Data and Medicine

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

SPECIAL THANKS TO:
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
BeautifulChemistry.net
EndPolio.org
Google Earth
Circos
Wikimedia Foundation

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Data and Medicine

This is really a magic era for
software. We can use computers now to

simulate so many different things. So every
person has a DNA sequence that's 3 billion

letters long, that's a really long sequence!
And in order for me to study it, I can't do

it by hand. I need to use computer programming
in order to go through this code that's 3

billion letters long in order to figure out
how your DNA code is associated with disease.

My interests are actually right at the interface
between biology and computer science. There

is a huge database that contains all known
organisms so humans, monkeys, mice, viruses,

bacteria. Usually now if a doctor is worried
about you having an infection, based on your

age and where your symptoms are, if it's in
your ear, your heart, or your brain, they

try to make a best guess as to what type of
infection you have. Then they'll send off

tests specifically for those bugs. So if they
think you have strep throat, they send off

the strep test. But the type of testing that
we do, since we can essentially test for any

type of infection with a single test so we
don't have to have a bias going into the testing

saying we think it's X, Y, or Z we just say
let's see what's in there. A Cottage Grove

teenager now says he's taking one life one
day at a time after being critically ill from

a mysterious illness. Mary Jolla has his story
and details into new DNA sequencing that helped

solve a medical mystery. It's spring and like
any other teenager, Joshua Osborn can't

be stuck indoors. Josh: "I feel wonderful
today. It's 80 degrees." It's a welcome change

from last summer, here in the hospital and
in a coma. His symptoms began last April with

fevers and headaches and he only got worse.
Clark: "And he needed to be hospitalized."

Josh may not remember the hospital stay but
his dad, Clark does. They tested for everything

that they knew. They tested for viruses and
bacteria and ultimately he had a brain scan

and two or three spinal taps. He had all these
crazy tubes. I remember that weekend when

they were doing it, it was so intense it was
like he was going to die that week. We got

Josh's samples from his doctor, because his
doctor was giving up. They had no idea. They

sunk millions of dollars into this kid and
they have used hundreds of test. Hundreds--

sent to the CDC, sent to multiple labs, and
they couldn't get an answer back. And they,

I mean so much money right, and they turned
to us and they were like, "We need to know

what it is." So this is where we have the
gene sequencers. We got a small amount of

Josh's cerebral spinal fluid which is the
fluid that bathes the brain, with very powerful

computer algorithms we took out all the human
sequences that were present in the data. And

then searched all the non-human sequences
that we got against a giant database that

contains gene sequences of all known organisms.
And very quickly we saw that the sequences

were all for a particular organism that Josh
likely contracted when he visited Puerto Rico

about nine months before. And fortunately,
that organism, it's a bacterium. And there

is a very straightforward treatment for it:
penicillin. The doctor gave him the drugs

that same day and he was fine 24 hours later.
All I can tell you is that, I'm happy to be

alive and I have dreams and I'm looking forward
to accomplishing them. Data analysis is changing

all medicine. It's not just changing how diseases
are diagnosed. Data is changing how we discover

cures to diseases. And even after a cure is
known, data is used for delivering medicine

to patients, for example, to fight polio in
Africa by distributing vaccines to everybody

who needs it. The magic of polio is finding
all the kids and getting them to have the

vaccine three times. And so we're taking satellite
photographs and using visual analysis to figure

out what the population is. And so we can
look and see if we're giving out a certain

amount of vaccine are we really reaching all
the kids? And amazingly what we found, on

the boundaries between political areas there
are various settlements that one group thought

that the other group was taking care of. We
also can take the phone that has the GPS tracking

and when they come back at the end of the
day, plug it in, and see where they've been

every minute. And that's making all the difference
because just getting coverage up from 80%

of kids to 90% of kids--that's the difference
between success and failure. And literally

the software that lets us look at the movements
of the teams, looks at the satellite maps,

gathers all the statistics together and tracks
this thing, that's what's going to make this

the second disease we finally get rid of.
So it's systems thinking, and the magic of

software are really at the center.