By CRG staff - interview with Steven Salzberg

All the legal fuss about gene patents may be for naught. Operating under the belief that "any individual should be allowed to interrogate his or her genome ... regardless of whether a private company claims to 'own' the rights to particular gene mutations," Steven Salzberg, Director of the Center for Bioinformatics and Computational Biology at the University of Maryland, and colleague Mihaela Pertea created a program to screen an individual's genome for BRCA mutations-apparently without violating Myriad's patents on those genes. The software is available for free download, but there is a catch: you'll need to have your genome sequence handy. Yet as the cost of whole-genome sequencing continues to drop, it will become more and more economical to circumvent specific diagnostic tests such as Myriad's with computational screens. In other words, the Salzberg Screen just might be the harbinger of a future in which, at least in diagnostic testing, gene patents are essentially obsolete.

How is the Salzberg Screen different from anything that's already out there?

It's the first purely computational screen that starts with the whole genome sequence- the "shotgun sequence" as we call it-from sequencing your genome with one of the new sequencing machines, the so called "next generation" sequencer.


I understand this project is a direct response to gene patents. Is it more specifically a response to the Myriad case as well?

No, it predates that-we heard about that lawsuit after we had already done most of the work. We were just about to submit the paper when we heard about the lawsuit.


Was the main idea from the beginning to effectively circumvent patents?

I think you could fairly say it was one of the main ideas. We just wanted to demonstrate that with current technology, we're now at the point where it's pretty easy to interrogate your genome for any mutation that you want to if you have the genome sequence. And you can do that computationally: once you sequence your genome, it's a one-time assay. You can sequence your genome once and test it many times-you can continue to test it computationally the rest of your life. Whenever a new mutation is discovered that you're interested in, you can just download some software and screen your genome. That's the way things will work in the future. We are a little ahead of the curve, but that's the idea: in research, we like to be ahead of the curve. We're not there yet, because people aren't routinely getting their genome sequenced, but it's going to happen, it's just a matter of time.


And the limiting factor now is the price of whole genome sequencing?

Yes, the price of whole genome sequencing is now under $10,000, just to do the raw sequencing ... but that's all you need for our test, that raw sequence. Our test is free, the software is free, and you can run it on your computer. It would probably take all day or overnight, since there's a lot of data in a genome sequence, but you can probably do it on your desktop computer. And the cost of sequencing is still dropping fairly rapidly. The Myriad test, which I believe is one of the most expensive, costs upwards of $4,000. We're already pretty close to the same cost, and once you have your genome you can test for any mutation in any gene-so why would you pay per gene to have them tested? It doesn't make any sense economically.

You have said that "the door to this new technology is already open and cannot be closed." Do you think that gene patents could get in the way of this?

Patents can slow things down and they can get in the way, but I don't think that they are going to stop progress. They certainly impede progress ... but remember, the U.S. is not the only country in the world, and the patents that are being filed in the U.S. are not recognized by many other countries. So if you can't get your genes tested here, you may be able to go somewhere else-the world is a small place.


Although it seems this software does not violate Myriad's patents directly, are you concerned that they might sue you for indirectly violating their patents?

I'm not really concerned, but I guess you could say I have a mild concern about that. I don't think it would really benefit them to go after me. I think right now Myriad is going to be mostly interested in just keeping their patents from being completely invalidated. The current court ruling is that the patents are not valid-and if that ruling holds up, game over for them.

For the very short term, you're not going to see large numbers of people getting their whole genome sequenced; but in the medium term, maybe four or five years out, I think it's going to become increasingly feasible for people to do that. If it's cheaper, people will do it.

If you can get one gene sequenced and tested for $4,000 or else get your whole genome sequenced for $4,000 and then test that one gene, I think everyone would do the latter, because once you sequence your genome you can then hang onto it and test for other mutations in the future-mutations that haven't been discovered yet.


Have you had any pushback, anyone telling you that making the screen available was a bad idea?

No, not really. I talked to the people in my group about it, and they were all very interested in the topic. I'd say they mostly thought it was a good idea ... though I'm not sure they would have all done it themselves!                                                    


To download the software, visit

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