CRISPR in Rare Disease Treatment

A Patent Landscape Overview | 2020 - 2025

A newborn baby, jaundiced and fragile, cradled in the arms of researchers who had just rewritten a single letter in his DNA. Within weeks of receiving a personalized CRISPR-based therapy, his liver began to function. The treatment had worked.


Known publicly as Baby KJ, this child was born with a severe metabolic disorder caused by one misspelled nucleotide out of three billion. His story, part medical miracle, part legal battleground captures the extraordinary tension at the heart of gene-editing medicine.

While researchers were celebrating in the lab, a different kind of battle was unfolding in courtrooms and patent offices. That battle would ultimately determine whether cures like Baby KJ's could ever reach the millions of patients who need them most.

300Mpeople living with rare diseases worldwide
95%of rare diseases have no approved treatment
2023CASGEVY - first approved CRISPR medicine

1. What Is CRISPR?

CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. It was not invented, it was discovered. In 1987, Japanese microbiologist Yoshizumi Ishino first observed mysterious repetitive sequences in bacterial DNA. Scientists confirmed only in 2007 that these sequences formed an adaptive immune system that bacteria had evolved to remember and destroy previously encountered viruses.

The transformative leap came in 2012, when Jennifer Doudna at UC Berkeley and Emmanuelle Charpentier published a landmark paper in Science. They demonstrated that the CRISPR-Cas9 system could be reprogrammed using a synthetic guide RNA to cut any DNA sequence, essentially converting a bacterial immune system into universal molecular scissors capable of editing the genome of any living organism.

Core Components

ComponentRoleMechanism
Guide RNA (gRNA)Targeting mechanismShort synthetic RNA matches a specific genome sequence; binds its complementary DNA like a key finding its lock, directing Cas9 to the correct location
Cas9 ProteinMolecular scissorsMakes a precise double-strand break at the target site; cell's natural repair machinery then either knocks out or corrects the gene
DNA Repair TemplateCorrection blueprintWhen correction rather than deletion is needed, this template instructs the cell's repair mechanism to copy the correct sequence as used in Baby KJ's treatment
Table 1: CRISPR Core Components and Their Roles in Gene Editing

How CRISPR Works: Five Stages

1

Design

Program guide RNA to match the target DNA sequence

2

Delivery

Package CRISPR components into viral vectors, lipid nanoparticles, or via electroporation

3

Bind

Guide RNA scans genome and binds to its complementary sequence

4

Cut

Cas9 makes a controlled double-strand break at the target location

5

Repair

Cell's own machinery disables the gene or incorporates the correction template

Figure 1: The CRISPR-Cas9 Editing Process — Five Stages from Design to Repair

Next-Generation CRISPR Variants

VariantKey InnovationPrimary Application
Base EditingChanges a single DNA letter without cutting, reducing risk of unintended editsPoint mutations in rare diseases
Prime EditingWorks like search-and-replace, covering all 12-point mutations and small indelsPrecision rare disease correction
CRISPR-Cas12Enhanced DNA specificity and activates collateral cleavageDiagnostics and gene editing
CRISPR-Cas13Targets RNA rather than DNA — no permanent genome alterationViral diseases and gene expression
CRISPRa / CRISPRiActivates or silences genes using deactivated Cas9 — no cuttingGene regulation and functional studies
Table 2: Next-Generation CRISPR Variants and Their Primary Applications

2. Why the World Needs CRISPR

Around 80% of rare diseases are genetic in origin caused by mutations in single genes. For decades, medicine could only treat downstream consequences, manage symptoms or replace deficient proteins. The root genetic cause remained untouchable. CRISPR changes this at platform level.

Unlike previous therapeutic approaches, CRISPR operates as a platform. The same core machinery can be redirected to any gene in any patient simply by changing the guide RNA sequence. A company that demonstrates the safety and efficacy of CRISPR delivery for one liver-based rare disease has, in principle, cleared the path for dozens more — using largely the same platform, delivery vehicle, and manufacturing infrastructure.

The Platform Advantage Aurora Therapeutics, co-founded by Jennifer Doudna, is explicitly building around this model — using artificial intelligence to design patient-specific guide RNAs for inborn errors of metabolism. The platform economics of CRISPR represent a structural shift in the economics of rare disease drug development.

3. CRISPR Patents: The Battle for Ownership

Intellectual property rights over foundational CRISPR technology represent one of the most commercially consequential patent disputes in biotechnology history. At stake are licensing fees and royalty streams potentially worth billions of dollars, control over which companies can develop CRISPR therapeutics and on what terms, and the degree to which patent monopolies translate into treatment prices beyond reach for most patients.

UC Berkeley — CVC Group

Jennifer Doudna, Emmanuelle Charpentier

Filed: May 2012 — cell-free biochemical setting
Claim: In vitro CRISPR-Cas9 programmed with synthetic gRNA
Argument: 2012 work inherently disclosed eukaryotic application
US licensee: Caribou Biosciences → Intellia Therapeutics
EU position: Stronger position after Broad EPO revocation
Charpentier: Independently licensed to CRISPR Therapeutics AG

Broad Institute — MIT & Harvard

Feng Zhang and colleagues

Filed: December 2012 — paid for accelerated processing
Claim: First to demonstrate CRISPR in living eukaryotic cells
Argument: Eukaryotic function required inventive steps beyond in vitro
US position: 31 granted US CRISPR patents as of 2025
EU position: Primary European patent revoked 2020
US licensee: Editas Medicine (primary therapeutic licensee)

Patent Milestone Timeline

2012
Both Groups File

Both UC Berkeley and Broad Institute file US patent applications within months of each other. The race begins.

2014
First US Patent Granted

Broad Institute receives the first US CRISPR patent through expedited processing, establishing an early advantage.

2017
PTAB Rules for Broad

USPTO PTAB rules Broad patents valid and non-overlapping with UC Berkeley claims. Broad retains US patents.

2020
EPO Revokes Broad Patent

European Patent Office revokes Broad's first European CRISPR patent on a procedural technicality. Editas stock falls 17% in one day. UC Berkeley gains European advantage.

2022
PTAB Reaffirms Broad

PTAB reaffirms Broad's priority for eukaryotic cell editing following interference proceedings. Broad retains US position.

2025
Appeals Court - Partial UC Win

US Court of Appeals finds PTAB legally erred in its conception analysis; case remanded for reconsideration. Dispute continues.

Figure 2: Key Patent Milestones in the UC Berkeley vs. Broad Institute Dispute (2012 – 2025)
Current Status (2025) The dispute remains unresolved after more than a decade. The US Court of Appeals found that the Patent Trial and Appeal Board legally erred in its conception analysis in 2025, remanding the case for reconsideration. This represents a partial procedural win for UC Berkeley, but the ultimate question of priority in eukaryotic editing remains to be finally determined. Meanwhile, both sides have built commercial licensing ecosystems that continue to operate during the litigation.

4. Patent Landscape: Filing Trends and Global Distribution

Gene editing and cell therapy patent applications grew steadily from 593 in 2020 to a peak of 928 in 2023, before declining to 897 in 2024 and 759 in 2025. The peak filing momentum concentrated between 2022 and 2024 reflects accelerating clinical validation and commercial investment. The moderation from 2024 reflects consolidation of foundational positions rather than reduced innovation.

YearPatent Applications FiledCount
2020
593
2021
680
2022
812
2023
928
2024
897
2025
759
Figure 3: Annual CRISPR & Gene Editing Patent Applications Filed (2020–2025)

Top Assignees - Institutional Dominance

MIT (175, 17%), University of California (172, 17%), and the Broad Institute (170, 17%) dominate with near-equal shares, together accounting for over half of all patent activity among the top 10. Regeneron Pharmaceuticals is the only purely commercial pharmaceutical company among the top 10 assignees, reflecting the field's deep academic roots.

AssigneeRelative ShareCountRank
MIT
175#1
University of California
172#2
Broad Institute Inc
170#3
University of Pennsylvania
98#4
Harvard University
88#5
University of Texas
73#6
CRISPR Therapeutics AG
69#7
Shanghai University
68#8
Stanford University
57#9
Regeneron Pharmaceuticals
50#10
Figure 4: Top 10 CRISPR Assignees by Patent Count (2020 - 2025) - Percentage share shown in brackets; bar length reflects relative count

Geographic Distribution - US and China Lead

The United States dominates with 3,091 priority filings, followed by China at 1,394 together accounting for the overwhelming majority of first filings globally. The European Patent Office (228) and South Korea (121) represent the next significant contributors, while India, Singapore, Japan, and Australia contribute smaller but meaningful volumes.

JurisdictionRelative ShareCountRank
United States (US)
3,091#1
China (CN)
1,394#2
EPO (EP)
228#3
South Korea (KR)
121#4
United Kingdom (UK)
89#5
India (IN)
34#6
Singapore (SG)
29#7
Japan (JP)
23#8
Australia (AU)
19#9
Figure 5: Top Jurisdictions by CRISPR Priority Filings (2020–2025)

5. CPC Classification Analysis

C12N2310/20 (CRISPR systems) dominates with 2,055 patents confirming CRISPR-based editing as the primary technology focus followed by C12N9/22 (ribonucleases/Cas proteins) at 1,715 and A61P35/00 (antineoplastic agents) at 1,526, reflecting oncology as the leading therapeutic indication. C12N15/113 (guide RNA technologies) at 1,469 underscores the centrality of non-coding nucleic acids to the platform.

CPC CodeDescriptionTotal Patents
C12N2310/20CRISPR Systems2,055
C12N9/22Ribonucleases / Cas Proteins1,715
A61P35/00Antineoplastic Agents1,526
C12N15/113Non-coding Nucleic Acids / Guide RNA / Gene Silencing1,469
C12N15/86Viral Vectors996
C12N2510/00Genetically Modified Cells950
C12N15/907Gene Modification in Mammalian Cells823
A61K40/11Nucleic Acid-Based Therapeutics752
C12N15/11DNA or RNA Fragments / Modified Non-coding Nucleic Acids680
A61K40/31Therapeutic Nucleic Acid Compositions660
Table 3: Top 10 CPC Classification Codes in CRISPR & Gene Editing Patents (2020 - 2025)
Classification Insight The dominance of C12N2310/20 and C12N9/22 reflects the platform nature of CRISPR IP the core tool (the CRISPR system and its Cas proteins) is the most heavily patented layer. Oncology's prominence in A61P35/00 confirms that cancer treatment remains the primary commercial application, even as rare disease filings grow rapidly.

6. The First Approved CRISPR Drug - CASGEVY

In December 2023, CASGEVY (exagamglogene autotemcel) became the world's first approved CRISPR-based medicine. It received simultaneous regulatory authorization from the UK MHRA, the US FDA, and the European EMA for the treatment of sickle cell disease and transfusion-dependent beta-thalassaemia in patients aged 12 and older.

CASGEVY uses CRISPR-Cas9 to edit a patient's own haematopoietic stem cells outside the body, reactivating fetal haemoglobin production to compensate for the defective adult haemoglobin that causes both diseases. Clinical trial data through 2024 showed approximately 90% of treated patients remaining free from severe vaso-occlusive crises for more than 12 consecutive months after infusion, with a mean VOC-free duration of 29.3 months.

First Approval Significance CASGEVY is not merely a drug, it is proof of concept for the entire CRISPR therapeutic platform. Its approval validated that ex vivo CRISPR editing can produce durable, clinically meaningful responses in humans with serious genetic disease. The next frontier in vivo CRISPR delivery directly into the body — is now in Phase III trials.

7. The Clinical Pipeline

Beyond CASGEVY, the CRISPR therapeutic pipeline is advancing rapidly. The most advanced program is Intellia Therapeutics' NTLA-2001 for transthyretin amyloid cardiomyopathy (hATTR), which completed Phase III enrolment with a filing planned for the second half of 2026. If approved, it would be the first in vivo CRISPR therapy administered directly into the body rather than requiring cells to be edited externally.

DiseaseStageKey PlayerApproach
Sickle cell / beta-thalassemiaApproved (2023)Vertex / CRISPR TherapeuticsEx vivo stem cell editing — reactivates fetal haemoglobin
hATTR (transthyretin amyloidosis)Phase III / filing 2026Intellia TherapeuticsIn vivo liver editing — knocks out the TTR gene
Hereditary angioedema (HAE)Phase I/IIIntellia TherapeuticsIn vivo editing of the KLKB1 gene in the liver
Leber congenital amaurosis (LCA10)Phase I/IIEditas MedicineIn vivo retinal editing — targets the CEP290 gene
Duchenne muscular dystrophyClinical / non-profitCure Rare DiseaseExon skipping via CRISPR
Inborn errors of metabolism (PKU)Preclinical / earlyAurora TherapeuticsAI-designed personalised guide RNAs — platform approach
HIVPhase IMultiple groupsExcision of integrated viral DNA from the host genome
Table 4: CRISPR Clinical Pipeline by Disease Area, Stage, and Approach (as of 2026)

8. Conclusion

CRISPR-Cas9 has come a long way in a remarkably short time — from a bacterial immune mechanism observed in a laboratory to a medicine that can rewrite a child's DNA and give them a chance at a normal life. The approval of CASGEVY in December 2023 was not just a scientific achievement; it was proof that gene editing can move from discovery to patient bedside.

The patent data tells the story of how much the world has invested in this technology. Filings grew from 593 in 2020 to a peak of 928 in 2023. The United States and China together account for the overwhelming majority of foundational filings. UC Berkeley, MIT, the Broad Institute, and Harvard together account for nearly half of all CRISPR patents underlying the central role that academic research has played in building this field.

Yet the long-running patent dispute between UC Berkeley and the Broad Institute, still unresolved after more than a decade, remains a reminder that groundbreaking science inevitably raises difficult questions about ownership, access, and who ultimately benefits. CPC data confirms that cancer treatment and CAR-T immunotherapy are the most active patent areas, while nucleic acid delivery, lipid nanoparticles, and precision editing tools like base editing signal where the next wave of innovation is heading.

Strategic Implications for IP Professionals The CRISPR landscape presents a unique dual challenge: the foundational dispute remains live, but a rich secondary ecosystem of application-specific, delivery-specific, and variant-specific patents has developed around it. Freedom-to-operate analysis in this space must account for both the core Cas protein and guide RNA patents and the growing body of downstream filings covering specific diseases, delivery mechanisms, and manufacturing processes. Legal Advantage LLC provides patent landscape searches, FTO analyses, and IP strategy support across the gene editing and rare disease sectors.

© 2026 Legal Advantage LLC | For informational use only CRISPR & Rare Disease Patent Landscape 2020 - 2025