Sequenom Inc v Controller of Patents (2025)

Summary

“The present appeals involve an interpretation of the exclusions from patentability in respect of diagnostic processes/methods under Section 3(i) of the Patents Act, 1970 (hereinafter ’the Act’).” (para 2) “These are two appeals filed under Section 117A of the Act” (para 3), and “The Appellants had preferred the following two Patent Applications: No. 2476/DELNP/2011 (hereinafter ‘first patent application’)” and “No. 3139/DELNP/2012 (hereinafter ‘second patent application’)” (para 4); “the purpose of the inventions is to detect foetal genetic traits, including the presence and absence of foetal nucleic acid, foetal sex and foetal chromosomal abnormalities, such as aneuploidy” (para 84). “Vide the first impugned order the Respondent has refused the grant of the corresponding patent application on the grounds that the subject invention lacks inventive step under Section 2(1)(ja) of the Act, and is not patentable under Sections 3(b), 3(d), 3(i) and 3(j) of the Act. Further, vide the second impugned order the Respondent has refused the grant of the patent application on the ground that the Claims thereto are not patentable under Section 3(i) of the Act.” (para 5) The appellants submitted that “the subject inventions in these appeals do not relate to a diagnostic method” (para 22).

The Court held that “this exclusion was only intended to safeguard the autonomy and efficacy of the medical profession in delivering essential care, not to create a blanket bar on patent protection for all innovations relating to diagnosis or treatment” (para 73), that “the intention is to exclude process claims and not product claims” (para 75), and that “Section 3(i) does not make any distinction between in vivo or in vitro processes” (para 79). Of the second patent application it held that “when the language of the Section 3(i) of the Act uses the word diagnostic, the same would include positive and negative diagnosis” (para 102), that “the inventions are liable to be excluded under Section 3(i) of the Act” (para 103), and that “the subject invention would also be hit by section 3(b) of the Act” (para 105). Of the first it held that “the mere fact that it is an in vitro method would by itself be insufficient to make the invention patentable, so long as the purpose of the process is to diagnose a medical condition” (para 113), and that “the appeal of the Appellants against the refusal of grant of subject patent application fails and is liable to be dismissed.” (para 115) “Accordingly, the present two appeals along with pending applications, if any, are disposed of in the above terms.” (para 116)

What the court decided

1. The scope of section 3(i). The Court held that “this exclusion was only intended to safeguard the autonomy and efficacy of the medical profession in delivering essential care, not to create a blanket bar on patent protection for all innovations relating to diagnosis or treatment” (para 73), that “the intention is to exclude process claims and not product claims” (para 75), and that “Section 3(i) does not make any distinction between in vivo or in vitro processes” (paras 73, 75, 79)
2. Screening and confirmatory diagnosis. “The fundamental difference being, as per the Appellants, that diagnostic tests are definitive whereas screening tests may give false-positives.” (para 92) The Court held: “A perusal of the Complete Specifications and the Claims would show that the tests when performed reveal the clear possibility of existence of aneuploidy or any other foetal disorder.” (para 99) “A review of the above material would show that these resources clearly distinguish between two different stages, the screening stage, and the confirmatory diagnostics stage. The publications record that any positive test results after the initial screening would require confirmation by amniocentesis and CVS before acting upon the same. However, the sensitivity and specificity of the Appellants’ test would show that it is extremely accurate having 98.6% sensitivity and 99.8 % specification.” (paras 92, 99–100)
3. Elimination from confirmatory testing. “Considering the Complete Specifications along with the medical literature relied upon by Appellants’, it is clear that upon performing the Appellants’ test a large number of pregnant women would be eliminated from the process of undergoing the confirmatory diagnostic test. This is especially true in view of the high percentage of sensitivity and specificity of the result of the test as claimed by the Appellants. Hence, a decision is made that no further treatment is required for such women.” (para 101)
4. Positive and negative diagnosis. “In the opinion of this Court, when the language of the Section 3(i) of the Act uses the word diagnostic, the same would include positive and negative diagnosis. The persons who are eliminated from undergoing further confirmation tests in respect of any medical condition, genetic abnormality etc., shows that there is a tangible result achieved by the method/ test which is being performed. It would defeat the purpose of Section 3(i) of the Act, if a test is held to be patentable merely because the test does not confirm the presence of a particular medical condition, although it does eliminate the need for further examination in respect of that medical condition.” (para 102)
5. The concern for innovation. “There is enormous concern expressed that if such a test is not allowed to be patented, it could lead to stultifying of innovation. The Court has already held above in respect of issue (i), that product claims are not excluded under Section 3(i) of the Act. Thus, equipment and devices are not excluded by 3(i) of the Act and only processes and methods which may be required to be performed by professionals for diagnosing would be excluded. The subject innovation in fact falls in the narrow compass, i.e., grant of a patent would exclude use of the said method for detecting the medical condition. Therefore, the inventions are liable to be excluded under Section 3(i) of the Act.” (para 103)
6. Sex determination and section 3(b). “In addition, the Court is also conscious of the fact that one of the embodiments in the Complete Specification of the second patent application, also deals with determination of presence of ‘Y’ chromosome nucleic acid, which would also be prohibited in terms of Section 3A of the 1994 Act” (“Pre-Conception and Pre-Natal Diagnostic Techniques Act, 1994”) (para 104), and “Thus, the subject invention would also be hit by section 3(b) of the Act.” (paras 104–105)
7. The first patent application. “The Claims in the said two applications were identical, except in respect of the polynucleotide sequences of ‘sequence identifier no.’ (hereinafter ‘SEQ ID No.’) mentioned in Claim 1, of the subject patent applications, i.e., SEQ ID 1 to 89 and SEQ ID 90 to 261, respectively.” (para 4) “The present patent application is also very similar to the patent application in C.A.(COMM.IPD-PAT) 13/2022 and the purpose of this application is also to detect foetal genetic traits including the presence or absence of foetal nucleic acid and quantity thereof, to check foetal sex and foetal chromosomal abnormalities.” (para 108) “The process of amendment conducted by the applicant would show that the purpose of this invention is also to generate biomarkers. The process is based on methylation of the nucleic acid in a sample and after determining the foetal nucleic acid, the same is then compared to determine the existence of abnormalities including aneuploidy.” (para 110) “As noted above, it is clear from the reading of the two patent applications that the same are in respect of identical inventions, which differ only in respect of the polynucleotide sequence of SEQ IDs. Thus, the analysis of the Court in respect of the subject patent application in C.A.(COMM.IPD-PAT) 13/2022 would squarely cover and bind the Appellants in respect of the present patent application as well.” (paras 4, 108, 110–111)
8. Grants in foreign jurisdictions. “This Court notes that the subject invention may have been patented in some foreign jurisdictions, however, the statutory prohibition in India being what it is, the mere grant in foreign jurisdictions would not lead to grant of the patent in India.” (para 112)
9. In vitro methods. “While there can be no doubt that the subject invention could be a useful invention, the mere fact that it is an in vitro method would by itself be insufficient to make the invention patentable, so long as the purpose of the process is to diagnose a medical condition. Thus, as the subject invention through the method or process of methylation of the samples derived from the pregnant woman, albeit in a laboratory set up, provides a result which would be sufficient to eliminate the pregnant woman from further tests, the same would be hit by Section 3(i) of the Act.” (para 113)
10. Disposition. Of the second patent application: “Accordingly, the appeal of the Appellants against the non-grant of subject patent application is dismissed in above terms.” (para 107) Of the first: “In view of the above discussion, this Court is of the view that the appeal of the Appellants against the refusal of grant of subject patent application fails and is liable to be dismissed.” (para 115) “Accordingly, the present two appeals along with pending applications, if any, are disposed of in the above terms.” (paras 107, 115–116)

What the court did not decide

Of the second patent application: “The Patent Office has also raised issues of lack of novelty and inventive steps. Since, the subject invention is being held to be non-patentable under Sections 3(b) and 3(i) of the Act” (“Patents Act, 1970”) “the said two issues are not being gone into.” (para 106) Of the first: “Insofar as opinion of the Patent Office on inventive step or Section 59 of the Act is concerned, the same is not being gone into inasmuch as this Court is of the opinion that subject patent is hit by Section 3(i) of the Act.” (para 114)

Subsequent treatment

• Followed — In Hirotsu Bio Science v Assistant Controller of Patents and Designs (2026) the Delhi High Court (Tejas Karia J, 17 January 2026) relied on paras 100–101 and 113 of this judgment, recording that it “emphasized that when the language of Section 3(i) of the Act” (“Patents Act, 1970”) “uses the word diagnostic, it would include both positive and negative diagnoses” (para 30); it held that “In the same way, in the present invention, the method leads to the identification of cancer with high accuracy” (para 32), and dismissed the appeal against the refusal under s.3(i) of a cancer-detection method (para 40).
• Followed — In Geron v Assistant Controller of Patents and Designs (2026) the Delhi High Court (Manmeet Pritam Singh Arora J, 17 March 2026) quoted paras 102–103 of this judgment as having “clarified further that the bar of Section 3(i) of the Patents Act would also apply to diagnostic methods that though do not confirm pathology but influence the medical practitioner’s treatment decision” (para 22), relied on it in holding that “The method, even though it does not reveal cancer, since the finding is the factor for deciding the treatment for the patient, will fall under the diagnostic method” (para 32), and dismissed the appeal (para 37).