Diagnostic Patents After Sequenom

By: Gideon B. Eckhouse  |   February 22, 2018

The discovery of cell-free fetal DNA ("cffDNA") was a groundbreaking and innovative discovery that has formed the basis for a number of patent filings. In the recent patent dispute between Illumina and Ariosa Diagnostics, we can compare patent claims that were found valid and infringed to those that were found not eligible under the seminal CAFC case of Ariosa Diagnostics v. Sequenom.

In 2015 The Court of Appeals for the Federal Circuit applied the Supreme Court’s Mayo Collaborative Services v. Prometheus Laboratories, Inc. precedent to invalidate claims directed toward methods of determining fetal genetic characteristics (Ariosa Diagnostics, Inc. v. Sequenom, Inc.). In that case, the Court first examined whether claims for amplifying and detecting cell-free fetal DNA are directed toward naturally occurring phenomenon. Since the method begins and ends with cffDNA it only includes natural phenomenon. Further, the claims do not transform the cffDNA and only amplify it using “well-understood, routine, and conventional activity.”

This decision was hailed by many as the death of diagnostic method patents. Recently, Illumina, Inc. won a patent dispute over Ariosa Diagnostics, Inc. applying patent that claimed diagnostic methods based on the use of cffDNA. For example claim 1 of U.S. Patent Number 8,318,430, relates to a method of a method for determining a presence or absence of a fetal aneuploidy in a fetus for maternal blood samples containing fetal and maternal cell-free genomic DNA. The method includes  performing performing massively parallel sequencing generating libraries of at least 100 non-random polynucleotides among other steps. While the claims of the ’430 patent and related patent 7,955,784 were challenge for invalidity in view of prior art, enablement, and written description, they were not challenged for patent eligibility under Section 101. What might differentiate the ’430 patent from Sequenom are the claim elements of at least 100 non-random polynucleotide sequences and “massively parallel sequencing.” If these methods are not well-understood, routine, and conventional then the claims may not be invalid under Section 101.