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Submission + - Sequencing a Human Genome in a Week ( 2

blackbearnh writes: The Human Genome Project took 13 years to fully sequence a single human's genetic information. 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 in itself. 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 in a session titled The Freedom to Cure Cancer: Open Source Software in Genomics, and gave O'Reilly Radar a sense of where the state of the art in genome sequencing is heading. "Now the difficulty is pushing further and further down the pipeline, if you will. 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. These ones that are in genes change the protein that that gene is encoding. These ones are in regulatory regions. These ones are in non-repetitive regions. So we can do all of those things relatively easily. Now the difficulty is following up on all of those and figuring out what they mean for the cancer. And, okay, we know they're different. We know that they exist in the cancer genome, but which ones are drivers and which ones are passengers? And what that means is which are the ones that were the cancer initiating events and which are the ones that are just coming along for the ride and don't really have anything to do with the tumor genesis or the disease itself but, just because cancer is so out of control and lots of things have gone wrong in the cell, finding 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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  • I'm just saying that maybe security and privacy controls need to be built into sequencing software before we can read a sequence like a newspaper and start evaluating people and treating them differently based on their genome.

    • Why?

      The tools used to evaluate a genome are there to do so objectively. Adding in supposed safe-guards might compromise this. More importantly, what you're asserting is the kind of thing for which we have laws. I know this is hyperbole but do you also want to install privacy controls and security measures into people's eyeballs so we don't treat them differently based on their race or any apparent affliction?

      Just my two cents...

I've noticed several design suggestions in your code.