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Data and Medicine

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    Data and Medicine
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    This is really a magic era for
    software. We can use computers now to
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    simulate so many different things. So every
    person has a DNA sequence that's 3 billion
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    letters long, that's a really long sequence!
    And in order for me to study it, I can't do
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    it by hand. I need to use computer programming
    in order to go through this code that's 3
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    billion letters long in order to figure out
    how your DNA code is associated with disease.
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    My interests are actually right at the interface
    between biology and computer science. There
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    is a huge database that contains all known
    organisms so humans, monkeys, mice, viruses,
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    bacteria. Usually now if a doctor is worried
    about you having an infection, based on your
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    age and where your symptoms are, if it's in
    your ear, your heart, or your brain, they
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    try to make a best guess as to what type of
    infection you have. Then they'll send off
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    tests specifically for those bugs. So if they
    think you have strep throat, they send off
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    the strep test. But the type of testing that
    we do, since we can essentially test for any
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    type of infection with a single test so we
    don't have to have a bias going into the testing
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    saying we think it's X, Y, or Z we just say
    let's see what's in there. A Cottage Grove
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    teenager now says he's taking one life one
    day at a time after being critically ill from
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    a mysterious illness. Mary Jolla has his story
    and details into new DNA sequencing that helped
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    solve a medical mystery. It's spring and like
    any other teenager, Joshua Osborn can't
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    be stuck indoors. Josh: "I feel wonderful
    today. It's 80 degrees." It's a welcome change
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    from last summer, here in the hospital and
    in a coma. His symptoms began last April with
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    fevers and headaches and he only got worse.
    Clark: "And he needed to be hospitalized."
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    Josh may not remember the hospital stay but
    his dad, Clark does. They tested for everything
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    that they knew. They tested for viruses and
    bacteria and ultimately he had a brain scan
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    and two or three spinal taps. He had all these
    crazy tubes. I remember that weekend when
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    they were doing it, it was so intense it was
    like he was going to die that week. We got
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    Josh's samples from his doctor, because his
    doctor was giving up. They had no idea. They
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    sunk millions of dollars into this kid and
    they have used hundreds of test. Hundreds--
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    sent to the CDC, sent to multiple labs, and
    they couldn't get an answer back. And they,
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    I mean so much money right, and they turned
    to us and they were like, "We need to know
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    what it is." So this is where we have the
    gene sequencers. We got a small amount of
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    Josh's cerebral spinal fluid which is the
    fluid that bathes the brain, with very powerful
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    computer algorithms we took out all the human
    sequences that were present in the data. And
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    then searched all the non-human sequences
    that we got against a giant database that
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    contains gene sequences of all known organisms.
    And very quickly we saw that the sequences
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    were all for a particular organism that Josh
    likely contracted when he visited Puerto Rico
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    about nine months before. And fortunately,
    that organism, it's a bacterium. And there
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    is a very straightforward treatment for it:
    penicillin. The doctor gave him the drugs
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    that same day and he was fine 24 hours later.
    All I can tell you is that, I'm happy to be
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    alive and I have dreams and I'm looking forward
    to accomplishing them. Data analysis is changing
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    all medicine. It's not just changing how diseases
    are diagnosed. Data is changing how we discover
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    cures to diseases. And even after a cure is
    known, data is used for delivering medicine
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    to patients, for example, to fight polio in
    Africa by distributing vaccines to everybody
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    who needs it. The magic of polio is finding
    all the kids and getting them to have the
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    vaccine three times. And so we're taking satellite
    photographs and using visual analysis to figure
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    out what the population is. And so we can
    look and see if we're giving out a certain
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    amount of vaccine are we really reaching all
    the kids? And amazingly what we found, on
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    the boundaries between political areas there
    are various settlements that one group thought
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    that the other group was taking care of. We
    also can take the phone that has the GPS tracking
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    and when they come back at the end of the
    day, plug it in, and see where they've been
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    every minute. And that's making all the difference
    because just getting coverage up from 80%
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    of kids to 90% of kids--that's the difference
    between success and failure. And literally
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    the software that lets us look at the movements
    of the teams, looks at the satellite maps,
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    gathers all the statistics together and tracks
    this thing, that's what's going to make this
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    the second disease we finally get rid of.
    So it's systems thinking, and the magic of
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    software are really at the center.
Data and Medicine

Learn how computer science is saving lives through genetic sequencing and harnessing the power of data to fight disease.

Josh and his family
The Derisi Lab - UCSF
Bill and Melinda Gates Foundation
Daniela Witten - Biostatistics at U of WA
WISC-TV News 3; Madison, WI
Google Earth
Wikimedia Foundation

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