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DNA Helix

Absence of “High Penetrance” in SNP Genomic Services

June 3rd, 2008 by Andrew Yates

deCODEme, 23andMe, and Navigenics all offer services that only test for “low penetrance genes,” or genes which only sometimes produce an expected trait. Why do these services not test for high penetrance genes, which do produce an expected trait?

The official line is that low penetrance genes are more common and thus more relevant. From Dr. Nierenberg of Navigenics:

“In the case of the BRCA genes, only a relatively small proportion of the population – as low as 5% – carry one or more of these genes. We are focused on SNPs that are apparent within whole populations. We make it clear in our literature that we do not test for this type of gene.”

“We make it clear in our literature?” that’s PR-speak for “we know you’re right, our service would be much more useful if we included those tests, but we can’t, so we pretend sour grapes.”

The real reason is that many of the most important tests are patented or are not identified by SNPs (like deletions or repeating sequences). However, I can’t blame a company representative for a positive spin on the product.

My problem is that the PR is confusing the public about the possibility of genetic testing. By telling consumers that they’re the best, the big three SNP services imply to consumers that they are the best that genetic testing has to offer. This is not true, and it’s making the industry as a whole look flaky.

The reality is that except for a few enthusiasts (like anyone in the DNA Network, including myself), existing SNP genomic services just aren’t that useful. It’s not useful to know that one has a 7% lifetime risk rather than a 5%. I need to know risks of about 40% and higher. No test offered by deCODEme, 23andMe, and Navigenics gives me this information. Even Kari Stephansson of deCODE has admitted “we are marketing these tests without any claim that they will impact on people’s lives.”

Myraid Genetics, unmentioned in the press recently, has a good selection of medically relevantly genetic tests not offered in SNP services and is a good example of the potential usefulness of genetic testing today:

Myraid

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    The official line is that low penetrance genes are more common and thus more relevant. From Dr. Nierenberg of Navigenics:

    “In the case of the BRCA genes, only a relatively small proportion of the population – as low as 5% - carry one or more of these genes. We are focused on SNPs that are apparent within whole populations. We make it clear in our literature that we do not test for this type of gene.”

    Yeah, and it just so happens that the 10% (not 5%) actually has medically actionable validity....

    -Steve
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    The SNP services also can't offer these tests because they are too medically useful. They are too firmly established as medical tests to be sold as informational tests. So they can only sell newly discovered, not patented, tests which aren't as good as the older medical tests. If they give people actionable medical information, it becomes very difficult to argue that the test is for informational purposes only.
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    It is all medically useful or useless. Either way it IS medicine. Test for disease risk? Then you are performing medicine. Check out the state laws in 42 of our great States.

    -Steve
    www.thegenesherpa.blogspot.com
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    Steve: I don't disagree, but that is the logic the SNP services are using... we'll see how long it holds up.
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    Kevin speaks of those pesky sequences that are patented which makes the genomic information services seem so worthless. But...faith....one just may glean some certainity of data by comparing it with data that is certiain such as the SNPs for blue eyes and the person has blue eyes; this could be a baseline however crude. Also a disorder would have more than one SNP associated with it such as a possibility for a defective neuron being combined with something that would suggest Autism would make the possibility for a disorder in the Autism family to be more certain than not (note, I did not say probability, that is another matter).
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    Mr. Andrew Yates offers the following comment in Absence of “High Penetrance” in SNP Genomic Services about espousing the uselessness of genetic testing by companies such as Navigenics:
    “The reality is that except for a few enthusiasts (like anyone in the DNA Network, including myself), existing SNP genomic services just aren’t that useful. It’s not useful to know that one has a 7% lifetime risk rather than a 5%. I need to know risks of about 40% and higher.”
    In response to Mr. Andrew Yates I offer the following information about lifetime risk assessments offered by Navigenics (www.navigenics.com).
    On the Navigenics HealthCompass six conditions have a lifetime risk potential that exceeds 35% (Five conditions exceed 40%). Since some conditions are less common in the population, it is useful to also consider relative risk, as opposed to absolute risk.
    Half of all 23 conditions reported have a relative risk (compared to the average genetic risk in the general population) greater than 2; seven conditions, greater than 3; and three conditions greater than 4. For comparison, this level of relative risk is in line with other well-accepted, commonly used risk factors such as positive family history and environmental risk factors (high lipids, age at menopause etc.)

    I hope this clarifies things for Mr. Yates who can now feel better about being an enthusiast.
    I would also ask Mr. Yates to reconsider his statement about why Navigenics is not doing BRCA testing. Patent considerations aside, it is of import only in about 5% of breast cancer cases (those with “extreme” positive family histories and early age of onset). The contribution of BRCA1/2 mutations in sporadic breast cancers has not been determined conclusively. Our preference is truly to offer a test that is applicable to the majority of individuals. We are cognizant that in a minority of people BRCA testing is important and have addressed this issue on our web site in several places. We realize that no test is complete in and of itself; otherwise people would have heart surgery based only on a treadmill. So, I would ask Mr. Yates to please give us credit for more than trying to get around patent considerations. We are enthusiasts as well.
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    The SNP services offer tests that are somehow related to medical field.So it is relevant inspite of the fact that it offers little benefit.
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    What is the relevance of low penetrating genes?
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    High penetrance genes testing is not included in SNP. Why is that so?
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    “In the case of the BRCA genes, only a relatively small proportion of the population – as low as 5% - carry one or more of these genes. We are focused on SNPs that are apparent within whole populations. We make it clear in our literature that we do not test for this type of gene.”

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  1. Challenge to Michael Nierenberg, Medical Director of Navigenics | Think Gene
    November 10, 2008 @ 11:15 pm

    [...] Nierenberg, Medical Director of Navigenics comments on “Absence of “High Penetrance” in SNP Genomic Services” regarding my statement “existing SNP genomic services just aren’t that [...]

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