The CRISPR Patent Battle: Who Owns Gene Editing?

The Most Valuable Invention in Biology

When Jennifer Doudna and Emmanuelle Charpentier published their landmark paper in Science in June 2012, they did more than describe a new way to edit genes. They lit the fuse on what would become the most consequential patent fight in the history of biotechnology — a legal battle that would span more than a decade, cross international borders, reshape the pharmaceutical industry, and force uncomfortable questions about who truly "owns" a technology that could redefine medicine.

At stake was not just credit or prestige, though both mattered enormously. The real prize was control over a multi-billion-dollar platform technology. Whoever held the key CRISPR patents would collect royalties on every drug, every therapy, every agricultural product, and every research tool built on CRISPR-Cas9 gene editing. The patent holder would decide which companies could develop CRISPR therapies, on what terms, and at what cost.

This is the story of that fight — who the combatants were, what they claimed, how the legal system sorted through their competing arguments, and what the outcome means for the future of gene editing.

The Discovery: Two Papers, Seven Months Apart

Doudna and Charpentier: The 2012 Science Paper

In June 2012, Jennifer Doudna of UC Berkeley and Emmanuelle Charpentier, then at Umea University in Sweden, published a paper in Science titled "A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity." The paper demonstrated that the CRISPR-Cas9 system — a naturally occurring immune defense in bacteria — could be reprogrammed to cut specific DNA sequences in a test tube. Critically, they showed that a single guide RNA (sgRNA) could be engineered to direct the Cas9 protein to virtually any target sequence, making the system remarkably simple and programmable.

The paper was immediately recognized as transformative. Previous gene-editing tools like zinc finger nucleases (ZFNs) and TALENs required laborious protein engineering for each new target. CRISPR-Cas9 required only a short RNA sequence. The implications were obvious: if this system could work inside living cells, it would democratize gene editing.

But the 2012 Science paper had a notable limitation. All of the experiments were conducted in vitro — in test tubes, using purified components. Doudna and Charpentier showed that CRISPR-Cas9 could cut DNA, but they had not yet demonstrated that it could edit genes inside the cells of living organisms, particularly the complex eukaryotic cells of plants and animals.

UC Berkeley filed a patent application on behalf of Doudna and Charpentier on May 25, 2012, before the Science paper was even published. The application was broad, claiming the use of CRISPR-Cas9 for gene editing in all cell types — prokaryotic and eukaryotic alike.

Feng Zhang: The 2013 Science Paper

Seven months later, in January 2013, Feng Zhang of the Broad Institute of MIT and Harvard published a paper in Science demonstrating that CRISPR-Cas9 could edit genes inside human cells and mouse cells. Zhang's paper, along with a simultaneously published paper from George Church's lab at Harvard, showed that the system worked in eukaryotic cells — the type of cells that make up the human body.

Zhang had filed his patent application on December 12, 2012, months after UC Berkeley's filing. But here was the critical difference: Zhang requested — and paid for — an accelerated examination of his patent. The Broad Institute's application sailed through the USPTO, and the first CRISPR patent was granted to Zhang and the Broad Institute on April 15, 2014. UC Berkeley's application, filed earlier but processed at normal speed, was still sitting in the queue.

By the time the dust began to settle, the Broad held a portfolio of patents specifically covering the use of CRISPR-Cas9 in eukaryotic cells — the application that mattered most for human medicine. UC Berkeley held claims to the foundational CRISPR-Cas9 technology more broadly, but had not yet secured patents specifically directed to eukaryotic applications.

The stage was set for a collision.

The Patent Interference Proceedings

What Is a Patent Interference?

Under U.S. patent law as it existed before 2013 (when the America Invents Act transitioned the system to "first to file"), the critical question was not who filed first, but who invented first. When two parties claimed to have invented the same thing, the USPTO could declare an "interference" — a legal proceeding to determine priority of invention.

UC Berkeley petitioned the USPTO to declare an interference between its pending patent application and several of the Broad's granted patents. Berkeley's argument was straightforward: Doudna and Charpentier invented CRISPR-Cas9 gene editing first, their patent application was filed first, and their broad claims should encompass all uses of the technology, including in eukaryotic cells.

The Broad countered with a fundamentally different framing. Zhang's work in eukaryotic cells, the Broad argued, was not merely an obvious extension of the Doudna-Charpentier in vitro work. Getting CRISPR to work inside the complex environment of a mammalian cell required significant additional innovation — adapting the system for nuclear localization, optimizing guide RNA design, and demonstrating actual genome editing in living cells. The Broad characterized this as a separate, independently patentable invention.

The PTAB Decision: 2017

In February 2017, the Patent Trial and Appeal Board (PTAB) issued its decision, and it was a decisive win for the Broad Institute. The three-judge panel ruled that there was no interference-in-fact between the two sets of claims. In plain language: the Broad's patents on CRISPR in eukaryotic cells and UC Berkeley's claims on CRISPR generally were directed at different inventions.

The PTAB found that a person of ordinary skill in the art, reading Doudna and Charpentier's 2012 paper, would not have had a reasonable expectation that CRISPR-Cas9 would work in eukaryotic cells. The biochemistry of cutting DNA in a test tube is substantially different from editing a genome inside the nucleus of a living human cell, surrounded by chromatin, histones, and complex repair machinery. The Board pointed to evidence that several labs had attempted and initially failed to get CRISPR working in mammalian cells, suggesting that Zhang's success was not obvious or inevitable.

This was a crucial legal distinction. If eukaryotic CRISPR was obvious from Doudna's in vitro work, then Berkeley's earlier filing date should give it priority. But if it was a separate, non-obvious invention, the Broad's patents could stand independently.

The Appeal: Federal Circuit, 2018

UC Berkeley appealed to the Court of Appeals for the Federal Circuit, the specialized appellate court that handles patent cases. In September 2018, the Federal Circuit affirmed the PTAB's decision. The court agreed that the Broad's eukaryotic CRISPR patents did not interfere with UC Berkeley's foundational claims. The two parties' inventions were legally distinct.

Round Two: The 2022 Decision

The story did not end there. After the America Invents Act changed U.S. patent law to a "first to file" system (for applications filed after March 16, 2013), a new proceeding was initiated. This time, the question was different — not who invented first, but whether the Broad's later-filed applications for eukaryotic CRISPR were patentable over UC Berkeley's earlier-filed application.

In February 2022, the PTAB again ruled in the Broad's favor. The Board found that Zhang's eukaryotic work was sufficiently inventive and non-obvious to warrant separate patents, even though Berkeley's application was filed earlier and claimed the technology broadly. The Board noted that the prior art did not render it obvious that CRISPR would work efficiently in mammalian cells, and that Zhang had provided specific innovations to make it function in that context.

UC Berkeley appealed once more, but the Federal Circuit upheld the decision in 2023. The Broad's eukaryotic CRISPR patents were secure.

The Split: Who Owns What

The practical outcome of the patent proceedings created an unusual and consequential division of intellectual property:

The Broad Institute holds patents covering the use of CRISPR-Cas9 in eukaryotic cells — meaning human cells, animal cells, and plant cells. Any company developing a CRISPR-based human therapy, agricultural product, or animal treatment needs a license from the Broad (or its licensees).

UC Berkeley (along with Charpentier and the University of Vienna) holds patents on the foundational CRISPR-Cas9 technology — the basic system of using a guide RNA to direct Cas9 to a target DNA sequence. These patents cover uses in prokaryotic cells (bacteria) and in vitro applications, as well as broader method claims. UC Berkeley was eventually granted its own U.S. patents, and these foundational claims have value in areas like research tools, diagnostics, and industrial biotechnology.

This split created a complex licensing landscape. For the most commercially valuable application — human therapeutics — companies generally needed licenses from both parties. For research tools and bacterial applications, UC Berkeley's patents were more directly relevant.

How the Patent War Shaped the Industry

The Three CRISPR Companies

The patent battle did not play out in a vacuum. Even as the legal proceedings unfolded, three major CRISPR therapeutics companies were founded, each aligned with one of the key scientists:

Editas Medicine (founded 2013) was built around Feng Zhang's work and licensed its core CRISPR technology from the Broad Institute. Editas held an exclusive license to the Broad's eukaryotic CRISPR patents for human therapeutics. The company's lead programs focused on genetic eye diseases and sickle cell disease.

Intellia Therapeutics (founded 2014) was co-founded by Jennifer Doudna and licensed its CRISPR technology from UC Berkeley and Doudna's intellectual property. Intellia pursued in vivo CRISPR therapies, most notably a groundbreaking program for transthyretin amyloidosis (ATTR) that demonstrated, for the first time, effective in vivo CRISPR gene editing in humans in clinical trials.

CRISPR Therapeutics (founded 2013) was co-founded by Emmanuelle Charpentier and licensed technology from Charpentier's patent estate. CRISPR Therapeutics partnered with Vertex Pharmaceuticals to develop Casgevy (exagamglogene autotemcel), which in 2023 became the first CRISPR-based therapy approved by regulators anywhere in the world, for the treatment of sickle cell disease and beta-thalassemia.

Each company's patent position reflected the fragmented IP landscape. In practice, most companies developing CRISPR therapeutics needed to navigate licenses from multiple parties. Cross-licensing agreements, sublicenses, and patent pools became essential to the business of CRISPR medicine.

The Licensing Landscape

The Broad Institute licensed its eukaryotic CRISPR patents through a complex web of agreements. Editas Medicine held the primary exclusive license for human therapeutics, but the Broad also granted non-exclusive licenses to other companies for specific applications. The Broad's licensing strategy evolved over time, with the institute signaling its willingness to license broadly for research and more selectively for commercial therapeutics.

UC Berkeley, through its technology transfer office and a licensing arrangement managed partly by the innovation company Caribou Biosciences (co-founded by Doudna), pursued its own licensing program. Caribou itself developed CRISPR-based cell therapies, particularly allogeneic CAR-T cell therapies for cancer.

Charpentier's patent rights were licensed through CRISPR Therapeutics and, for certain fields, through ERS Genomics, a company she co-founded specifically to manage her CRISPR intellectual property.

The result was a patent thicket — overlapping claims held by different parties, each controlling a piece of the puzzle. Companies entering the CRISPR space had to assemble licenses from multiple sources, adding cost and complexity. Some industry observers compared it to the early days of the automobile, when a tangle of competing patents nearly strangled the industry until a patent pool was formed.

The European Patent Office: A Different Outcome

While the U.S. proceedings dominated headlines, the battle played out differently at the European Patent Office (EPO). European patent law applies different standards for patentability, and the EPO's proceedings followed a different procedural path.

The Broad Institute initially secured a key European patent (EP 2771468) covering the use of CRISPR-Cas9 in eukaryotic cells. However, in January 2018, the EPO revoked this patent on procedural grounds related to the priority claim. The Broad had listed certain inventors on the priority application (the earlier U.S. filing from which the European patent claimed priority) that did not match the inventors on the European patent itself. Under European patent law, this discrepancy invalidated the priority claim, and without that earlier priority date, the Broad's European patent was exposed to prior art — including the Doudna-Charpentier publications.

The EPO's Technical Board of Appeal upheld this revocation. The practical effect was significant: in Europe, UC Berkeley and Charpentier's patent position was relatively stronger than in the United States. European companies seeking CRISPR licenses needed to navigate a different IP landscape than their American counterparts.

UC Berkeley and the University of Vienna secured European patents covering the CRISPR-Cas9 system, giving Doudna and Charpentier's side a more dominant position in European jurisdictions. This geographic split in patent rights added another layer of complexity for companies operating globally.

Base Editing and Prime Editing: The Next Patent Frontier

The CRISPR patent war was not confined to the original Cas9 technology. As the field advanced, new gene-editing approaches emerged — and with them, new patent battles.

David Liu and Base Editing

David Liu, a chemist at the Broad Institute and Harvard, developed base editing in 2016. Base editors use a modified, catalytically impaired Cas9 (called a nickase) fused to a deaminase enzyme to convert one DNA base to another — for example, changing a C to a T — without making a double-strand break in the DNA. This was a significant advance because it avoided some of the unpredictable outcomes (insertions and deletions) associated with traditional CRISPR-Cas9 editing.

Liu's base editing patents were filed through the Broad Institute, extending the Broad's patent portfolio into next-generation editing technologies. Beam Therapeutics, co-founded by Liu, Feng Zhang, and Keith Joung, was established in 2017 to commercialize base editing. Beam licensed exclusive rights to the Broad's base editing patents.

Prime Editing

In 2019, David Liu's lab introduced prime editing, which uses a Cas9 nickase fused to a reverse transcriptase enzyme, guided by a prime editing guide RNA (pegRNA). Prime editing can make virtually any type of small edit — insertions, deletions, and all twelve types of point mutations — without requiring double-strand breaks or donor DNA templates. It is sometimes described as a "search and replace" function for the genome.

Prime editing patents were again filed through the Broad Institute. Prime Medicine, founded in 2019, licensed these patents to develop prime editing therapies. The Broad's control of both base editing and prime editing patents significantly expanded its dominance in the gene-editing IP landscape.

The Strategic Implications

The Broad's accumulation of patents across CRISPR-Cas9 (eukaryotic applications), base editing, and prime editing gave it an unparalleled position in the gene-editing patent landscape. Companies developing next-generation editing therapies found themselves needing Broad licenses regardless of which editing modality they used. This concentration of IP rights in a single institution raised concerns among some industry participants and academic researchers about access, cost, and innovation.

However, the Broad and its licensees argued that strong patent protection was necessary to incentivize the enormous investment required to translate gene-editing discoveries into approved therapies. The cost of bringing a gene therapy through clinical trials and regulatory approval runs into the hundreds of millions of dollars, and patent protection provides the commercial certainty that investors require.

The Nobel Prize: Recognition Without Resolution

In October 2020, the Nobel Committee awarded the Nobel Prize in Chemistry to Jennifer Doudna and Emmanuelle Charpentier "for the development of a method for genome editing." The prize recognized their 2012 discovery of the CRISPR-Cas9 genetic scissors.

Feng Zhang was not included. The Nobel Prize can be awarded to a maximum of three individuals, and the committee chose to recognize the scientists who first characterized the CRISPR-Cas9 system as a programmable gene-editing tool. Zhang's contribution — demonstrating that the system worked in eukaryotic cells — was acknowledged as significant by the scientific community, but the Nobel Committee focused on the foundational discovery.

The Nobel decision did not resolve the patent dispute, nor was it intended to. Patent law and scientific credit operate under different frameworks. The patent system asks who made a specific, claimed invention and whether that invention was novel and non-obvious. The Nobel Prize asks who made the most important contribution to science. Zhang won the patent battle for eukaryotic applications; Doudna and Charpentier won the Nobel Prize for the underlying discovery. Both outcomes can be simultaneously correct under their respective systems.

The Nobel also did not include other scientists who made important early contributions to CRISPR biology, such as Francisco Mojica, who first identified CRISPR sequences in archaea in the 1990s, or Virginijus Siksnys, who independently demonstrated CRISPR-Cas9 DNA cleavage around the same time as Doudna and Charpentier. The history of CRISPR, like most major scientific discoveries, involved contributions from many researchers across multiple institutions and countries.

What the Patent Battle Means for the Future

For Patients

The fragmented patent landscape has, so far, not prevented CRISPR therapies from reaching patients. Casgevy was approved in 2023, and multiple other CRISPR-based therapies are advancing through clinical trials for conditions including cancer, hereditary blindness, high cholesterol, HIV, and rare genetic diseases. The patent holders have, to date, been willing to license their technology for therapeutic development, though the terms of these licenses are often confidential.

However, the cost of navigating the patent thicket adds to the already staggering expense of gene therapy development. Whether this ultimately affects patient access and drug pricing remains an open question. Some patient advocates have argued that the broad patenting of fundamental biotechnology tools could slow the development of therapies for rare diseases, where the commercial market may be too small to justify the licensing fees.

For the Industry

The CRISPR patent battle established important precedents for the biotechnology industry. It demonstrated that improvements to a foundational technology — like making an in vitro system work in living cells — can be independently patentable, even if the foundational invention was made first by someone else. This has implications for other platform technologies in biotech, from RNA therapeutics to synthetic biology.

The battle also highlighted the importance of patent strategy. The Broad's decision to seek accelerated examination of Zhang's application proved to be a masterstroke of patent prosecution. UC Berkeley's failure to pursue expedited review of its earlier-filed application cost it dearly. In the world of patent law, filing first is only an advantage if you also prosecute effectively.

For Science

Perhaps the most troubling aspect of the CRISPR patent war is what it revealed about the relationship between scientific discovery and commercial ownership. CRISPR-Cas9 is a product of billions of years of bacterial evolution, discovered and characterized by publicly funded researchers at universities and academic institutions. The idea that a naturally occurring biological mechanism can be privately owned through patents strikes some as fundamentally problematic.

Others counter that patents do not cover the natural phenomenon itself, but rather the specific, human-designed applications of that phenomenon. Nobody "owns" CRISPR-Cas9 as it exists in bacteria. The patents cover the engineered tools and methods that humans created to harness the system for gene editing.

This philosophical tension is not unique to CRISPR, but the sheer importance of the technology — and the vast sums of money at stake — has made it particularly acute. As gene editing moves from laboratory curiosity to clinical reality, the question of who owns the tools of genetic medicine will continue to shape the field for decades to come.

A Timeline of Key Events

Year	Event
2012	Doudna and Charpentier publish CRISPR-Cas9 paper in Science; UC Berkeley files patent application
2012	Feng Zhang files patent application for CRISPR in eukaryotic cells (December)
2013	Zhang publishes eukaryotic CRISPR paper in Science; Editas Medicine and CRISPR Therapeutics founded
2014	Broad Institute granted first CRISPR patent (U.S. Patent 8,697,359); Intellia Therapeutics founded
2015	UC Berkeley petitions USPTO for patent interference
2016	David Liu publishes first base editing paper
2017	PTAB rules no interference-in-fact; Broad's patents stand; Beam Therapeutics founded
2018	Federal Circuit affirms PTAB decision; EPO revokes Broad's European CRISPR patent
2019	David Liu publishes prime editing paper; Prime Medicine founded
2020	Nobel Prize in Chemistry awarded to Doudna and Charpentier
2022	PTAB again rules in Broad's favor under first-to-file analysis
2023	Federal Circuit affirms 2022 PTAB decision; Casgevy approved as first CRISPR therapy

Conclusion

The CRISPR patent battle is more than a legal curiosity. It is a case study in how the patent system handles transformative scientific discoveries, how academic institutions compete for commercial rights, and how intellectual property shapes the development of an entire industry. The Broad Institute won the fight for eukaryotic CRISPR patents in the United States, while UC Berkeley and Charpentier secured stronger positions in Europe and in foundational claims. The three major CRISPR companies — Editas, Intellia, and CRISPR Therapeutics — each built their businesses on the patent estate of their scientific founders, and the broader industry assembled complex webs of licenses to bring gene-editing therapies to patients.

As CRISPR technology continues to evolve — with base editing, prime editing, and newer approaches expanding the toolkit — the patent landscape will grow more complex, not less. The next generation of patent battles is already underway, with new claims being filed on CRISPR delivery systems, next-generation Cas proteins, epigenetic editing, and RNA editing technologies.

The fundamental question posed by the CRISPR patent war — who owns the tools to rewrite the code of life — does not have a simple answer. But the way society answers it will determine who benefits from the gene-editing revolution, how quickly new therapies reach patients, and whether the promise of CRISPR is realized broadly or narrowly. The stakes could not be higher.

Sources and Further Reading

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816-821.
Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., & Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819-823.
Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., Norville, J.E., & Church, G.M. (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121), 823-826.
Komor, A.C., Kim, Y.B., Packer, M.S., Zuris, J.A., & Liu, D.R. (2016). Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 533(7603), 420-424.
Anzalone, A.V., Randolph, P.B., Davis, J.R., Sousa, A.A., Koblan, L.W., Levy, J.M., Chen, P.J., Wilson, C., Newby, G.A., Raguram, A., & Liu, D.R. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature, 576(7785), 149-157.
United States Patent and Trademark Office, Patent Trial and Appeal Board. The Broad Institute, Inc. v. The Regents of the University of California. Interference No. 106,048 (2017).
The Regents of the University of California v. The Broad Institute, Inc., No. 2017-1907 (Fed. Cir. 2018).
United States Patent and Trademark Office, Patent Trial and Appeal Board. The Regents of the University of California v. The Broad Institute, Inc., Interference No. 106,115 (2022).
European Patent Office, Technical Board of Appeal. Decision on EP 2771468 (2020).
The Nobel Prize in Chemistry 2020. NobelPrize.org. Nobel Prize Outreach AB. Retrieved from https://www.nobelprize.org/prizes/chemistry/2020/summary/
Sherkow, J.S. (2017). Patent protection for CRISPR: An ELSI review. Journal of Law and the Biosciences, 4(3), 565-576.
Contreras, J.L., & Sherkow, J.S. (2017). CRISPR, surrogate licensing, and scientific discovery. Science, 355(6326), 698-700.