Search for tag: "genomics"

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Lynn: My name is Lynn Jorde. I'm the Chairman of the Department of Human Genetics at the University of Utah School of Medicine. I'm here today with Dr. Eric Green, who is the director of the National Human Genome Research Institute.

So, we've heard a lot about the ever decreasing cost of genome sequencing, about a million fold in the last decade. Does this mean that everyone should be sequenced? Or if not, who should be sequenced?

Dr. Green: So from a research perspective, I think there's great power in getting tremendous amounts of data from as many people as possible and using this in very robust ways to try to understand many aspects of health and disease. I think your question though, is aimed more at, "Should everybody get their genome sequenced as part of their medical care?" I'm not sure we're quite there yet. That might be where we are eventually, but just because we have the technical capabilities of doing that, I think we're far away from knowing what to do with that information in a clinical context to say that this should be sort of used for everybody. Rather, I think it's most useful now in very discreet areas where there's clear evidence that having genomic information will be helpful to that patient.

Lynn: Some critics have said that the Human Genome Project, of which you and many of us have been a part, hasn't really delivered on one of the original promises to revolutionize medicine. How would you respond to that?

Dr. Green: When the Genome Project ended 13 years ago, there was incredible celebration. In fact, many of use were euphoric about having achieved the goals that were set out for the Genome Project. I think in our exuberance lots of promises were made and lots of claims were made to have this was going to revolutionize this, that and the other and lead to great medical advances. I think much of that exuberance might have been over interpreted as meaning those advances were going to take place quickly.

There was no reason to believe it was going to happen that quickly. Actually, if you look back in the history of bio-medical research, there is usually periods measured in decades between very basic discoveries, such as the discovery of antibiotics, the discovery of the basic biochemistry of cholesterol metabolism and the actual changes in medical practice that led to advances in medicine. Decades. Here we are only 13 years in to having information about our genome available to us. So we've not seen the revolution, that I think will eventually come. I think for that we've been criticized.

I think we just have to take a step back, recognize that we're 13 years in. There's some vivid examples where genomics has had a profound effect on medicine, but they're the earliest examples. Even in aggregate those don't represent a revolution, but they're highly illustrative of what is coming.

So I think, when we look back at the history of genomics, say 10, 20, 30 years from now, I think that will be the fair time to assess whether or not our claims that were made when the Genome Project ended, were accurate or not. It's just too soon to do it now.

Lynn: So we're seeing investigations now, of all sorts of traits. The genetics of IQ, people claim to have found genes that influence things like aggressive behavior, anxiety. This gets pretty controversial. Are there areas that should be off limits, at least off limits to NIH funding?

Dr. Green: Absolutely. People get very uncomfortable with some of these ideas of doing genomic studies to better understand the basis for IQ, for aggression, various other attributes. It's also controversial scientifically, so before we even think about whether or not we want to limit this, I do want to put some reality on this. I think most scientists would agree that getting an accurate assessment of intelligence is not simple. Getting an accurate assessment of behavior is not simple. I think it is scientifically controversial whether we can even make major gains in this by doing these studies. So I think that really has to temper our enthusiasm for it. But then, of course, there's the ethical and societal implications of this. Are people going to be comfortable with it?

I think we need to be very cautious. When we are going to use these new tools of genomics, especially at this early stage, to prioritize things that are going to have great societal benefit. There's so many major medical challenges, disease areas, that will benefit from using these tools first and foremost, those are the areas that should be prioritized and I think that's where we should be putting our energies. At the same time, we should be very careful looking at what some of these other studies that might be envisioned, how they'll be perceived and how practical they are. I think they're going to end up being a low priority. In some cases, one might imagine doing some studies, along those lines. I just don't think they're going to be at a very high priority.

There's a lot of controversy of whether they'll be successful. It just doesn't seem to be the thing to be emphasizing right now. So, my enthusiasm level is low. I think in general people are making decisions about where money is going are going to deprioritize them. I'm not sure I want to say there should be a ban, but there should be careful scrutiny put on these. Research dollars are precious and we need to go to things that are more practical, and things that will have a higher impact on human health and disease.

Lynn: Over the past two years there's been quite a lot of controversy about patenting human genes. So, how does patenting, or not, affect scientists and consumers? Could it affect interests on the part of the private sector in investing and genetic and genomic research?

Dr. Green: There's not simple answers. The whole intellectual property construct and the ability to get patents and protecting people's advances are very important for the private sector and their ability to invest in things and feel comfortable that they will get a return on investment and so forth.

On the other hand, there's something a little special about the human genome. It is very basic, fundamental to humankind. It is our blueprint and the potential to have fundamental information about our blueprint be used. And a fast note, any day we be restricted makes many people uncomfortable. I think one of the things genomics has done, and its sort of cultural values associated with data sharing, is making as many things available to everybody, freely, widely. I think has served us very well. I think the fundamentals of understanding how the genome works in human genes and so forth, having no restrictions on their use, I think is very, very important.

There's a vision associated with using information about one's genome to tailor their medical care. I think many of us get very uncomfortable if in the process of doing so, if too many patents were laid down they would look like tollbooths across the double helix. Every single time we would go to one to analyze one part of someone's genome, we would have to pay a toll, and that would greatly hinder advances.

So, I think many of us have taken a position that it's so basic, that information, that just raw information, which is easy to get about the human genome and about genes, should sort of be off limits for patenting. Now, if you use that information you come up with a great intellectual advance and you design things around it and you come up with something that is more than just the basic fundamental information, yes, that should probably be fair game for patenting, for getting intellectual property and so forth. I think it's that raw information about genes that has made many people uncomfortable and have said that should be off limits for patenting.

Lynn: A big part of this then is the public understanding of traits, of what it means when we say a gene is associated with a trait. This gets us to the question of genomic literacy. What can we do to increase genomic literacy among the public so that they will better understand these kinds of issues?

Dr. Green: Genomics is a relatively young discipline. It's only been around a little over a quarter century. We are fortunate that it's been wildly successful. I think we're all very proud of that, but that's actually created a bit of a challenge for us. The challenge is that this field of science is finding it's way into medicine faster than any of us could have anticipated.

As a result of that, we have some complicated concepts, but also some basic language of genomics that it's finding its way into medical care. Yet, most people don't necessarily know the basics of this. They haven't been given the opportunity to learn it. Many of the healthcare professionals weren't taught this when they were in school. So this is happening so fast and furious that our ability to educate the public, educate healthcare professionals, is lagging behind.

As a result of that, this becomes very important when patients go to see their healthcare professionals and now will start hearing, in some context, about genomics. They don't really understand those words, they don't understand that language. If the patients don't understand it, they're going to go home and talk to their family. They may not understand it. They talk to their friends, they may not understand it.

So we have a societal responsibility to increase literacy about basic language of genomics, because that is a language that will increasingly be used by healthcare professionals, as part of patient care. It's not anybody's fault that we find ourselves in this situation. We're victims of our own success. We've been successful scientifically and now we need to sort of redouble our efforts to think about how to raise genomic literacy more broadly across society.

Lynn: Looking forward to the next decade, the next two decades, what excites you the most about genomic medicine?

Dr. Green: I think what excites me more than anything is the optimism that I have that what is going to transpire over the next decade is going to be significantly greater than what has transpired over the even last decade or the last two decades. I think we're so much more poised to accelerate progress than we ever have been in the last 25 years of genomics.

So, what I anticipate, what I'm excited about, is on multiple, multiple fronts, multiple areas, whether it's cancer, whether it's rare disease, whether it's infectious disease, whether it's in thinking about how to prescribe medications in a more precise and rational way, it just seems in so many areas, the progress I anticipate over the next ten years, I actually believe will be even more remarkable than what I've seen. Yet, I've been shocked by how much we have seen medical applications of genomics begin to be realized on a timeframe that I simply would not have predicted when I got involved in this field initially. I'm even more excited about the next generation of biodmedical researchers and healthcare professionals who I think are going to be the ones that are going to truly realize genomic medicine.

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Interviewer: A new tool that could completely change how we diagnose infectious diseases, up next on The Scope.

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Interviewer: I'm talking with Gabor Marth, professor of human genetics at the University of Utah and co-director of the USTAR Center for Genetic Discovery.

Diagnosing infectious diseases is still a significant problem in medicine. Right now in the clinic, you either do a culture or maybe a PCR test to see what's infecting a person. You have co-developed a tool called Taxonomer that's taking a completely different approach.

Gabor: Taxonomer is a software tool that is able to look at DNA fragments, which is what current technologies are able to produce from blood from an infectious disease patient, and identify the organisms that are present in that sample.

These types of tools, in my opinion, are very likely to replace the tests that you mentioned, that are based on specific hypotheses. We have to know what the strains that we are looking for in these patients, whereas tools like Taxonomer will be able to look at the DNA sequences and tell you upfront what pathogenic organisms are causing the patients disease.

Interviewer: So if you have a patient that's sick, you take a little blood, you have to get the DNA from that blood sequence for all the genetic material, I guess. And then that sequence information goes in the Taxonomer, and Taxonomer catalogues everything that's in there.

Gabor: Yes, as you mentioned, in traditional clinical tests you would have to ask "Does this patient have this particular strain of, which specific pneumonia strain this particular patient has." Sometimes these experiments fail. Some of the strains go better in the media that are used in laboratory tests than others. When the same data goes to a Taxonomer you just get an unbiased view of which strains and what proportions are present in the patient. That will help the physician diagnose the patient much faster, and in a much more objective manner.

Interviewer: So there are some really stand-out characteristics of Taxonomer. These are based on the software called Iobio, which is what you developed, correct?

Gabor: Taxonomer itself is the engine, it is the software that is able to take a DNA fragment and tell you which organism that DNA fragment presents. And it's married to Iobio, which is a web-based analysis platform that my laboratory is developing, that allows interactive, real-time and high visual representation of the data.

Interviewer: So yes, one way I've heard it described is that it's like putting a super computer in the hands of your average user, it has that much power behind it. But it's accessible on the internet.

Gabor: This is actually an accurate description because the computational power that allows Taxonomer to run is enormous but all that is hidden from the user. It's what's called the backhand of the architecture, there is a powerful computer sitting in the background that performs the computation in very, very intensive classification job. But what the users see is almost immediate response and almost immediate results.

Interviewer: And so before, this type of analysis took a lot longer and probably had to be done by a specialist, right? A bio-informatic specialist. But now anybody could do it. Is that the idea?

Gabor: Many, many things that the average user will be able to do. Of course, this is not to say that there is no longer need to for a . . .

Interviewer: We don't need you anymore.

Gabor: More involved analysis and expert analysis, but what Taxonomer will be able to do, it will be able to give a scientist, or even a lay-person, an immediate view of what is the overwhelming characteristics of the data. For example, we have examples of an Ebola patient. And when you look at the viral composition of the blood taken from this Ebola patient, you will see that pretty much 100% of the viral load in this individual is Ebola. So that's a very, very obvious and easily interpretable answer to the question of what's making this person sick.

Interviewer: Well like you said, a lot of the strength of this tool is that it's very visual, and that helps people take in information in a different way. Can you talk about that a little bit? Why you think that's an important component.

Gabor: That's how the human mind works. Experts can be trained to look at large data files and textual outputs coming from software and interpret that data in a scientifically meaningful fashion. But our human brain doesn't quite work that way. We like to see things, we like to use the brains innate analytical abilities to start from an image to develop an understanding. And that is the underlying philosophy behind the Iobio project.

Interviewer: In a few years how do you envision Taxonomer, in particular, being used?

Gabor: I view this that its applicability is going to be very wide. This is going to be a very wide and generally applicable tool. Some of the applications that we can foresee today will be infectious disease identification in the clinic that will require expert review of the data. Moving forward, the obvious application will be pathogen identification in the field, under field conditions.

Once the technologies are developed for portable and faster DNA sequence can be used under field conditions. This is only scratching the surface, checking sanitary conditions in restaurants and many applications that we can think of now and many even more applications that will become clear in the future.

Announcer: Interesting, informative, and all in the name of better health. This is The Scope Health Sciences Radio.