Background
Illumina, Inc. and Verinata Health held U.S. Patent Nos. 9,580,751 and 9,738,931, which claimed methods for preparing a DNA sample enriched with cell-free fetal DNA (cffDNA) from a blood sample drawn from a pregnant woman. The inventive insight behind the patents was the discovery that cffDNA is significantly shorter in size than the cell-free maternal DNA present in the same sample. By selectively removing larger DNA fragments, the inventors could produce a sample with a dramatically higher proportion of fetal DNA, making non-invasive prenatal testing far more practical and accurate.
Ariosa Diagnostics — maker of the Harmony Prenatal Test — argued the patents were invalid under § 101 because they were merely directed to the natural phenomenon that cffDNA is shorter than maternal cfDNA. The district court agreed and granted judgment that the claims were ineligible. Illumina and Verinata appealed to the Federal Circuit, which had previously ruled against a related Sequenom patent (Ariosa Diagnostics v. Sequenom, 2015) in a closely watched case that the diagnostic-patent community hoped would be reconsidered.
The Court’s Holding
The Federal Circuit reversed. Judge Lourie, writing for the majority, held that the claims were not directed to the natural phenomenon of fetal DNA size at Alice step one, and therefore eligibility analysis did not need to proceed to step two. The key distinction was that the claimed method was not merely observing or measuring cffDNA’s shorter length — it was a process for physically acting on that difference to produce a new, enriched biological sample. The claims recited concrete preparation steps (e.g., removing large DNA fragments by size selection) that changed the composition of the sample, rather than simply detecting or reporting a naturally occurring property.
The majority distinguished Ariosa v. Sequenom, where the invalidated claims were directed to detecting paternally inherited cffDNA that is naturally present in maternal blood — an observation of a phenomenon. Here, the preparation steps actively created something new: a sample that does not exist in nature, enriched beyond the natural ratio. Judge Reyna dissented, arguing the majority had created a new “bucket” of eligibility analysis for method-of-preparation claims that was inconsistent with Mayo and Sequenom and that would allow patentees to circumvent the natural-phenomenon exception by appending physical processing steps to their claims.
Key Takeaways
- Method-of-preparation claims in the life sciences can be patent eligible even when they exploit a natural phenomenon, provided the steps physically create a product or composition that does not exist in nature in the same form.
- The court drew a key line between claims that detect or report a natural phenomenon (likely ineligible) and claims that act upon a natural phenomenon to produce a physically distinct result (potentially eligible).
- This decision offered a path for diagnostic and genomic patent applicants to structure claims around preparatory steps rather than detection steps alone, improving their § 101 odds.
- The dissent’s concern about inconsistency with earlier precedent leaves open the possibility of en banc or Supreme Court reconsideration in future diagnostic patent cases.
Why It Matters
For the life sciences and diagnostics industry, Illumina v. Ariosa was a significant, if incomplete, win after years of decisions that made biological and diagnostic patents difficult to secure. The Federal Circuit had previously invalidated the foundational cffDNA discovery patent in Ariosa v. Sequenom despite acknowledging it was a genuine and valuable breakthrough — a result widely criticized as unjust. The Illumina decision showed a path forward: draft method claims around what the process does physically, not just what it measures, and distinguish the claimed steps from mere observation of nature.
For companies investing in prenatal testing, genomics, and precision medicine, the ruling mattered commercially as well as doctrinally. It affirmed that Illumina’s enrichment-based technology for non-invasive prenatal testing was protectable, helping to sustain a competitive moat in a multi-billion-dollar market. More broadly, it injected a degree of optimism into a biotech patent community that had grown accustomed to seeing diagnostics-related patents fall under the natural-phenomenon exception.