T 1627/09 (Desaturases/WASHINGTON) 10-10-2013

Admissibility of the opposition

1. In substance, the appellant has argued that the notice of opposition did not comply with Rule 76(2)(c) EPC (see Section X, supra).

2. According to Rule 76(2)(c) EPC, the notice of opposition must contain a statement of the extent to which the European patent is opposed and of the grounds on which the opposition is based, as well as an indication of the facts, evidence and arguments presented in support of these grounds, i.e. the substantiation.

3. The appellant's objection is directed to the substantiation of the ground of insufficient disclosure only, its argument being that the respondent had not provided any proof in this respect. The appellant has not objected as regards the substantiation of the other grounds for opposition (in the present case, lack of inventive step and of industrial application, pursuant to Article 100(a) EPC).

4. For the opposition to be admissible, it is sufficient that the notice of opposition fulfills the requirements of Rule 76(2)(c) EPC in respect of one of the grounds of opposition (see decision T 653/99 of 18 September 2002; point 2 of the Reasons). On this basis alone the opposition is to be considered as admissible.

5. Furthermore, the appellant has not disputed the fact that the notice of opposition contains an indication of the facts, evidence and arguments presented by the respondent in support of its objection of insufficient disclosure (see inter alia Example 1 of document D1) but argues that a proof of this assertion is lacking in the notice of opposition. In this respect, the Board notes that document D1 contains a clear statement that "No desaturation of EDA to DGLA was observed with D8S-3" (column 42, lines 36 to 37) but no experimental evidence. However, Rule 76(2)(c) EPC does not require that proof of the facts be contained in the notice of opposition. An indication thereof is necessary and sufficient (see decision T 426/08 of 1 December 2008; see point 5.1.3 of the Reasons).

6. Therefore, the requirements of Rule 76(2)(c) EPC have been met and the opposition division correctly decided that the opposition was admissible.

Admissibility of document D16

7. The appellant has argued that the opposition division erred in admitting document D16 into opposition proceedings.

8. Document D16 was enclosed with the respondent's letter submitted on 6 March 2009 in preparation for the oral proceedings before the opposition division. It was filed in direct response to the appellant's argument of 20 February 2009 that no experimental data were disclosed in columns 41 to 42 of document D1 (see point 5, supra).

9. If the way in which the department of first instance has exercised its discretion on a procedural matter is challenged in an appeal, it is not the function of the Board of appeal to review all the facts and circumstances of the case as if it were in the place of the department of first instance, and to decide whether or not it would have exercised such discretion in the same way as the department of first instance. A Board of appeal should only overrule the way in which a department of first instance has exercised its discretion if the Board concludes it has done so according to the wrong principles, or without taking into account the right principles, or in an unreasonable way (cf. Case law of the Board's of Appeal, 7th edition, IV.E.3.6, page 983; and decisions cited therein).

10. The opposition division held that document D16 was submitted within the time limit set in the summons to attend oral proceedings in order to support facts and arguments already on file, and decided to admit it.

11. The Board concludes that the opposition division correctly exercised its discretionary power and sees no reason to overturn its decision.

Admissibility of the auxiliary requests

12. The admissibility of the first auxiliary request was not disputed, and the amendments in it do not raise any new issues. Therefore, the Board decides to admit it into the appeal proceedings.

13. The second to fifth and seventh auxiliary requests which were filed on 10 September 2013 are amendments to the appellant's case after it had filed its grounds of appeal. They may be admitted and considered at the Board's discretion. The discretion shall be exercised in view of inter alia the complexity of the new subject-matter submitted, the current state of the proceedings and the need for procedural economy (see Article 13(1) RPBA).

14. In claim 1 of each of the second to fifth and seventh auxiliary requests, the protein or the nucleic acid sequence for which protection is sought is defined by reference to SEQ ID NO:4 and by further features relating to a process for obtaining it.

15. The appellant was perfectly aware from the onset of the opposition proceedings of the fundamental deficiencies associated with SEQ ID NO:4. As can be seen from document D3, it must even have been aware of the sequencing errors in SEQ ID NOs: 3 and 4 when the patent application was still pending.

Therefore, it could have been foreseen, when preparing for the oral proceedings before the opposition division, that a claim in which the desaturase was defined by reference to SEQ ID NO:4 only was at a high risk of being refused (see the summons of 15 December 2008). However, neither in the opposition proceedings nor with its grounds of appeal did the appellant take the opportunity to file any request in which the claimed protein or nucleotide acid would have been defined in another way, for example by reference to a process of manufacture.

16. Under these circumstances, the Board regards the filing of the second to fifth and seventh auxiliary requests one month before oral proceedings as the clearly belated introduction of fresh cases rendering the case more complex and giving rise to new objections under Articles 84 and 123 EPC.

17. Therefore, using the discretionary power conferred to it by Article 13(1) RPBA, the Board decides not to admit the second to fifth and seventh auxiliary requests into the appeal proceedings.

18. The sixth auxiliary request was filed together with the grounds of appeal. It comprises claims 1 to 5, corresponding to claims 14 to 18 as granted. The respondent has been aware of those claims from the onset of the opposition proceedings and admission of the sixth auxiliary request does not create any new issues. Therefore, the Board decides to admit the sixth auxiliary request into the appeal proceedings.

19. The eighth auxiliary request was filed in direct response to the refusal by the Board of the sixth auxiliary request (see paragraph 42 below) for reasons of insufficient disclosure. Claim 1 of the eighth auxiliary request differs from claim 1 of the sixth auxiliary request by its reference to "a sequence selected from SEQ ID NO:5 and SEQ ID NO:6", while the former feature "at least 15 contiguous nucleotides of a sequence shown in SEQ ID NO:3" was deleted.

20. The oligonucleotides of SEQ ID NO:5 and SEQ ID NO:6 are primers designed to be completely degenerate to sequences overlapping the first and the third of the His-box regions of the delta 6-desaturase of Caenorhabditis elegans (see bottom of page 21 of the patent application WO 00/34439). They were used in combination to amplify by PCR and clone a delta 8-desaturase from E. gracilis (see page 6, lines 29 to 30 and Example 3 on pages 21 to 22 of patent application WO 00/34439). They were however not used in any hybridization assay. Therefore, the feature introduced in claim 1 of the eighth auxiliary request has been taken out of its context and would, if the request were admitted into the proceedings, give rise to an objection under Article 123(2) EPC. Moreover, issues under Article 123(3) EPC might arise in view of the fact that the primers defined by SEQ ID NO:5 and SEQ ID NO:6, due to their degenerate nature, encompass a sizeable number of primer sequences which are not present in SEQ ID NO:3.

21. Therefore, using the discretional power conferred to it by Article 13(1) RPBA, the Board decides not to admit the eighth auxiliary request into the appeal proceedings.

Main request (claims as granted)(Article 83 EPC)

22. Claim 1 is directed to an active desaturase comprising an amino acid sequence consisting of the sequence of SEQ ID NO:4 or having at least 60% identity thereto.

23. The pivotal question to be answered is whether such an active desaturase is actually disclosed in the patent application (WO 00/34439).

24. Example 7 in the patent application describes how the inventors have put into practice the teaching of Examples 3 and 4 to prepare a plasmid (pJW541) containing an open reading frame encoding a protein designated EFD1 (stating for Euglena Fatty Acid Desaturase 1). Example 8 reports that the translation of that open reading frame indicated a protein of 422 amino acids, the sequence of which is represented in Figure 3 under the designation "egd1" together with the sequences of FAT-3 and FAT-4, two desaturases of C. elegans. This 422 amino acid sequence is further designated as SEQ ID NO:4 in the sequence listing. Example 9 reports that, to confirm the presumed desaturase activity of the encoded protein, the EDF1 cDNA was transferred from plasmid pJW541 to a yeast expression vector, pYES2, under the control of a galactose-inducible promoter. The resulting expression vector, pYES2-541, was introduced into S. cerevisiae. Yeast cultures were supplemented with various fatty acid soaps and the fatty acids of the cultures were analysed by methyl-ester derivatization and gas chromatography. The patterns of desaturation activity indicated that pYES2-541 expressed a delta 8-desaturase activity.

25. The respondent has argued that the protein defined by SEQ ID NO:4 does not exhibit any desaturase activity. In support of its argument, it has referred to documents D1 and D16.

26. Example 1 of document D1 (see columns 40 to 42) describes inter alia the preparation of a plasmid, pDMW261, comprising an in vitro synthesized codon-optimized gene for expression in Yarrowia. The synthetic gene sequence, designated D8S-3, encodes a protein having an amino acid sequence identical to the amino acid sequence of SEQ ID NO:4 of the patent application (see SEQ ID NO:7 of document D1). Following transformation of the pDMW261 construct into Yarrowia lipolytica, a feeding experiment using eicosadienoic acid (EDA) was conducted (see column 42, lines 1 to 12 and 32 to 35 together with column 3, line 38). The cells were collected by centrifugation, lipids were extracted, and fatty acid methyl esters were prepared by trans-esterification and subsequently analyzed. No experimental evidence is provided in this last respect. However, it is clearly stated that no desaturation of EDA to dihomo-gamma-linoleic acids (DGLA) was observed (see column 42, lines 35 to 36 together with Table 2 on column 11). This has led the respondent to the obvious conclusion that the protein having the sequence of SEQ ID NO:4 has no desaturase activity. Detailed experimental evidence supporting this conclusion is provided by document D16 (see the Section entitled "Co-Expression of the synthetic Delta-8 Desaturase "D8S-1" And A Synthetic Delta-9 Elongase" on pages 3 to 4). With the submission of document D16, the respondent has discharged its burden of proof.

27. The appellant has not presented any evidence to the contrary. Its argument that the results of D1 were not verifiable and as such not credible is not tenable in view of the convincing explanations provided by document D16.

28. The Board concludes that the protein defined by SEQ ID NO:4 has no desaturase activity.

29. The appellant has argued that the information contained in the application as filed would have been sufficient to allow the skilled person to prepare a cDNA encoding the delta 8-desaturase obtainable from Euglena gracilis, to express it and to confirm its enzymatic activity. It referred to three cloning approaches which would have been at the disposal of the skilled person. The first approach would have used the teaching of the Examples. The second approach would have relied on hybridization assays using the general information given on pages 11 to 12 of the patent application. The third approach would have been a genomic PCR approach relying on the general information given at lines 13 to 19 on page 11.

30. Since the skilled person relying on the patent application was not informed that the protein defined by SEQ ID NO:4 was inactive, and since the patent application neither disclosed any active sequence variants having at least 60% sequence identity nor which positions of SEQ ID NO:4 had to be modified in order to obtain a functional desaturase, it had to go back to E. gracilis and reclone the desaturase in order to put the claimed invention into practice. Even though each of the steps necessary for recloning could be performed by a person skilled in the art, it is the combination of all the necessary steps (isolation of total mRNA, PCR amplification and selection of a group of amplification products with homology to known desaturases, completion of the 5' and 3' ends by RACE amplification, cloning and expression of the full length sequence to assess its function) which creates an undue burden on the skilled person trying to perform the invention. The same applies to the two alternative approaches mentioned by the appellant.

31. Thus, contrary to the requirements of Article 83 EPC, the skilled person would not have been in a position to perform the claimed invention readily and without undue burden across essentially the entire scope of claim 1.

32. Therefore, the main request does not meet the requirements of Article 83 EPC.

First auxiliary request (Article 83 EPC)

33. Claim 1 is directed to an active delta 8-desaturase which comprises an amino acid sequence having at least 80% identity to the sequence SEQ ID NO:4.

34. In the patent application, such proteins are referred to once (see bottom of page 13, reading "Proteins of the invention also include proteins showing at least 60%, at least 70%, at least 80%, at least 90%, and at least 95% similarity (to the sequence of FIG. 6A or FIG. 7A) using blastp with default parameters)" (emphasis by the Board); the sequence represented in FIG. 7A is the sequence SEQ ID NO:4).

35. Thus, the only criterion provided to the skilled person trying to identify proteins according to claim 1 is the self-contained reference to a protein of sequence SEQ ID NO:4. However, as discussed in points 26 and 27 (supra), the protein encoded by SEQ ID NO: 4 has no delta 8-desaturase activity. As for the main request, the skilled person trying to perform the invention according to the first auxiliary request was therefore left with the undue burden of embarking on a research program with the aim of first cloning a protein with delta 8-desaturase activity and then locating in its sequence those portions which could be altered to the extent of no more than 20% of the total sequence without prejudicing the enzymatic activity.

36. The Board reaches the conclusion that the patent fails to disclose the subject matter of claim 1 of auxiliary request 1 in a manner sufficiently clear and complete for it to be carried out by a person skilled in the art. Therefore, this request does not meet the requirements of Article 83 EPC.

Sixth auxiliary request (Article 83 EPC)

37. Claim 1 of the sixth auxiliary request is directed to a method of identifying a nucleic acid sequence as one that encodes a desaturase. It comprises two steps, namely a step of hybridizing the sequence to at least 15 contiguous nucleotides of a sequence as shown in SEQ ID NO:3 and a step of identification as a desaturase for which no technical features have been indicated.

38. According to the claim language, as soon as hybridization occurs, a tested sequence is identified as encoding a desaturase, i.e. a protein having desaturase activity.

39. The appellant has argued that the step of identification was only a first step and that further confirmation steps as disclosed in the patent specification, i.e. cloning of a complete ORF and functional assays with the encoded protein, would be performed by the skilled person to confirm the function.

40. These confirmation steps are however not part of the claim and the question is whether the skilled person, taking into account the general knowledge and the disclosure in the patent application, was in a position to readily identify a nucleic acid sequence encoding a protein having desaturase activity by simply performing the steps of claim 1.

41. According to claim 1, the probe comprises any sequence having at least 15 contiguous nucleotides from anywhere within SEQ ID NO:3 and is not limited to e.g. sequences from the conserved His-box regions. The claim encompasses thus the use of short probes comprising sequences contributing to the inactivity of the protein encoded by SEQ ID NO:3 (see document D4 which provides a nucleotide sequence alignment of the coding region of SEQ ID NO:3 of the patent application against the corresponding coding region of SEQ ID NO:3 as shown in patent US 6,825,017 B1 - document D2), as well as probes comprising sequences from areas with high homology to e.g. the cytochrome b5 like motif at its N-terminus (see the paragraph bridging pages 25 and 26 of the patent application). In view of the inclusion of probes detecting inactive sequences, probes with high homology to cytochrome b5, and the limited specificity of probes as short as 15 nucleic acids, the Board concludes that the skilled person was not in a position to readily, and without undue burden, perform the invention across essentially the entire scope of the claim.

42. The Board decides that the sixth auxiliary request does not meet the requirements of Article 83 EPC.

43. In the absence of any allowable request, the appeal must be dismissed.