On October 26, 2014, 60 Minutes aired a story called “Breeding Out Disease” that included a segment about GenePeeks, a company that uses genetic information from prospective parents to make thousands of “digital babies” and ”calculate the risk of two people conceiving a child with any one of 500 severe recessive pediatric disorders.” When the topic of GenePeeks’ patents came up, that piqued my interest, and I decided to investigate further.

The GenePeeks Patents 

A search of the USPTO database identified two patents assigned to GenePeeks: U.S. 8,620,594 and U.S. 8.805,620, which stemmed from the same application.

The ’594 patent includes method and systems claims. Independent method claim 1 recites:

1. A method of generating a virtual progeny genome … for a potential progeny, the method implemented by a computer processor executing program instructions, the method comprising the steps of:

  1. using the processor, generating a first haplopath … including a single allele … of a genotype at each of a plurality of loci from a first genome profile of a first potential parent;
  2. using the processor, generating a second haplopath … including a single allele  of a genotype at each of the plurality of loci … from a second genome profile of a second potential parent;
  3. using the processor, combining said first haplopath … with said second haplopath … to generate a virtual progeny genome sampling … including two alleles … of a genotype at each of the plurality of loci … for a potential progeny;
  4. using the processor, comparing genotypes of said virtual progeny genome sampling to one or more databases of genotype-phenotype associations to determine a likelihood of expression of one or more phenotypes for the potential progeny having said virtual progeny genome sampling; and
  5. repeating steps (a)-(d), for a plurality of first and second haplopaths from, respectively, the first and second potential parents … to generate a virtual progeny genome … including a plurality of the virtual progeny genome samplings … ; and,
  6. generating for the potential progeny of said first potential parent and said second potential parent probabilities or probability distributions for said potential progeny expressing said one or more phenotypes based on the likelihoods determined for the plurality of virtual progeny genome samplings in the virtual progeny genome ….

The ’620 patent includes method and systems claims. Independent method claim 1 recites:

1. A method of selecting a donor or reproductive partner for a potential parent from a pool of sperm donors, or from a pool of oocyte donors or from a pool of potential reproductive partners, the method implemented by a computer processor executing program instructions, the method comprising the steps of:

  1. using the processor, generating a recipient haplopath … including a single allele … of a genotype at each of a plurality of loci … from a recipient genome profile of a potential parent;
  2. using the processor, generating a donor haplopath H … including a single allele … of a genotype at each of the plurality of loci … from a donor genome profile of a member of a pool of sperm donors, oocyte donors or potential reproductive partners;
  3. using the processor, combining said recipient haplopath H with said donor haplopath H to generate a virtual progeny genome sampling … including two alleles … of a genotype at each of the plurality of loci … for a potential progeny;
  4. using the processor, comparing genotypes of said virtual progeny genome sampling to one or more databases of genotype-phenotype associations to determine a likelihood of expression of one or more phenotypes for the potential progeny having said virtual progeny genome sampling; and
  5. repeating steps (a)-(d) for a plurality of recipient and donor haplopaths from, respectively, the recipient and donor potential parents … to generate a virtual progeny genome … including a plurality of the virtual progeny genome samplings …
  6. generating probabilities or probability distributions for said potential progeny expressing said one or more phenotypes based on the likelihoods determined for the plurality of virtual progeny genome samplings in the virtual progeny genome … and
  7. repeating steps (a)-(f) for each member of said pool of sperm donors, oocyte donors or potential reproductive partners.

As explained in the “Summary of Invention” section of the patents, the described methods predict “the likelihood that a hypothetical child of any two persons … will express any trait or disease that is subject to genetic influences that have been previously characterized, completely or partially.”

Are These Methods Patent Eligible?

The GenePeeks patents were granted in December of 2013 and August of 2014, respectively. Would they pass muster under the USPTO’s current patent eligibility guidance?

Both patents faced 35 USC § 101 rejections during prosecution, based on the assertion that the claims were directed to abstract ideas. In the ’594 patent, the rejections were overcome by arguing that the claims recited “specific steps” and “tangible operations,” and that certain claims passed the machine-or-transformation test of Bilski. Similar arguments were made in the ’620 patent, where it also was argued that the claims did not recite ideas that are “commonly performed by medical professionals” (as asserted in the rejection), but recite steps that medical professionals “do not and have never performed.”

Although both patents were allowed before the Supreme Court decided Alice Corp. v. CLS Bank International, the examination and allowance of the claims appears to be consist with the USPTO’s current implementation of Alice.