December 30, 2012
Full Genome Sequencing: Use Computers, Not MDs To Understand

The argument that full genome sequencing results require doctors to interpret gets it exactly wrong. We need computers to interpret our genes to us because doctors can't possibly model that much data in their minds.

Concerns about a lack of regulation become even more intense when you get into sequencing the entire genome or exome (a smaller part that contains important DNA sequences that direct the body to make essential proteins), wrote Dr. James Evans and Dr. Jonathan Berg, of the department of genetics and medicine at the University of North Carolina at Chapel Hill.

...

The U.S. Food and Drug Administration has been in talks with direct-to-consumer companies and is particularly interested in tests that influence medical decisions.

The cost of sequencing of one's entire genome has already fallen by orders of magnitude and is now below ten thousand dollars and still dropping. Once the cost hits below $1000 i want to get my full genome sequenced and keep that data stored where I can access it any time. As more discoveries are published about what each genetic variant means I do not want to take time off from work to go to a doctor's office to pay a doctor to look up to see if I have that variant.

Think about it will mean to know your 2.9 billion letter genetic sequence: The amount of data will be so large that to check on what it means will require interacting with a computer. Doctors won't know more than a few hundred genetic variants. The mind just can not remember that much info and it won't be worth trying. So we'll have to use computers to advise us on the ramifications of our genetic sequences.

We should be able to directly interact with computers in order to understand our genomes. The meaning of our genomes should not be accessible only to medical doctors and genetic counselors.

Share |      Randall Parker, 2012 December 30 07:51 PM 


Comments
Aaron Ashmann (halotek) said at December 31, 2012 2:10 AM:

Randall, I've studied health and nutrition for about 10 years now and nothing, and I mean nothing has shed my clarity of what I know than the DNA test I took. I was always wondering why I was sensitive to so many foods, but also was robust in certain areas. My non-secretor status was also eye opening. I recommend the test for everyone if they can handle it.

JP Straley said at December 31, 2012 7:51 AM:

Well, the question is whether we own our body or not?

If I own my body and thus my DNA, I also own the information coded in the DNA and I should be able to use or interpret this property. I may easily hire an agent to analyze and interpret my DNA.

Rent-seekers may claim that I will injure myself in hiring an "unqualified" person or agent to interpret, but almost certainly they will use some sort of expert system to interpret the information, so there is no reason whatever to interpose this rent-seeker between the generator and owner of the information (me) and the beneficiary of the information (which also happens to be me).

There is also the additional privacy that can be gained by using a private agent to analyze and interpret my DNA. The rent-seeker would never gain the advantage of his license if he did not convince government to grant such license, and this creates a partnership between the licensed DNA interpreter and government...likely to the detriment of my privacy.

kurt9 said at December 31, 2012 9:44 AM:

The FDA is trying to defend the medical guild. Like the guild system of the middle-ages, medical professionals have become nothing more than gate keepers which, in turn, is nothing more than rent-seeking parasitism.

kurt9 said at December 31, 2012 9:48 AM:

I have always believed that the FDA should be abolished. The only legitimate regulatory issues, that of content purity and proper labeling, can be enforced by the USDA. We don't need the FDA which, by the way, is responsible for the needless suffering and death of 3,000 Americans every single day. The FDA is a genocidal organization that carries out a Holocaust-equivalent on the American people every 3 years. Its time it be eliminated.

Randall Parker said at December 31, 2012 3:17 PM:

Aaron,

And imagine what your full genome sequence will be able to tell you about your ideal diet 5 years from now and, even more, 10 years from now. We'll get lots of useful info from our personal owners manual if we are only allowed to read it.

JP,

Yes, agreed: The key question is whether one owns one's own body. I say yes.

Kurt,

The medical guild should be replaced with huge amounts of data flowing to and expert systems, machine learning models, and other computer-based diagnostic and treatment tools. We should have microfluidic devices in our bedrooms and bathrooms collecting data to look for problems every day.

I think the FDA should lose authority over what drugs you can use when you've been diagnosed with less than 5 years left to live. It should also have no power to stop you from getting any kind of test you want directly.

Nanonymous said at January 2, 2013 4:45 PM:

Is it legal to hide from me the results of any other test if I explicitly request the results? Say, blood glucose or HDL levels. I don't think it would be legal. And I can go to any number of places that do these tests - all of them are full of clinical tecnicians, not doctors. DNA is not different in any way - it's just a test on something in my body. I will gladly consult my doctor on how to interpret glucose levels or DNA alleles and what, if anything, to do about it - OR, I am perfectly free to look up the existing literature or believe some erroneous information I find in the internet. Any attempt to hide my DNA from me is pure BS.

your full genome sequence will be able to tell you about your ideal diet 5 years from now and, even more, 10 years from now.

I'd be really surprised if anything even remotely resembling this happens in 5 years. It almost certainly won't. Remember - we still can't even predict something as simple as height based on genetic info (the predictions are not very good anyway.) And diet is literally several orders of magnitude more complex.

Interesting times are coming in any way. Tampering with DNA tests by planting synthetic DNA will probably be attempted (but should be easy enough to detect.) Drive-by exome sequencing by insurance companies will certainly be attempted in some cases. Keep your DNA data safe - safer than your credit card number.

Matt said at January 2, 2013 4:54 PM:

"Randall, I've studied health and nutrition for about 10 years now and nothing, and I mean nothing has shed my clarity of what I know than the DNA test I took. I was always wondering why I was sensitive to so many foods, but also was robust in certain areas. My non-secretor status was also eye opening. I recommend the test for everyone if they can handle it."

Aaron, could you explain which test you took, how you took it, and how you went about interpreting the results?

From an interested layman who doesn't know where to start with this stuff.

Thanks.

Aaron Ashmann (halotek) said at January 2, 2013 9:55 PM:

Matt, I took the test at 23andme.com

They have basic info on traits/genetic diseases and so on. A lot of time you will just have to search SNP databases and look at actually pubmed studies. It's not completely easy stuff.

Any example of this is I've always known what a non-secretor was, but didn't easily get this info from 23andme.com. It told me I had resistance to the common norovirus-- when I looked further into the data on this, It said i was a non-secretor.

Test was done via a spit test-- very simple. you purchase kit and then send back to lab.

Btw, the 23andme.com test is worth it for your ancestral genealogy alone.

Lastly , interpreting results is not easy. most studies have a star ranking based on how much data we know. ALso, there is a lot of gene play going on so some genes, might tell you you process saturated fat well and others might say otherwise. you really have to look at your results carefully.

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