Daily Archives: January 14, 2014

Today, Illumina, the leading maker of DNA sequencers, announced a milestone in biotechnology: it is introducing a new machine that can sequence the genetic code of a human cell for $1,000.

The machine actually a combination of ten machines working together called the HiSeqX Ten will cost $10 million. Already, three have been bought by Macrogen, The Harvard-MIT Broad Institute in Cambridge, and the Garvan Institute of Medical Research in Australia. Illumina forecasts that it will sell five of the systems this year.

Eric Lander, one of the worlds leading geneticists and the director of the Broad, called the machines extremely exciting in Illuminas press release. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine, he said.

Its a milestone of huge psychological importance for the scientists who study human genetics and the industry of biotechnology companies creating new diagnostic tests and drugs using the technology. Initially, the number was put out there by researchers as kind of a thought experiment, or a mythic totem. Less than a decade ago, the cost of decoding a human genome was $250,000, but thanks in part to Illumina, the efficiency of the machines has risen at an exponential rate, outpacing the famous Moores Law that describes the improvement of the semiconductor chips used in supercomputers.

But actually hitting the $1,000 mark has proved elusive. Life Technologies, which was trying to give Illumina a run for its money, announced a year ago that it would launch a machine capable of cranking through DNA basepairs at this rate, but the machine still hasnt hit the market. Even if it had, there were reasons not to give it the title. For one thing, it was only counting the costs of the chemicals consumed in sequencing all that DNA, not the machine. (See: Not Quite The $1,000 Genome, But Close Enough)

But Jay Flatley, Illuminas Chief Executive, says that this time the calculations include the cost of the chemicals, of preparing the samples, and amortization for that extremely expensive machine. And in general, producing all that data is a huge step forward for biology. Meanwhile, many of Illuminas potential competitors, including companies like Life and Pacific Biosciences, have been left far behind.

They are brilliant, says Michael Pellini, the Chief Executive of Foundation Medicine, which uses Illuminas machines to analyze the genomes of cancer patients. Well ahead of the field. Nothing today has a dramatic impact on our business, but its good in general for the field. Someone still needs to adapt the technology to the field of oncology in a seamles way. Thats where we come in.

Other companies are racing to use the new technology, too. Earlier this week, Regeneron, a fast-growing biotechnology company, announced that it would be using the technology in research directed at discovering new drugs in collaboration with the Geisinger Health System in Pennsylvania.

Source: Forbes

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The $1,000 Genome Arrives -- For Real, This Time

A colour map shows gradients of myelin in a human brain, red and yellow indicating high myelin and darker colours indicating low myelin. | credits: New York Times Service

Deanna Barch talks fast, as if she doesnt want to waste any time getting to the task at hand, which is substantial. She is one of the researchers here at Washington University working on the first interactive wiring diagram of the living, working human brain.

To build this diagram she and her colleagues are doing brain scans and cognitive, psychological, physical and genetic assessments of 1,200 volunteers. They are more than a third of the way through collecting information. Then comes the processing of data, incorporating it into a three-dimensional, interactive map of the healthy human brain showing structure and function, with detail to 1.5 cubic millimeters, or less than 0.0001 cubic inches.

Barch is explaining the dimensions of the task, and the reasons for undertaking it, as she stands in a small room, where multiple monitors are set in front of a window that looks onto an adjoining room with an MRI machine, in the psychology building. She asks a research assistant to bring up an image.

Its all there, she says, reassuring a reporter who has just emerged from the machine, and whose brain is on display.And so it is, as far as the parts are concerned: cortex, amygdala, hippocampus and all the other regions and subregions, where memories, fear, speech and calculation occur. But this is just a first go-round. It is a static image, in black and white.

There are hours of scans and tests yet to do, though the reporter is doing only a demonstration and not completing the full routine.

Each of the 1,200 subjects whose brain data will form the final database will spend a good 10 hours over two days being scanned and doing other tests. The scientists and technicians will then spend at least another 10 hours analyzing and storing each persons data to build something that neuroscience does not yet have: a baseline database for structure and activity in a healthy brain that can be cross-referenced with personality traits, cognitive skills and genetics. And it will be online, in an interactive map available to all.

Dr. Helen Mayberg, a doctor and researcher at the Emory University School of Medicine, who has used MRI research to guide her development of a treatment for depression with deep brain stimulation, a technique that involves surgery to implant a pacemaker-like device in the brain, is one of the many scientists who could use this sort of database to guide her research.

With it, she said, she can ask, how is this really critical node connected to other parts of the brain, information that will inform future research and surgery.

The database and brain map are a part of the Human Connectome Project, a roughly $40m five-year effort supported by the National Institutes of Health. It consists of two consortiums: a collaboration among Harvard, Massachusetts General Hospital and UCLA to improve MRI technology and the $30m project Barch is part of, involving Washington University, the University of Minnesota and the University of Oxford.

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The brain, in exquisite detail