Monthly Archives: May 2012

23andme’s First Patent

Update, June 1: 23andme has added an addendum to their announcement. In particular, the addendum clarifies and seems to promise that the patent will not be enforced with respect to performing interpretations: “Other entities can present information about the genetic associations covered in our patents without licensing fees.” This is reassuring news and it’s great to see 23andme outline such a limitation on patent enforcement! It allays my feared hypothetical situation regarding a “swiss cheese” effect on genome interpretation efforts (described below). — Madeleine


This morning I noticed a post from 23andme’s blog last night: Anne Wojcicki announced that 23andme expects to be awarded its first patent today. It touched on a lot of issues I care about, so I’ve written this personal post in response to it.

From what I understand, the 23andme patent seems to be a patent on genetic variant interpretation: in specific, on the interpretation of some variants (including one in the gene SGK1) as being associated with differences in an individual’s risk of developing Parkinson’s disease. Technical methods for determining the variants are listed, but they seem to be an enumeration of all extant methods for assessing genetic variants (including techniques used in whole genome sequencing).

In other words: this seems to be a patent regarding the reporting and usage of an observation that a naturally-occurring genetic variant is associated with a particular trait. As noted by 23andme’s announcement, these patents are controversial.

Patent Wars

While my first love is genetics, I am also a programmer — and in software, patents are very broadly hated by programmers. This American Life has an excellent episode documenting the tangled mess that is the software patent industry. It has become an arms race; even the most well-intentioned companies feel obligated to build up patent arsenals. Software patents are a different beast to biotechnology patents, but in some ways larger issues remain true: applied too broadly, in a field of rapid progress, patents have the potential to create a tangled web of litigation. The intended purpose of patents to protect innovation and encourage commercialization through exclusive access to innovation has instead become outright warfare.

A web of litigation in the mobile phone industry. ©2010 George Kokkinidis / Design Language, used with permission

I worry that this vision of patent warfare could exist in the realm of genome interpretation. The multitude of patents on the meaning of genetic variants seems to make the process of whole genome interpretation almost impossibly hazardous. I think it is vital to everybody that we are able to not merely return your “A’s, C’s, G’s, and T’s”, but also give you explanations like “you have A here, and according to these studies this means you are much less likely to be infected with stomach flu”. Will each one of those explanations run the risk of violating a patent? Will genome interpretations become like Swiss cheese as they must carefully avoid mentioning each of the patented genes (which are possibly the most important ones)? Is part of 23andme’s purpose here to build up its own arsenal of interpretations, as both defense and weapon against other interpretation efforts?

Will patents on the observed associations of genetic variants turn whole genome interpretation efforts into swiss cheese? Image credit: Madeleine Price Ball, CC-BY-SA

23andme is far from the first in this field (there are hundreds or thousands of patents like this one) and it is possible that they have no intention to engage in such wars. Nevertheless, as far as I am aware they have not released an assurance that the patent will not be used in this way (of course, neither has anyone else). In the software industry, some groups have made assurances regarding their patents — promises that the patents will only be used for defensive purposes (e.g. Twitter) or limits on their offensive uses (e.g. Red Hat). That said, such promises are easily broken.

Also troubling to me is the exact wording in the announcement itself:

“We believe patents should not be used to obstruct research or prevent individuals from knowing what’s in their genome. We believe that everyone has a right to know their genomes — their sequence of As, Ts, Cs, and Gs — and should be able to access them should they want to. This has been our guiding principle since day one, and 23andMe has pioneered the ability for individuals to have unfettered access to their genomes.”

I’m reading between the lines, but… if access to your genome means that you only have access to the uninterpreted sequence of A’s, T’s, C’s, and G’s — a completely unintelligible mess to the vast majority of humanity — then I think that falls short of “unfettered access”.

Patenting Nature

There is an important difference between software patents and gene interpretation patents. While software is clearly the product of design (hence the term “software engineer”), patents on the interpretations of genes are the product of discovery. Indeed, the word “discovery” dominates 23andme’s own announcement of the patent. As that announcement noted, whether this is patentable material is the subject of hot debate. Is this patenting a “law of nature”? While using the laws of nature is fundamental to any process, patent law has held that the “laws of nature” themselves are not patentable.

I am a researcher and not a lawyer, but I’ll try to summarize my understanding of the recent “Prometheus” case referenced by 23andme’s announcement. In a unanimous decision, the Supreme Court struck down the patentability of the act of monitoring the levels of a drug metabolite (the product of the drug as the body breaks it down) and the use of this information to adjust dosage of that drug. This correlation was held to be a “law of nature”, and therefore unpatentable. Some phrases from the decision that stood out to me were these:

“But to transform an unpatentable law of nature into a patent eligible application of such a law, a patent must do more than simply state the law of nature while adding the words ‘apply it.’”

“… the claimed processes are not patentable unless they have additional features that provide practical assurance that the processes are genuine applications of those laws rather than drafting efforts designed to monopolize the correlations.”

Patenting the observed naturally-occurring traits associated with a naturally occurring genetic variant strikes me as a very similar “law of nature”. Perhaps even moreso — at least the drug itself was some level of non-natural engineering? This is far from resolved, however. The more relevant case — the “Myriad” case regarding a patent on BRCA variants and their associations with breast cancer risk — has been remanded to the Federal Circuit for reconsideration in light of the Prometheus case. I am optimistic that the act of reading and interpreting genetic variants will be held to be non-patentable, and that all my worries written here will be moot and forgotten …. but this remains to be seen.

Cashing In On Crowdsourcing?

The discoveries made by 23andme have come from their “23andWe” program — a crowdsourcing of scientific research. A recent Nature Reviews Genetics article describes such programs as “participant centered initiatives” — “tools, programs and projects that empower participants to engage in the research process”. Crowdsourcing is a powerful tool to rapidly meet a goal, and an exciting consequence of the internet’s transformational facilitation of connecting and communicating. But it holds some darker questions: to what extent does such a program exist to benefit the participant — and to what extent is the participant used as a resource to benefit the organization? Although the lines might be fuzzy to draw, the ownership and profit from user-generated data has become a clear motivation for companies (c.f. Facebook).

The Personal Genome Project has a lot of overlap with 23andWe in style. We want to collect similar information from participants — we ask people (if they are willing) to share information regarding their health and traits, as well as genome data. But there is also a key difference between the two projects: we do not hold this data privately for our own research. We release the data publicly for all others to see, and this is something we are uniquely able to do due to our open consent process. We want everyone — including our participants — to have as much access to the data as we do, and the same potential to make interesting discoveries.

As such, I see Personal Genome Project participants as very much our “peers” in this research endeavor. For this reason I prefer to use the phrase “peer production” rather than “crowdsourcing” to describe some aspects of our work (a term that can also be applied to projects like Linux and Wikipedia): not merely a project that solicits participant contributions, but one that genuinely shares those contributions as freely as possible.