Data and Medicine



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.

10 comments

  1. i like computer science but dont want to be programmer and i have some interest in medicine i think im gonna do something like this for India

  2. I'm a medical student but I'm so interested in computer science too.
    l really don't know what to do 😕

  3. I'm gonna study computer science in college this year, but want to side focus on biology in order to help people research diseases. Now to pay tuition haha

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