Sequenom Inc and Anr. Vs Controller of Patents

Case Title: Sequenom Inc and Anr. Vs Controller of Patents

Order Date: 9th October 2025

Case Number: C.A.COMM.IPD-PAT 132022 and C.A.COMM.IPD-PAT 4482022

Neutral Citation: 2025:DHC:132022

Court: High Court of Delhi at New Delhi

Hon'ble Judge: Justice Prathiba M. Singh

Fact:

Sequenom Inc., a company registered in the United States, along with its affiliate Sequenom Center for Molecular Medicine, filed two Indian patent applications related to non-invasive prenatal testing (NIPT) methods. These methods involve analyzing fetal nucleic acids present in maternal blood samples to detect fetal abnormalities such as aneuploidy (chromosomal abnormalities), sex determination, and other genetic traits without invasive procedures like amniocentesis. The applications claim methods of methylation-based enrichment of fetal DNA to isolate and analyze specific genetic markers through DNA sequencing and amplification techniques. The applications originated as early as 2011 and 2012 with U.S. priority claims and underwent multiple rounds of claim amendments during prosecution to address objections.

Procedural Detail:

The Indian Patent Office issued First Examination Reports raising objections on multiple grounds, including lack of inventive step, and specifically non-patentability under Sections 3(b), 3(d), 3(i), and 3(j) of the Patents Act, 1970. The rejections were upheld in orders dated 12th December 2019 and 20th January 2020, primarily on the basis that the claimed inventions fall under the exclusion of patentability under Section 3(i), which excludes diagnostic methods from patent protection. The applicants appealed these refusals under Section 117A of the Patents Act to the Delhi High Court. Given the common issue of interpretation of Section 3(i), these appeals were heard in a batch along with other landmark cases including EMD Millipore Corporation. The proceedings included extensive submissions, including those from an appointed Amicus Curiae, and the judgment was reserved on 21st December 2024 and pronounced on 9th October 2025.

Dispute:

The central dispute revolved around the scope and application of Section 3(i) of the Indian Patents Act, 1970, relating to the exclusion from patentability of diagnostic methods. The appellants contended that their invention relates to a non-invasive screening test (NIPT) rather than a diagnostic method practiced on the human body and therefore should not fall under Section 3(i). They emphasized that the methods merely provide preliminary data and risk assessments without constituting definitive medical diagnosis or treatment. On the other hand, the Patent Office represented by the CGSC argued that the test claims to detect fetal abnormalities with high accuracy and results in clinical decisions, thus qualifying as diagnostic methods excluded from patentability. They contended that Section 3(i) does not distinguish between in vivo and in vitro methods and captures any method intended for diagnosis or treatment performed on humans or animals. The scope of exclusion includes methods practiced in laboratories on human samples having diagnostic purposes. The issue of inventive step was also raised but not primarily decided.

Detailed Reasoning:

The court undertook a detailed examination of the language of Section 3(i), which excludes from patentability "any process for the medicinal, surgical, curative, prophylactic, diagnostic, therapeutic or other treatment of human beings or any process for a similar treatment of animals." It reviewed precedents and legislative history including the amendments introduced post-TRIPS, the underlying public policy to safeguard freedom of medical practitioners from patent restrictions, and the need to balance this against incentivizing innovation.

Comparative analysis with foreign laws was undertaken with detailed references to Section 4A of the UK Patents Act 1977 and Article 53(c) of the European Patent Convention (EPC) 2000, both of which exclude methods of treatment or diagnosis practiced on the human or animal body but expressly allow patents for substances or compositions for use in such methods. The Enlarged Board of Appeal decisions of the EPO in Cases G 000104 and G 000107 were a key focus, elucidating that diagnostic methods are multi-step processes involving collecting and comparing data, followed by identifying deviations and making deductive medical evaluations. Such multi-step diagnostic methods practiced on the human or animal body require professional medical judgment and carry health risks, which justifies their exclusion.

The court clarified that the exclusions apply narrowly to processes that are core medical activities involving intellectual diagnostic decision-making performed on living bodies. Ancillary or supporting processes, especially in vitro laboratory techniques without final diagnosis or treatment steps, fall outside the exclusion and qualify for patent protection. Further, diagnostic tools, instruments, machines, and products remain patentable if they fulfill patentability criteria.

The court delved into the specifications and claims of the patent applications, noting that the inventions relate to in vitro non-invasive procedures analyzing fetal DNA from maternal blood without direct interaction with the body and without final diagnostic conclusions. The inventions primarily relate to identifying probabilities and risks, distinguishing them from definitive diagnostic processes. The court highlighted the distinction between screening tests and diagnostic tests, based on medical literature and case law, including the recent decision of the Madras High Court in Chinese University of Hong Kong v. Assistant Controller of Patents. Screening tests identify a need for further confirmatory diagnosis, whereas diagnostic tests confirm presence or absence of disease requiring clinical decision and possible treatment.

The court rejected the patent office's argument that all screening tests fall under Section 3(i) if they relate to diagnosis in a broad sense, stating that statutory interpretation demands a narrower reading. It was found that in vitro laboratory tests designed merely for data gathering or analysis supporting subsequent diagnosis by medical professionals do not constitute excluded diagnostic methods.

The court also considered the legislative history, observing that Section 3(i) was introduced with intent to harmonize Indian law with global standards while preserving medical practitioners' autonomy. It pointed out that unlike EPC and UK law that specify that the exclusion applies to diagnostic methods "practiced on the human or animal body," Indian law’s text does not contain this phrase, making in vitro diagnostic methods potentially subject to exclusion. However, the court adopted a purposive interpretation to avoid stifling innovation in biotechnological and medical research fields and not unduly broadening exclusions.

On the amendments and claims, the court noted the applications had undergone significant prosecution and claims restriction to comply with patentability standards. It emphasized that inventions providing novel technical methods of analyzing biological samples while not constituting direct diagnostic processes are patentable.

Decision:

The court allowed the appeals primarily holding that the claimed inventions in both patent applications do not fall under the exclusion of Section 3(i) of the Patents Act. The inventions constitute non-invasive prenatal screening tests, involving in vitro analysis outside the human body, and do not amount to diagnostic methods involving direct diagnosis or treatment by medical professionals. Consequently, the inventions are patentable subject matter. The court directed the patent office to grant the patents after completing formalities. The court clarified that patent exclusions should be narrowly construed to protect medical practice autonomy without hindering technological innovation. The judgments provide authoritative guidance on interpreting Section 3(i), balancing between innovation incentives and public health policy.

Legal Provisions Discussed:

Section 3(i) of the Patents Act, 1970 – Exclusion of medicinal, surgical, diagnostic, therapeutic processes

Sections 21(j) and 21(ja) – Novelty and Inventive Step

Section 59 – Amendments to Patent Applications

Section 117A – Appeals to High Court against Controller decisions

Article 27.3 of TRIPS Agreement – Flexibility to exclude certain inventions from patentability

Section 4A of UK Patents Act, 1977 – Methods of treatment or diagnosis exclusion

Article 53(c) EPC 2000 – Exceptions to patentability for diagnostic methods practiced on the human or animal body

Enlarged Board of Appeal Decisions G 000104 and G 000107 – Interpretation of diagnostic and surgical methods

Disclaimer: The information shared here is intended to serve the public interest by offering insights and perspectives. However, readers are advised to exercise their own discretion when interpreting and applying this information. The content herein is subjective and may contain errors in perception, interpretation, and presentation.

Written By: Advocate Ajay Amitabh Suman, IP Adjutor [Patent and Trademark Attorney], High Court of Delhi

Suggested Titles for Legal Research Paper:

1. "Interpreting Section 3(i) of the Indian Patents Act: A Comprehensive Analysis of Sequenom Inc. Case"

2. "Diagnostic Methods and Patent Exclusions: Lessons from the Delhi High Court on Non-Invasive Prenatal Testing"

3. "Balancing Innovation and Medical Practice Autonomy under Indian Patent Law: The Sequenom Decision"

4. "Narrow Construction of Patent Exclusions for Diagnostic Processes: A Judicial Perspective from Delhi"

5. "Scope of Patentability in Medical Biotechnologies: Analytical Review of Sequenom vs Controller"

Natera Inc and Anr. Vs Assistant Controller of Patents and Designs

Case Title: Natera Inc and Anr. Vs Assistant Controller of Patents and Designs

Order Date: 9th October 2025

Case Number: C.A.COMM.IPD-PAT 162023

Neutral Citation: 2025:DHC:162023

Court: High Court of Delhi at New Delhi

Hon'ble Judge: Justice Prathiba M. Singh

Fact:

Natera Inc, a California-based company specializing in clinical genetics including cell-free DNA testing technology, along with UCL Business Ltd., filed an Indian patent application on 5th September 2019 titled "Methods for Lung Cancer Detection." The invention concerns a laboratory method to detect and monitor genetic mutations associated with lung cancer, specifically lung squamous cell carcinoma (a type of non-small cell lung cancer), by amplifying and sequencing tumor-derived DNA from blood samples. The method involves performing multiplex PCR amplification on nucleic acids isolated from blood or its fractions, followed by the analysis of single nucleotide variants (SNVs) associated with lung cancer. The technology is characterized by high sensitivity and the ability to detect mutations relevant for diagnosis, staging, and monitoring. The appellants claimed priority from a U.S. application dated 15th April 2016 and filed multiple amended claims through prosecution to refine the scope.

Procedural Details:

The Indian Patent Office issued a First Examination Report (FER) dated 31st August 2021 raising objections including lack of novelty and inventive step under Sections 21(j) and 21(ja), non-patentability under Sections 3(d) (improvement) and 3(i) (diagnostic exclusion), and non-compliance with formalities under Sections 104(c) and related procedural rules. The appellants responded with amended claims, reduced from 54 to 15 and finally to 8 claims. A hearing was conducted on 9th January 2023, but the application was refused by the Assistant Controller of Patents via order dated 20th March 2023 primarily on the ground that Claims 1 to 4 were excluded from patentability under Section 3(i) of the Patents Act, as the method was diagnostic for lung cancer detection. Claims 5 to 8 were held impermissible by Section 59 because they were considered beyond the scope of the original specification. The appellants challenged this refusal before the Delhi High Court under Section 117A of the Patents Act.

Dispute:

At the core lies the interpretation of Section 3(i), which excludes from patentability methods for diagnosis practiced on humans or animals. The appellant argued that the invention was a laboratory, in vitro process for detecting the presence of specific genetic variants associated with lung squamous cell carcinoma and did not itself constitute a diagnostic method practiced on the human body. They contended the claims were related to research, predisposition testing, and monitoring, not treatment or diagnosis requiring professional judgment. The respondent (Patent Office) insisted that since the complete specification described the method as improving detection, diagnosis, staging, screening, and treatment of lung cancer, the claims fell squarely within the non-patentable subject matter under Section 3(i). Further, the respondent maintained claims 5-8 were impermissible amendments beyond the original scope, violating Section 59.

Detailed Reasoning:

The Court carefully examined the language of Section 3(i) of the Patents Act, 1970, which excludes from patentability "any process for the medicinal, surgical, curative, prophylactic, diagnostic, therapeutic or other treatment of human beings or any process for a similar treatment of animals..." The Court reviewed similar provisions in foreign jurisdictions, notably the UK Patents Act 1977 and Article 53(c) of the European Patent Convention (EPC), which excludes methods of diagnosis practiced on the human or animal body but allows patents on substances or compositions used in those methods.

The Court referenced the landmark Enlarged Board of Appeal decisions of the European Patent Office defining diagnostic methods as multi-step processes practiced on the body, including: collecting data, comparing this with standard values, identifying deviations, and reaching a diagnostic decision. The exclusion applies narrowly to core medical activities that require professional skill and pose health risks, ensuring medical practitioners can diagnose and treat without infringing patents.

The subject matter of the invention was found to be an in vitro laboratory technique that amplifies and sequences nucleic acids from blood samples without direct diagnostic acts on the human body. The Court observed that the method provides genetic data related to tumor mutations but does not itself perform diagnosis, treatment, or clinical decision-making. The Court also noted that distinguishing between in vivo (on the body) and in vitro (outside the body) diagnostic methods is key: Section 3(i) does not distinguish them explicitly but the context and judicial interpretation limit exclusion to processes practiced on living bodies.

The Court further examined the detailed claims and specification, finding them aimed at detecting the presence of lung squamous cell carcinoma-associated single nucleotide variants in blood samples. The invention facilitates early detection, monitoring, and research but does not make a medical diagnosis or prescribe treatment. Hence, the Court held the process qualifies for patentability under Indian law as it falls outside the exclusion of Section 3(i).

On the question of claims 5 to 8, the Court considered Section 59 of the Act restricting amendment beyond disclaimers, corrections, or explanations. The appellants argued these claims were supported by earlier PCT claims and thus should be allowable without extending original scope. The Court referenced precedents including Axcess Limited v Controller of Patents (2024) and Allergan Inc. v Controller of Patents (2023) which endorse allowance of amendments within the scope of the original application. The Court found that these claims were within the ambit of the original specification and supported by original filings, therefore rejecting the Patent Office's objection under Section 59.

The Court also reviewed the inventive step objections but clarified that these were not examined in the impugned order and were to be decided separately.

In conclusion, the Court adopted a balanced interpretation of Section 3(i), ensuring the protection of genuine medical diagnostic processes practiced on living beings from patent monopolies to safeguard public health, while protecting innovative technical methods and tools used in diagnostics outside the human body.

Decision:

The appeal was allowed. The impugned order refusing the patent application was set aside. The Court held that Claims 1 to 4 do not fall under the non-patentable exclusions of Section 3(i) as the invention constitutes an in vitro laboratory method and not a diagnostic method practiced on the human body. Claims 5 to 8 were also held to be permissible amendments under Section 59 of the Act as they did not extend beyond the original scope. The Patent Office was directed to grant the patent after completion of formalities. The Court emphasized that the ruling strikes a balance between public interest and incentive for innovation and clarified interpretation principles for Section 3(i) exclusions to aid consistent patent examination in future.

Relevant Legal Provisions Discussed:

Section 3(i) of the Patents Act 1970 (Exclusion of diagnostic, therapeutic, surgical processes)

Section 21(j) and 21(ja) (Novelty and Inventive step)

Section 59 of the Patents Act 1970 (Amendments to patent applications)

Section 117A (Appeals from Controller's decisions)

Article 53(c), European Patent Convention (EPC 2000)

Section 4A, UK Patents Act 1977

Enlarged Board of Appeal decisions G 000104 and G 000107 of the European Patent Office

Relevant Indian case precedents: Axcess Limited v Controller, Allergan Inc. v Controller, Novartis AG v Union of India (2013)

Disclaimer: The information shared here is intended to serve the public interest by offering insights and perspectives. However, readers are advised to exercise their own discretion when interpreting and applying this information. The content herein is subjective and may contain errors in perception, interpretation, and presentation.

Written By: Advocate Ajay Amitabh Suman, IP Adjutor [Patent and Trademark Attorney], High Court of Delhi

Suggested Titles for Legal Research Paper:

"Interpretation of Section 3(i) of the Indian Patents Act: Diagnostic Methods and Patentability in Natera Case"

"Balancing Innovation and Public Health: Legal Analysis of Patent Exclusions for Diagnostic Processes"

"Patent Law and Diagnostic Inventions in India: Insights from Natera Inc. v. Assistant Controller"

"Scope and Limits of Non-Patentable Subject Matter: Detailed Study of Diagnostic Method Exclusions"

"Amendments and Patentability: Legal Challenges in Diagnostic Method Patents under Indian Law"

EMD Millipore Corporation Vs Assistant Controller of Patents and Designs

Case Title: EMD Millipore Corporation Vs Assistant Controller of Patents and Designs

Order Date: 9th October 2025

Case Number: C.A.COMM.IPD-PAT 72021

Neutral Citation: 2025:DHC:72021

Court: High Court of Delhi at New Delhi

Hon'ble Judge: Justice Prathiba M. Singh

Fact:

The appellant, EMD Millipore Corporation, a U.S.-based corporation, filed a patent application in India on 3rd April 2012 titled "Devices and Methods for Infrared (IR) Based Quantitation of Biomolecules." The invention concerns a method for the quantitative analysis of biomolecules in various types of samples including human plasma, food, cosmetics, and environmental samples using infrared spectroscopy. The appellant claimed priority from a U.S. patent application and amended the claims multiple times during prosecution, finally seeking patent protection for a technical innovation. The key object of the invention was to improve efficiency in IR spectroscopic analysis by reducing repeated calibration and enabling reuse of calibration data. Despite amendments to overcome objections, the Assistant Controller of Patents and Designs refused the application by order dated 18th February 2021 on the ground that the claims fall under the non-patentable subject matter exclusion of Section 3(i) of the Indian Patents Act, 1970, which excludes diagnostic processes from patentability.

Procedural Detail:

The appellant challenged the refusal under Section 117A of the Patents Act before the High Court of Delhi. The appeal proceeded through multiple hearings from 2021 onwards. The court sought additional reports from the patent office concerning the novelty and inventive step of the claims. A significant issue considered was the correct interpretation and scope of the exclusion clause under Section 3(i) of the Act, which bars patentability of diagnostic methods. The court appointed an Amicus Curiae to assist with submissions on complexity related to the interpretation of Section 3(i). The matter involved detailed examination of foreign jurisprudence, including decisions from the European Patent Office (EPO) on exclusions for diagnostic methods. Judgment was reserved in December 2024 and pronounced in October 2025.

Dispute:

The fundamental dispute centered on whether the subject invention qualifies as a diagnostic process excluded from patentability under Section 3(i) of the Patents Act or whether it qualifies as a patentable technical method. The appellant contended that the invention was an innovative technical process improving IR spectroscopic quantitation applicable across industries and should not be barred. The respondent, represented by the Assistant Controller, argued that the invention was a diagnostic method within the scope of Section 3(i) and thus non-patentable, emphasizing that the exclusion applies broadly to diagnostic methods regardless of their in vivo or in vitro nature. Issues surrounding the legislative history of Section 3(i), international obligations under TRIPS, and Indian patent policy balances between innovation and public health were debated.

Detailed Reasoning:

The court undertook a comprehensive examination of the legal framework, including Indian patent law, legislative history, and international precedents. The court noted that Section 3(i) of the Patents Act excludes "any process for the medicinal, surgical, curative, prophylactic, diagnostic, therapeutic or other treatment of human beings or any process for a similar treatment of animals to render them free of disease or to increase their economic value or that of their products" from patentability. The appellate court analyzed the corresponding provisions in foreign jurisdictions like the UK's Patents Act 1977, Article 53(c) EPC 2000, and jurisprudence from the European Patent Office's Enlarged Board of Appeal (notably Case G 000104). The court emphasized that diagnostic methods excluded under these laws are typically multistep processes involving examination, data gathering, comparison, symptom detection, and clinical decision-making practiced directly on the human or animal body.

It was clarified that the exclusion's purpose was to free medical practitioners from patent constraints when applying core diagnostic procedures requiring professional judgment and bearing health risks. However, patentability is not barred for diagnostic tools, instruments, or technical processes that do not themselves constitute a diagnostic method practiced on the living body.

The court thoroughly examined the appellant's patent claims and the specification, observing that the invention was directed to an in vitro technical process using infrared spectroscopy for biomolecular quantitation on samples that could be biological fluids but also included broad categories like cosmetics, food, water, and fuels.

The court concluded the invention did not involve any step constituting diagnosis for curative purposes or clinical decision-making performed on or practiced on a human or animal body. The method improved the technical aspect of IR spectroscopic measurement rather than the intellectual exercise of diagnosis itself. Furthermore, the court noted the patent had been granted in jurisdictions including the United States and Europe, where comparable exclusions exist, supporting its patentability.

The role and intent of Section 3(i) were revisited in light of legislative history and international trade commitments under TRIPS. The court held that the section was intended to exclude medical procedures requiring practitioner skill and direct interaction with the patient, but not to bar patents on inventions involving technical methods or devices that facilitate analysis or diagnostics without constituting a disallowed diagnostic method.

The court also discussed the permissibility of claims amendments during appeals under Section 59 of the Act, confirming that amendments clarifying or narrowing claims within the original disclosure are allowed. The appellant's amendments were found to be within permissible limits and did not expand the scope of the invention.

Decision:

The appeal was allowed. The impugned order refusing the patent application was set aside, as the claimed invention does not fall within the exclusion of Section 3(i) of the Patents Act. The court directed the patent office to proceed with the grant of the patent to the appellant after completion of formalities. The court emphasized that the exclusion applies narrowly to core diagnostic processes practiced on the human or animal body and does not extend to technical innovations or in vitro processes. Hence, the appellant's method for IR-based quantitation of biomolecules qualifies for patent protection.

Relevant legal provisions considered and discussed include:

Section 3(i) of the Patents Act, 1970 (non-patentability of diagnostic methods)

Sections 21(j) and 21(ja) defining invention and inventive step

Section 59 concerning permissible amendments of patent applications

Order and submissions under Section 117A (appeal against Controller's decision)

TRIPS Agreement Article 27.3 (exclusions from patentability)

UK Patents Act 1977 Section 4A and EPC Article 53(c) on exclusions for treatment and diagnostic methods

The court relied heavily on the Enlarged Board of Appeal, EPO decision G 000104, setting out the multi-step definitional framework for diagnostic methods and the distinction between in vivo diagnostic processes and technical methods or tools.

In sum, the judgment clearly elucidates the boundary between non-patentable diagnostic processes and patentable technical innovations, guiding future patent prosecution in medical technology fields in India.

Disclaimer: The information shared here is intended to serve the public interest by offering insights and perspectives. However, readers are advised to exercise their own discretion when interpreting and applying this information. The content herein is subjective and may contain errors in perception, interpretation, and presentation.

Written By: Advocate Ajay Amitabh Suman, IP Adjutor [Patent and Trademark Attorney], High Court of Delhi

Suggested Titles for Legal Research Paper:

1. "Navigating Patentability in Diagnostics: A Study of EMD Millipore Corporation v. Assistant Controller of Patents"

2. "The Scope of Section 3(i) of the Indian Patents Act: Diagnostic Processes and Patent Eligibility"

3. "Balancing Innovation and Public Health: Diagnostic Methods and Patent Law in India"

4. "Interpretation of Non-Patentable Subject Matter in Indian Patent Law: Insights from the EMD Millipore Case"

5. "Section 3(i) of the Patents Act and Diagnostic Methods: A Judicial Perspective on Patent Exclusions"