The Future Is Here Today...Robots, Genetics, AI, Longevity, Singularity

For the first time, researchers at Yale have used whole genome sequencing to make a clinical diagnosis.

For the first time, researchers at Yale have used whole genome sequencing to make a clinical diagnosis.

A doctor has some tried and true methods of helping her diagnose a disease: examining the lymph nodes, taking your temperature, that whole “turn your head and cough” thing. Now, we need to add one more: whole genome sequencing. Researchers at Yale have sequenced the genome of a patient in order to diagnose his condition, reportedly for the first time. Richard Lifton and his team examined the protein encoding portion of an infant’s DNA to determine whether or not he had Bartter’s syndrome (he didn’t). Though still too expensive to use in everyday clinical work, Lifton has shown that whole genome analysis is an effective and relatively quick method to diagnose some diseases. We’re going to be seeing a lot more of this.

The costs of whole genome sequencing has been falling since the completion of the Human Genome Project. Industry leaders Complete Genomics and Illumina are pushing prices below $50,000 per genome and we could see it drop to $1000 within the next year. Cheap genome sequencing will open up new avenues of diagnosis, but could also allow individuals greater insight into which diseases they should be on the lookout for. IBM announced that it will use silicon chip technology to speed up whole genome sequencing, and we’ve already seen a handheld device that finds special gene variations using CMOS components. As genetic analysis gets faster and cheaper, the medical system will have to adjust to take advantage of the new information, hopefully with amazing results.

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The SNP Dr from DNA Electronics will allow you to find important genes in your DNA in less than 30 minutes.

DNA Electronics' SNP Dr. will allow you to find important genes in your DNA in less than 30 minutes.

If your computer and your DNA had a baby, it would be the SNP Dr. from DNA Electronics. SNP Dr. is the world’s first hand held semi-conductor device that will be able to read your DNA in about 15-30 minutes. I was able to chat with DNA Electronics CEO Prof. Chris Toumazou who is also the founder of Toumaz Technologies, the company that brought you Sensium. Toumazou let me in on how SNP Dr. will change medicine and genetic testing, and what we can look forward to in the future of semi-conductors and biology.

The current means of looking at your genetic code involves actual looking. Optic sensors help to pour through your DNA and discover variations. That technique is slow and difficult to scale down. Semiconductors, though, are getting faster and smaller every day. So a semiconductor device like SNP Dr. can be cheap and easily produced at a hand held size. Imagine a world where genetic testing could be done with just some spit, a cotton swab, and your iPhone.

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Complete Genomics is pushing down the costs of sequencing the human genome.

Complete Genomics is pushing down the costs of sequencing the human genome.

It’s getting progressively cheaper to sequence your entire genome. Earlier in June, Illumina announced it would provide sequencing for close to $50k, half of their original price. Not to be outdone, Complete Genomics just released on Monday that it had gathered $45 million dollars in funding. The Silicon Valley based company is planning to use that money to further develop their streamline sequencing operations so that they can offer a complete genome for just $5000 by next year. CG’s goal is to finish 10,000 sequences by years end 2010. Even though that’s later than we had hoped, it’s still a whole lot of DNA and at the cheapest price for a whole genome seen so far. The question is, can they really pull it off?

We’ve been looking for a company, any company really, to break the $1000 price mark for a complete genome sequencing sometime in the next few years. That’s about the point where retail sales of the service will explode. With their exponentially decreasing price tag, Complete Genomics might be on that path. However, we know of at least one company that is trying to reach that goal by the end of this year. Stay tuned for that story in the next few weeks.

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Many people have heard of the original X Prize, which was a $10 million prize given to the first company that could build a spacecraft capable of carrying three people to 100 kilometers above the earth’s surface, twice within two weeks. Many people are unaware that this original X Prize has since spawned an entire family of other $10 million X Prize challenges that are ongoing today.

The Archon X Prize is offering $10 million “to the first Team that can build a device and use it to sequence 100
human genomes within 10 days or less, with an accuracy of no more than
one error in every 100,000 bases sequenced, with sequences accurately
covering at least 98% of the genome, and at a recurring cost of no more
than $10,000 per genome.”

The Archon X Prize will accelerate mankind’s efforts to achieve affordable and fast sequencing and analysis of the DNA for every individual on the planet. Once this capability is a reality it will unleash a revolution in our ability to make people healthier, fight disease, and even improve people beyond their original genetic and biological bodies.

Picture from Archon X Prize Website

The Short:
Technology Review reports that for just $1,350,000 USD you can have have the worlds fastest commercially available DNA sequencer, called the Heliscope. The machine developed by Helicos BioSciences takes just one hour to read 1.3 billion base pairs from a strand of DNA. Here is a picture of the beauty:

The Heliscope

HeliScope™ Single Molecule Sequencer

The Long:
The Heliscope is being marketed as a DNA microscope. It is unique in the field of DNA sequencing because it sequences an actual DNA strand whereas most other sequencing technologies use PCR to create millions of copies of an original DNA template and then parallelize the analysis of these millions of strands. Although PCR based technologies can compete with the Heliscope on speed, only the heliscope offers analysis of an actual single strand of DNA. The millions of copies created from PCR based technologies differ slightly from the original template strand due to very rare but significant copying errors that occur during the creation of the copies and hence some of the information from the original strand is lost. From the article:

“The technology is so new that it’s not yet clear what applications it
will be best suited to. But some scientists believe that
single-­molecule sequencing could be particularly important in
understanding how genetic variations contribute to disease. After all,
some rare mutations linked to disease may have been missed in previous
genomic studies because they weren’t copied during the amplification
process.”

Both PCR and single strand based analyses have their place in genetics, but if you are doing single strand analysis then Helicose has the machine for you!

Like other DNA sequencing technologies, the Heliscope uses fluorescently tagged DNA to “see” the DNA sequence, but the Heliscope is unique in its ability to see individual fluroescence of a single base as noted in these quotes:

“Once the fluorescently tagged base is incorporated into the new strand,
the HeliScope’s camera can spot the light it emits. “The imager detects
a plume–a 200-­nanometer cone of light–from the integration of a
single [base] onto a ­single strand of DNA,”

and

“But unlike those technologies, the HeliScope can distinguish the
unamplified fluorescent signal of a single base taking its place on a
growing DNA strand. One key to that ability is a nonstick material that
the company developed, which coats the surface of the flow cell and
allows it to be washed clean between reactions: residual fluorescent
bases would make it more difficult to accurately detect individual
sequencing reactions. “You need to make sure no extra base molecules
are sticking to the surface,” says Patrice Milos, chief scientific
officer at Helicos. “This was one of the biggest early challenges.”
After each cycle, the fluorescent markers are clipped from the newly
incorporated bases, and remaining chemicals are washed away. The
process is repeated sequentially with each of the four bases.”

I just read the following post from the 23andMe company blog. The most interesting revelation here is the demonstration of how easy it is for a person to find a compatible organ donor once their DNA is scanned and compared against the DNA of other individuals in the database.

Less than ten years ago an enormous scientific endeavor to decode a single human genome was completed with the expenditure of millions of dollars and more than a decade of intense effort. Today, for less than $1,000 you can have your own individual DNA analyzed in a matter of weeks! The ability to analyze the DNA of an individual cheaply and quickly represents a revolution in the way mankind will be able to manipulate the human body. Stick with us here at singularity hub and be in the know as the revolution unfolds.

In the next month or so I will be having my DNA analyzed by the two leading companies in the field, 23andMe and deCODEme. In depth analysis of my experience at both companies will be posted here as soon as possible so stay tuned.

Wired just setup a how-to wiki describing how to check yourself for genetic abnormalities. The wiki is pretty wimpy on details at the moment, but hopefully people will update it with more information soon. The wiki suggests the following 3 options for analyzing your DNA:

1. Visit a genetic counselor. These companies specialize in detecting specific genes

2. Scan your whole genome by using a testing company such as 23andMe or deCODEme. By scanning your entire genome you can check much more than your genes. You can check for a million or more genetic markers called SNPs.

3. Perform the test yourself at home! This requires a good deal of work on your part, but the tools required to analyze your genome at home do indeed exist and they will surely become more available, cheaper, and easy to use in the near future