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If We Can't Get Genome Accuracy Right, Personalized Medicine Is a Pipe Dream

If We Can't Get Genome Accuracy Right, Personalized Medicine Is a Pipe Dream | healthcare technology |

If genomes are going to revolutionize personalized medicine, the first step will be sequencing the genome accurately.

It bears repeating just how far this tech has come: the price of sequencing a genome is rapidly coming down, as is the time it takes to do a sequence. It’s getting so easy that the price point is already well within the means of many middle class Americans, and the technology might soon prove useful enough to save lives. Proponents say that, in the future, personalized medicine will allow doctors to determine the specific genetic variants that predispose their patients to certain diseases, which will then help doctors to devise individualized—and more effective—treatments.

But with roughly six billion base pairs in the human genome, creating a truly accurate gene sequence is no easy task. Even the best sequencing techniques can have an error rate around 1 percent, which adds up to hundreds of thousands of errors. When diseases depend on single nucleotide insertions or changes, those errors can mean the difference between a misdiagnosis and an accurate one.

A group of researchers with the US government’s National Institute of Standards and Technology is trying to solve that problem with a program called Genome in a Bottle. With academic and commercial partners, the group is trying to create what is essentially one “perfect” human genome that can be a reference for sequencing labs. Though every genome is different, the places where sequencing errors most commonly happen are fairly well understood, and by comparing one sequence with a reference genome, doctors and researchers would be able to tell if they’ve made a mistake.

“We’re sitting here with billions of data pairs—it boggles the mind try to get that much information accurately determined,” said Marc Salit of NIST’s Genome Scale Measurements Group. “Even when we think we’re getting it right, a few missing bases or additional ones can make a huge difference.”

Salit and his colleague, Justin Zook, recently published a study in Nature Biotechnologydiscussing their solution to the problem. According to Salit, by sequencing the same genome many times and comparing the base pairs, they can create a reference that is much more accurate than what we already have.

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Eric Schmidt's 2014 predictions: big genomics and smartphones everywhere

Eric Schmidt's 2014 predictions: big genomics and smartphones everywhere | healthcare technology |

What does 2014 hold? According to Eric Schmidt, Google's executive chairman, it means smartphones everywhere - and also the possibility of genetics data being used to develop new cures for cancer.

Schmidt says there's a big change - a disruption - coming for business through the arrival of "big data": "The biggest disruptor that we're sure about is the arrival of big data and machine intelligence everywhere - so the ability [for businesses] to find people, to talk specifically to them, to judge them, to rank what they're doing, to decide what to do with your products, changes every business globally."

But he also sees potential in the field of genomics - the parsing of all the data being collected from DNA and gene sequencing. That might not be surprising, given that Google is an investor in 23andme, a gene sequencing company which aims to collect the genomes of a million people so that it can do data-matching analysis on their DNA.

(Unfortunately, that plan has hit a snag: 23andme has been told to cease operating by the US Food and Drug Administration because it has failed to respond to inquiries about its testing methods and publication of results.)

Here's what Schmidt has to say on genomics: "The biggest disruption that we don't really know what's going to happen is probably in the genetics area. The ability to have personal genetics records and the ability to start gathering all of the gene sequencing into places will yield discoveries in cancer treatment and diagnostics over the next year that that are unfathomably important."

It may be worth mentioning that "we'll find cures through genomics" has been the promise held up by scientists every year since the human genome was first sequenced.

So far, it hasn't happened - as much as anything because human gene variation is remarkably big, and there's still a lot that isn't known about the interaction of what appears to be non-functional parts of our DNA (which doesn't seem to code to produce proteins) and the parts that do code for proteins.

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