In re Stanford University (Fed. Cir. 2021).
This case appears to potential be a good test case on patent eligibility for the U.S. Supreme Court. The Federal Circuit here held that Stanford’s bioinformatics innovation – “a method for resolving haplotype phase” – lacks eligibility under Section 101 because it is directed to an abstract idea under Alice Corp.
Gene inheritance is a super interesting biologic process. Each person inherits a set of chromosomes from each parent. At times, it is helpful to understand which genes came from which parent — especially if tracing disease patterns or researching various diseases. The problem though is that the chromosomes are not labelled “dad” & “mom” (except potentially the sex linked one).
The general purpose of the invention is to provide a better method for figuring out which genes are associated with which parent. The approach is to first obtain allele data from the subject as well as three other family members (two parents and a sibling). The claims then use a statistical inference process (Hidden Markov Model) to identify the likely inheritance state. The claims define key parameters of the model (the hidden states). In addition to HMM, the claims also require a series of error-reduction techniques that use population data as well as consideration of sequencing errors. The prior art includes other methods of resolving haplotype phase, and other would-be non-infringing methods have also been developed since then. [Read Claim 1]. Apparently, the prior-art method had ~80% accuracy while the invention here boosts accuracy to ~98% (for heterozygous positions).
Prosecution History: Stanford researchers filed a couple of provisional applications back in 2011 followed in 2012 by the non-provisional application at issue here (App. No. 13/445,925). After two rejections, an RCE, and several claim amendments, the examiner eventually issued a notice of allowance in 2016. Stanford paid the issue fee and the patent issued on September 13, 2016. The next day (on September 14, 2016), the USPTO withdrew the patent from issue on order of the Tech Center 1600 director, and the subsequently issued a new rejection focusing on patent eligibility. That rejection was affirmed by the PTAB and how has been affirmed by the Federal Circuit.
Patenting Math: On appeal, the Federal Circuit found the claims directed to an abstract mathematical calculation. In its analysis, the court broke-down the claim into a three step process:
- Receive data
- Process data
- Store or output data.
This is an information processing claim, but it does not “DO” anything with the information. The court explains “claim 1 recites no concrete application for the haplotype phase beyond storing it and providing it upon request.” Now, some data processing approaches have been patentable, but those have focused on improving computer functionality itself. The distinguishing point here is that Stanford’s innovation simply provides a better data output.
With Alice Step 2, the court found no inventive concept beyond the abstract idea. Rather, all of the innovative features were basically combining various mathematical algorithms to do a better job of processing data — but we already said that is an abstract idea.
That a specific or different combination of mathematical steps yields a greater number of haplotype predictions than previously achievable under the prior art is not enough to transform claim 1 into a patent eligible application.
Some of the dependent claims include a “diagnosis” or providing a “drug treatment.” However, the court found that the generalized element was equivalent to saying “apply it.” In other words, a specific application is required before a mathematical algorithm such as this will be deemed patent eligible.