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Biotech Science

Sequencing a Human Genome In a Week 101

Posted by kdawson
from the data-data-everywhere dept.
blackbearnh writes "The Human Genome Project took 13 years to sequence a single human's genetic information in full. At Washington University's Genome Center, they can now do one in a week. But when you're generating that much data, just keeping track of it can become a major challenge. David Dooling is in charge of managing the massive output of the Center's herd of gene sequencing machines, and making it available to researchers inside the Center and around the world. He'll be talking about his work at OSCON, and gave O'Reilly Radar a sense of where the state of the art in genome sequencing is heading. 'Now we can run these instruments. We can generate a lot of data. We can align it to the human reference. We can detect the variance. We can determine which variance exists in one genome versus another genome. Those variances that are cancerous, specific to the cancer genome, we can annotate those and say these are in genes. ... Now the difficulty is following up on all of those and figuring out what they mean for the cancer. ... We know that they exist in the cancer genome, but which ones are drivers and which ones are passengers? ... [F]inding which ones are actually causative is becoming more and more the challenge now.'"
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Sequencing a Human Genome In a Week

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  • by HotNeedleOfInquiry (598897) on Monday July 13, 2009 @07:43PM (#28684423)
    Suppose they sequence a specific human's genome. Now they do it again. Will the two sequences be the same?
  • Money well spent (Score:5, Insightful)

    by momerath2003 (606823) * on Monday July 13, 2009 @07:58PM (#28684573) Journal

    We pissed away $3 billion dollars and 13 years of time, when we could have waited a few more years and got it done in a week, and much, much cheaper. What a waste of time and money that was....

    I know I'm being trolled, but you're an idiot. It's pretty obvious that the ability to sequence the genome in a week could only result from techniques developed and information gathered in the original Human Genome project.

  • by QuantumG (50515) * <qg@biodome.org> on Monday July 13, 2009 @07:59PM (#28684591) Homepage Journal

    What's funny is that there is actually people who think like that. Apparently if we just sit around and wait, things will get better. I call this the dark side of the "invisible hand" of the market.. because it is invisible, people forget how it comes about. In order to get improvement in technology you need a market for that technology. And, typically, you need some loss-leader to create the market in the first place. Government funding serves this purpose well.

  • by goombah99 (560566) on Monday July 13, 2009 @10:37PM (#28685637)

    I suppose it's worth noting that the intermediate (raw) data sets can get pretty large. they are actually getting larger as the trend goes towards shorter less informative "reads" that require more of them to recover the connective information and to recover from errors and duplications. However that's a tend that has a stopping point. While more reads is better at some point there is almost no added value from more reads. So at that point that's the maximum amount of data you need to collect. it's won't increase ever. meanwhile hard drive and network speeds will go up factors of ten.

    thus the storage issues here are well tolerated at present and soon will become trivial.

  • wow. read a book. (Score:3, Insightful)

    by CFD339 (795926) <andrewp @ t h e n o r t h.com> on Tuesday July 14, 2009 @08:41AM (#28689333) Homepage Journal

    First, kinds of cancers were known to exist a century ago. Tumors and growths were not unheard of. Most childhood cancers killed quickly and were undiagnosed as specific disease other than "wasting away". When the average lifespan was 30-40 years, a great many other cancers were not present because people didn't live long enough to die from them.

    As we cure "other" diseases, cancers become more likely causes of death. Cells fail to divide perfectly, some may go cancerous others simply don't produce as healthy a replacement specialized cell. Your arteries harden, muscles don't repair as well, other tissues don't work as well (you get weaker, more wrinkled, easier to fall ill). Eventually either something fails that can't be repaired or enough cells go cancerous. Until we either figure out how to replace the body (seems unlikely as the brain and body are more tied together than sf movies like to present) or we figure out how to make cells repair/refresh themselves without shortening their telomeres -- I have no idea how likely that actually is.

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