The decision addresses a recurring deficiency in patent adjudication: the failure to deal with amended claims in a reasoned manner. Where the scope and character of an invention are defined through its claims, any omission to consider amendments that alter those claims renders the refusal susceptible to challenge. The judgment affirms that an order of refusal must engage with the claims as they stand at the time of decision, and not as they existed at an earlier stage of prosecution.
Factual Background
1. The Subject Application and the Technology
The subject patent application related to stem cell-derived pancreatic beta cells, referred to as SC-beta cells. The research addressed a longstanding problem in diabetes treatment: existing methods for generating insulin-producing cells from pluripotent stem cells produced cells that functioned abnormally and could not secrete appropriate insulin levels in response to glucose. The Harvard invention claimed a method of producing non-native pancreatic beta cells that exhibit functional characteristics closer to mature adult beta cells, including glucose-stimulated insulin secretion, expression of specific genes, and mono-hormonal properties.
The term ‘non-native’ was defined in the specification to mean cells that are markedly different in certain aspects from beta cells existing in nature, particularly in gene expression profiles, while still exhibiting similar functional behaviour. These cells are generated in vitro from stem cells through a multi-step laboratory protocol and do not naturally occur in the human body.
2. The Critical Amendment: Original vs Amended Claim 1
The amendment that the Controller failed to consider changed the fundamental character of the principal claim. The original Claim 1 was a composition claim, directed at a pharmaceutical formulation comprising the non-native pancreatic beta cell together with carriers, additives, and diluents. The amended Claim 1 removed the composition entirely and claimed only the non-native pancreatic beta cell itself.
This distinction was legally significant. The objections under Sections 3(e) and 10(4) and 10(5), which the Controller had raised in the context of a composition claim (requiring synergy data, disclosure of all components and their amounts), could not be applied in the same way to a claim directed at the cell itself. The amended claim required a wholly different analysis.
| Original Claim 1 (Composition Claim) | Amended Claim 1 (Cell Claim) |
| A composition comprising a non-native pancreatic beta cell, and one or more pharmaceutically acceptable carriers, additives, and/or diluents, wherein: (a) the non-native pancreatic beta cell comprises one or more crystalline insulin granules; (b) the non-native pancreatic beta cell expresses the following genes: INS, PDX1, NKX6-1, and ZNT8; (c) the non-native pancreatic beta cell exhibits an in vitro glucose stimulated insulin secretion (GSIS) response to a first glucose challenge; and (d) the non-native pancreatic beta cell does not express one or both of somatostatin and glucagon; and wherein said composition is in the form of an in vitro cell cluster. | A non-native pancreatic beta cell, wherein: (a) the non-native pancreatic beta cell comprises one or more crystalline insulin granules; (b) the non-native pancreatic beta cell expresses the following genes: INS, PDX1, NKX6-1, and ZNT8; (c) the non-native pancreatic beta cell exhibits an in vitro glucose stimulated insulin secretion (GSIS) response to a first glucose challenge; and the non-native pancreatic beta cell does not express one or both of somatostatin and glucagon. |
| Character: Pharmaceutical composition with carrier. | Character: The non-native cell itself, not a composition. |
| Statutory exposure: Section 3(e) synergy objection applies directly to composition. | Statutory exposure: Composition objection falls away; analysis under 3(j) and 10 must be reconsidered. |
Issues Before the Court
- Whether the refusal order was vitiated by the Controller’s failure to consider the amended claims filed with the post-hearing written submissions.
- Whether such failure materially affected the assessment under Sections 3(j), 3(e), and Section 10 of the Patents Act, 1970.
- Whether the matter required reconsideration by the Controller with a fresh opportunity of hearing to the Appellant.
Submissions of the Parties
1. Appellant: Harvard College
The Appellant submitted that the impugned order proceeded entirely on the basis of the original claims and did not engage with the amended claims submitted along with the post-hearing written submissions. The amendments, it was argued, materially altered the nature of the invention, and accordingly required a fresh examination on all statutory grounds.
On the substantive questions, the Appellant contended that the non-native SC-beta cells are structurally, functionally, and genetically distinct from native beta cells. They exhibit altered gene expression profiles, enhanced glucose responsiveness, and mono-hormonal features not found in nature. The cells are generated through a multi-step, laboratory-directed differentiation process that does not occur naturally, and are accordingly not excluded by Section 3(j) as parts of an animal. Reliance was placed on Imclone LLC v. Assistant Controller of Patents (Madras High Court, 2024), BTS Research International Pty. Ltd. v. Controller General of Patents (Calcutta High Court, 2025), and Diamond v. Chakrabarty (US Supreme Court, 1980).
2. Respondent: Controller General of Patents
The Respondent submitted that the refusal was justified on grounds of non-patentability under Section 3(j) and lack of sufficient disclosure under Section 10. The Respondent argued that Section 3(j) excludes plants and animals in whole or any part thereof, irrespective of whether those parts are cultured, maintained, or differentiated in vitro. Accepting the Appellant’s characterisation of SC-beta cells as synthetic would create a loophole permitting any naturally derived biological material to be rebranded as synthetic simply by virtue of laboratory handling.
The Respondent also argued that the terms ‘non-native’, ‘native’, and ‘gene expression profile’ as used in the claims were unclear because no standard for a native cell or a standard gene expression profile was defined in the specification. The Respondent relied on Association for Molecular Pathology v. Myriad Genetics (US Supreme Court, 2013) for the proposition that naturally occurring material, even if isolated, is not patentable.
Judicial Reasoning
The Court confined its examination to the manner in which the impugned order was passed. It did not address the substantive merits of patentability under Sections 3(j), 3(e), or Section 10. The determination was procedural, but the procedural error identified was fatal to the order.
1. The Amended Claims Were Acknowledged but Not Considered
The Court recorded that the amended claims had been placed on record through the post-hearing written submissions. The Controller had referred to them in the impugned order as an ‘Alternative set of Claims’. However, the order proceeded to decide the application solely on the basis of the original claims. The Court observed:
Although the Impugned Order has mentioned the amended claims placed on record through the post-hearing Written Submissions as ‘Alternative set of Claims’, the same are not considered while passing the Impugned Order.
Merely recording the existence of amended claims does not constitute consideration of them. The Controller was required to examine the amended claims and provide reasons that reflected that examination.
2. The Amendment Changed the Entire Basis of the Refusal
The Court examined the nature of the amendment and found that it fundamentally altered the character of Claim 1. The original claim was a composition claim; the amended claim was directed at the non-native pancreatic beta cell itself. The Court observed:
It is clear from the amended claims that they are not composition claims… the entire basis of the Impugned Order may undergo change if the amended claims are considered by the learned Controller.
The objections under Sections 10(4) and 10(5) relating to definitiveness and sufficiency were assessed in the context of a composition claim and its requirement to disclose all components, their amounts, and synergy. Once the claims shifted to a claim directed at the cell itself, the reasoning adopted by the Controller in the impugned order could not be sustained without independent reconsideration of each objection on its own terms.
3. Non-Consideration of Amended Claims Is a Glaring Error
The Court applied the principle settled in Jitendra Kohli v. Controller of Patents (2022:DHC:1904), where the Delhi High Court had held that failure to consider amended claims is a glaring error warranting remand. The Court quoted:
The amended claims have not been taken into consideration… This is clearly a glaring error.
The Court also drew support from Akebia Therapeutics Inc. v. Controller of Patents and Designs (CMA(PT)/64/2024, Madras High Court, 20 March 2025), where an amendment that changed the nature of claims from method to composition claims was held to require a fresh evaluation by the Controller. The Court in Akebia had similarly set aside the impugned order and remanded the matter with a direction that the reconsidering officer should not be the same officer who issued the original order.
4. Scope of Remand
The Court set aside the impugned order and remanded the matter to the Controller. The directions issued were:
- The Controller is to pass a detailed order on the subject application after considering the amended claims filed with the post-hearing written submissions.
- An opportunity of hearing must be given to the Appellant before passing the fresh order.
- The fresh order must be passed within six months from the date of communication of the judgment.
- The Controller must consider the amended claims independently and without being influenced by conclusions already reached regarding the original claims in the impugned order.
The Court expressly clarified the limits of its intervention:
It is clarified that this Court has not considered the merits of the respective cases, and the Subject Application shall be decided in accordance with law without being influenced by any observations made in this Judgement.
Precedents Applied and Discussed
| Case | Principle Applied |
| Jitendra Kohli v. Controller of Patents 2022:DHC:1904 (Delhi HC) | Failure to consider amended claims at the time of deciding the fate of the application is a glaring error. The matter must be reconsidered afresh with the amended claims taken into account on all counts including novelty, inventive step and patentability. |
| Akebia Therapeutics Inc. v. Controller of Patents and Designs CMA(PT)/64/2024 (Madras HC, 20 March 2025) | Where an amendment changes the nature of claims from one type to another (in that case, method to composition), it is crucial for the Controller to address the amended claims. Rejection substantially on the ground that claims were amended is not tenable. |
| Imclone LLC v. Assistant Controller of Patents 2024 SCC OnLine Mad 8397 (Madras HC) | Antibody generated by significant technical human intervention, including deletion and replacement of genetic material and hybridoma process, held patentable. Relied upon by Appellant for proposition that SC-beta cells similarly involve human technical intervention. |
| BTS Research International Pty. Ltd. v. Controller General of Patents 2025 SCC OnLine Cal 2943 (Calcutta HC) | Section 3(j) exclusion must be narrowly construed. Inventions involving genetic engineering or non-natural cell creation are not excluded. Tri-hybrid cells held outside Section 3(j). Court recognised that man-made cellular constructs fall outside the scope of the exclusion. |
| Association for Molecular Pathology v. Myriad Genetics 2013 SCC OnLine US SC 47 (US SC) | Relied upon by Respondent. Naturally occurring DNA held unpatentable; cDNA (synthetic) treated differently. Appellant countered that SC-beta cells are analogous to cDNA as they do not exist in nature and are generated only through human intervention. |
| Diamond v. Chakrabarty 1980 SCC OnLine US SC 128 (US SC) | Relied upon by Appellant. Something with new and different characteristics created by human effort is considered an invention and not a natural product. Supports patentability of man-made biological constructs. |
Doctrinal Context
The judgment sits within a line of authority from the Delhi High Court and Madras High Court that treats non-consideration of amended claims as a jurisdictional error, not merely a factual oversight. Where claims are amended during prosecution, the legal character of the invention, as defined by those claims, changes. The statutory analysis must follow the claims as they stand, not as they previously stood.
The principle has particular significance in complex technology fields such as biotechnology, where amendments frequently shift claims between different categories: composition claims, method claims, product claims, and cell or organism claims. Each category carries different statutory exposure under Sections 3(c), 3(e), 3(i), 3(j), and 10 of the Patents Act, 1970. An objection that is squarely applicable to a composition claim may not apply at all, or may apply differently, to a claim directed at the biological entity itself.
The judgment also reinforces a second principle: a reasoned order is a prerequisite of a valid exercise of the Controller’s power under Section 15 of the Patents Act. Reasons must address the claims and grounds that are actually in issue at the time of the decision. A refusal order that provides detailed reasoning on claims that have been superseded by amendment is not a reasoned order on the application as it stands.
Implications for Practice
The decision reinforces the importance of claim amendments made during prosecution. Where an applicant submits amended claims along with post-hearing written submissions, those claims become the operative claims on which the Controller must decide. Applicants should ensure that amended claims are clearly identified, formally presented, and that the written submissions explain why the amendments address the outstanding objections and how they alter the statutory analysis.
Further, the decision clarifies that where amended claims change the nature of the invention, a fresh evaluation is required on all relevant statutory provisions.Also establishes that refusal orders must address the claims in their amended form and provide reasons that correspond to those claims.
Conclusion
The judgment does not resolve the substantive questions of whether SC-beta cells are excluded under Section 3(j), whether the claims satisfy the disclosure requirements of Section 10, or whether the terminology used in the amended claims is sufficiently definite. Those questions return to the Controller for determination. What the Court has determined is the threshold condition: any future order must engage, in terms, with the amended claims and provide reasons that reflect that engagement.
Governing Law
Patents Act, 1970: Section 3(c), Section 3(e), Section 3(i), Section 3(j), Section 10(4), Section 10(5), Section 15, Section 117 | Patents Rules, 2003: Rule 129, Rule 138 | Code of Civil Procedure, 1908: Section 151
