Monday, June 15, 2009

The Genome Scan Dirty Little Secret

You know what I love, you take a company who is inferring that science IS clinical utility and then you hire them to perform interpretation on something that in it's current for is often uninterpretable......and then you sell that for something on the lines of 90-48, 000 USD.

My business is healthcare, my business is also risk prediction, but what my
business is most is disease prevention......

My profession is physician, my oath is to do no harm and if I must harm, do so healing or palliating suffering....A noble profession to be sure.

But no one, I repeat no physician is leading the charge to do whole genome scans for risk prognostication.

Maybe for certain disease detection, but not for true risk prediction.

But, guess what? The business people are...... The business side of Genomics is all about getting "these little babies" into the hands of everyone......

Billions of people at 99 dollars a piece is a lot of money.....but the one thing that may hobble this model is what I like to call the dirty little secret of whole genome scanning.

You can read about it at my other posts
1. We have no clue what it really means.....Merry Christmas
2. Nature is So Wrong
Ok Guys, Seriously.
4. Rading the Medical Commons, A Pirate's Life for Me

Or you can let me recap. Currently DTC genomic companies are testing 1 million single nucleotide polymorphisms. We have in our body combined, 6 billion of these little nucleotides....

Sure the SNPs were safe, heck a SMALL minority had some science behind them.....but
most were razzle dazzle and hyped by researchers to the press.....

Oversold and Overhyped.......If you thought that was something, wait to see the hype from the "Whole Genome" crowd.....

You see, even the most skilled, erudite, knowledgeable geneticist can be hobbled by the explanation of certain genomic changes......

A. If they changes often aren't in genes, then the biology needs to be elucidated, that takes years.

B. If the changes are in genes but that no one has seen before, how do you know what to predict will happen?
C. If we see a change which has been seen but has a wide variety of phenotypes, how do we explain the risk?

D. Most importantly, how do we modify disease risk based on genomic information for most of these things?????

My point is, you have disparate DTC companies calculating risks in different ways and even worse, recommending or "inferring" recommendations for lifestyle changes. Unfortunately, the quit smoking and lose weight isn't exactly "Science" or medicine, which is why they can get away with it.....

What about when a whole genome comes along at 30x coverage? Well, Illumina plans to do that and "outsource" the interpretation to these companies who are "interpreting" based on some very, very soft science already.

What in the hell do they plan to do with this whole genome interpretation?

In my mind these are the keys to get whole genome scan to utility.
1. Formalize some sort of standard interpretive algorithm AND THEN TEST IT CLINICALLY

2. Research the phenotypes which emerge from each and every genomic change out there.....Some like George Church plan to do this in the wide open....which may not attract the millions of people and dozens of years needed for this one....
3. Study the actions which will be proposed for each of the genomic changes to reduce disease risk or to treat disease.....

IFF you can get 5 common diseases captured with this, then you will have a successful system. But then the problem with this is what Illumina already knows...."you will be diagnosing disease and thus enter the realm of clinical test"

Which they have already prepared for by mandating physician ordering of their whole genome scan....

A long post I know......And a long way to go before this is useful at 99 USD per person.

The Sherpa Says: The incidentalome is just the beginning of the nightmare about to be unleashed with whole genomes.....


Lois Wingerson said...

Thanks for this very thoughtful and timely post.

Still waiting to see any useful clinical result of genomic scanning for the general population, which is always too eager for a quick, easy fix for health problems.

What do we truly know about staying healthy? Family history offers a free, quick clue to your risk. Don't smoke, eat and drink prudently, exercise . . . BORing (but true).

Meanwhile (unlike you, good doctor) industry has no primum non nocere mandate. I suppose the best we can hope for just now is that until there's good science the $99 USD will come out of pocket, not out of taxpayer dollars.

So caveat emptor. I'm spending my $99 on popcorn and home movies, thanks very much.

Lois Wingerson
Author Mapping Our Genes and Unnatural Selection

Steve Murphy MD said...

Thank you for your comments. Where could I purchase your book?