

The new technologies will sequence a person's DNA quickly and cost-effectively so it routinely can be used by biomedical researchers and health care workers to improve the prevention, diagnosis and treatment of human disease.

"NHGRI and its grantees have made significant progress toward the goal of developing DNA sequencing technologies to sequence a human genome for $1,000 or less," said Eric D. Green, M.D, Ph.D., director of NHGRI, one of the National Institutes of Health. "However, we must continue to support and encourage innovative approaches that hold the most promise for advancing our knowledge of human health and disease."

NHGRI's Revolutionary Genome Sequencing Technologies grants have as their goal the development of breakthrough technologies that will enable a human-sized genome to be sequenced for $1,000 or less.

"Next generation sequencing technologies used in laboratories today have allowed significant advances in the scale and scope of biological research," said Jeffery Schloss, Ph.D., NHGRI's programme director for technology development. "Still, there are other improvements that remain to be made before such sequencing tools can be used routinely in the laboratory and clinic."

The new grants will fund 10 investigator teams to develop revolutionary technologies that may make it possible to sequence a genome for $1,000. The collective approaches incorporate many complementary elements that integrate biochemistry, chemistry and physics with engineering to enhance the whole effort to develop the next generation of DNA sequencing and analysis technologies.

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