Gene Essence: what bad personal genomics looks like

I mentioned yesterday that one of the companies recently targeted by the California health department was an outfit called Gene Essence. Gene Essence is a 23andMe-style genome scan service launched back at the end of March (covered by Hsien) by Biomarker Pharmaceuticals, a company that aims to develop "genomic and proteomic aging-intervention technologies" to "provide interventions that will extend a healthy human lifespan by slowing the process of aging, and delaying the onset of age-related diseases."

I haven't heard anything about Gene Essence since its launch was announced, so I was curious to see how the service had evolved. The first signs were good: the company is using the Affymetrix 6.0 SNP array, a solid platform that provides information on around 1 million genetic variants throughout the genome - although I can't find any information on where the testing is actually being performed.

Unfortunately, it's all downhill from there. The company thoughtfully provides a demo report allowing customers to see what they'll be getting for their $1,195 - and based on what that shows me I can't imagine anyone purchasing this service, especially given that both 23andMe and deCODEme both offer infinitely superior products at a lower price.

To see just how bad Gene Effects' service is, first check out the 23andMe and deCODEme demo versions, here and here. Now take a look at the demo page where Gene Effects displays your "genetic susceptibility" for a set of different common diseases. Apparently the demo sample has a genetic susceptibility of 100% for atherosclerosis; but does that mean he is 100% likely to get atherosclerosis, that he has the maximum possible genetic risk for the disease, or simply that he has the riskier version all of the known polymorphisms associated with the disease? It's impossible to tell from the page itself - and if you click on the bar for that condition you end up on this absolutely incomprehensible "detail page", which is no help at all.

OK, so let's try reading the manual. The "How to Read This Report" page is unhelpful, but the "Sample Reports" page provides some useful detail - and after a bit of digging it becomes clear that the "genetic susceptibility" score is an indicator of how many of the known risk variants a person carries, scaled by the relative effect of each variant on disease risk. We're supposed to be using the "adjusted trend" column, which "takes into account the fact that for each condition, a different proportion of the population will have a genetic trend value lower than yours". This doesn't make it any clearer what this actually means in terms of risk prediction; but rather than provide a useful clarification the page goes on to lay out a series of generic disclaimers (e.g. "SNPs are simply markers for the disease or condition and do not necessarily carry any predictive value in terms of assessing one’s susceptibility to a given disease").

In other words, the company provides a series of alarming and confusing predictions, and then simply tells you they don't necessarily mean anything.

There's no estimate of the individual's actual risk of the disease (as you would find in a 23andMe, deCODEme or Navigenics report), no indication of the fraction of the total variance in disease risk that is captured by the polymorphisms in your report, and no reference to whether the described associations are actually reliable and well-validated (for instance, it gives you information on 14 different variants associated with bipolar disease, not one of which has actually been independently replicated). That renders the information essentially meaningless and potentially seriously misleading for the typical customer.

By this stage anyone that Gene Essence somehow convinced to purchase their product would be desperately looking for a way to get some return on their $1,195 purchase. Well, they could always download their raw data and run it through Promethease, which would give them access to the information on each of their genetic variants from the public SNPedia database - except when they click on the "Complete SNP Data" page they'll find no straightforward way to download their entire data-set, but rather a box in which they can type a SNP identification number and download their genotypes one by one. A million of those is going to take some time, even if this feature was actually working (which it isn't, at least for the demo account).

In summary: based on the demo (which is all a potential customer would have to go on) this service is currently seriously bad; I find it hard to imagine that any potential personal genomics customer would pick it over its vastly more professional-looking, rigorous and user-friendly rivals. The fact that Gene Essence actually charges more for its service than 23andMe is utterly absurd. This is an example of what happens when a company tries to jump on the genome scan bandwagon without investing sufficiently in the knowledge-base and user interface required to present extremely complex data to a customer with a limited understanding of genetics.

This hardly inspires any further confidence in the company:

A person who declined to identify herself and who answered the phone at the number listed on Gene Essence's Web site said she didn't know anything about that business or Robert Danielzadeh, identified by the state as its chief executive.

I suggested yesterday that the best outcome in California might be a compromise, in which respectable personal genomics companies are allowed to continue operating (with slightly increased regulatory oversight) while amateurish efforts like Gene Essence slide quietly out of existence. While I don't agree with Steve Murphy that a doctor's explicit permission should be required to authorise a genome scan, there should be a minimum standard of validation and information reporting - and the current version of Gene Essence falls well below that standard.


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