Mass genome sequencing is finally happening

Posted by liza On June - 7 - 2010

The new frontier for disease cure and prevention is somewhere in our gene, that we have all known for a while. Until not so long ago, high costs and long timings have prevented to exploit the incredible possibilities of genome sequencing.

Now that the wall of costs has been broken, the first mass DNA sequencing workshop could finally begin. This month, researchers at Kaiser Permanente, a volunteer based DNA bank, together with the University of California, began the highly automated, large-scale process of analyzing that DNA, which is being extracted from tens of thousands of saliva samples donated since 2008.

The main goal is to computer cross-analyze the genes of people with diseases like cancer and multiple sclerosis, which will possible lead to pinpoint the genes responsible for the illnesses.

The process will be completed in less than 18 months, a speed that would have seemed preposterous to contemplate a decade ago.

What makes the Kaiser study unique is that members of a single, colossal cohort will have their genomes scanned uniformly, then paired with their medical histories. “It is absolutely the largest study of its kind, and it has enormous statistical power”, said Winifred K. Ross, project manager for the National Institute of Aging.

Experiments like this one underscore how quickly gene-scanning technology is moving from the lab to the home. Last week, officials of the University of California, Berkeley, disclosed that 6,000 incoming freshman and transfer students will be asked to swab their cheeks at home for DNA, to participate in a collective lesson in genetics and a preview of the predicted era when medicine will be tailored to each person’s genetic makeup. Each student who agrees to participate will be able to tap in a security code on a laptop and check whether they carry gene variants that might affect their ability to process lactose, alcohol or folate, a vitamin found in leafy greens.

Ten years from now every new-born will know wether he’ll suffer from diabetes in his teens or a heart condition in his fifties. Not from a pediatric psychic, that is not in sight yet, but from the analysis of the genetic code of the baby. The costs of DNA mapping have already sensibly diminished, but they will drop to less than $1000 in the near future, making this a standard after-birth procedure. The human Genome Project, the first human genome sequencing ever published was completed in 2001 at a cost of $4 billion. Two years ago scientists James Watson and Craig Venter had their genomes mapped with about $1m, and Dr. Stephen Quake, a Stanford engineer, recently decoded is own with less than $50,000 and just a three-member staff. Dr Jay Flately from Illumina, an American company specialized in personalized medicine development by applying innovative genetic technologies, stated in an interview with The Times that most kids will have this simple procedure done within 2019. It will be enough to collect a drop of blood with a heel-prick blood test, similar to the one that is already used to screen for inherited diseases such as cystic fibrosis. “The limitations are sociological; when and where people think it can be applied, the concerns people have about misinformation and the background ethics questions. I think those are actually going to be the limits that push it out to a ten-year timeframe” he said. This procedure will in fact raise eyebrows on privacy concerns: what if an insurance company manages to get its hands on your own sequenced genome and prices your health insurance accordingly? But, as Dr. Flatley added “people have to recognize that this horse is out of the barn, and that your genome probably can’t be protected, because everywhere you go you leave your genome behind.” A used coffee mug or a fallen out hair are enough to track a person’s DNA anyway. This is why it will be very important for proper legislation to be passed. The benefits will be so great that will most likely wipe out the initial concerns. Knowing which kind of cancer or cariovascular problems could affect us, is crucial to early prevention and drugs and dietary advice.

Genome sequencing just became faster and cheaper

Posted by liza On August - 15 - 2009

It took Christopher Columbus 36 days to reach America. Now you fly to New York in about 8 hours. The first commercial computer, the UNIVAC I costed about $1,550,000 and weighed 13 tons. How much did you spend for your laptop?

Tech devices have been getting smaller, faster and cheaper. We all noticed that. This development is becoming reality in the DNA research field as well, as Dr. Stephen Quake, a Stanford engineer, has recently proven the world.

He recently decoded is own genome sequence with less than $50,000 and just a three-member staff thanks to his Heliscope Single Molecule Sequencer. This innovative machine can sequence a human genome in four weeks with a small technical staff. Companies and labs who have been providing this service relied on hundreds of machines and large staff to get the job done. The most recently sequenced human genome before Dr. Quake’s costed about $250,000 to be decoded, and his machine brings the cost to less than a fifth of that. Not to mention that it is much faster. He said the much-discussed goal of the $1,000 genome could be attained in two or three years. That is the cost at which genome sequencing could start to become a standard part of medical practice. Once again, we are watching modern technology became obsolete live.

We are driving fast down the road of routine full genome sequencing. This will lead to a better understanding of our personal disease risk-factors and prevention.

“You have to have a strong stomach when you look at your own genome,” Dr. Quake said. Looking at his own, he discovered a variant associated with heard disease. Luckily he inherited only from one parent, which leaves him with another healthy gene copy.

The cost of the device is “about $1 million, depending on how hard you bargain,” Dr. Quake said. Funny enough it is about the same as the UNIVAC I. Will genome sequencing devices become part of household first-aid kits in a decade time?