http://ipkitten.blogspot.com/2022/08/epo-under-fire-for-its-approach-to-st26.html
There is an international requirement for the DNA, RNA and protein sequences disclosed in a patent application to be provided in a sequence listing. Sequence listings are used by patent offices to search the prior art for the listed sequences. As of 1 July 2022, the old international standard for sequence listings, ST.25, was replaced by the new ST.26 standard. The shift to ST.26, and the introduction of the new WIPO software for preparing ST.26 sequence listings has the aim of increasing public access to patent sequences. However, concerns have been raised over the requirement to convert ST.25 to ST.26 sequence listings for newly filed European divisional applications. epi has submitted a paper to the EPO arguing that forcing applicants to convert ST.25 sequence listings to the ST.26 format runs the risk of adding matter and creating legal uncertainty for years.
Benefits of WIPO Sequence and ST.26
WIPO has worked hard to communicate the benefits of ST.26. A stated aim of the introduction of ST.26 is the harmonisation of patent office practice on sequence listings. The switch to ST.26 should also improve access to patent sequence data, given that ST.26 is designed to be more compatible with public sequence databases. ST.26 also accommodates a greater variety of sequence information relating to non-standard sequence features, and thus reflects the growing use of non-standard sequence types and residues in patent applications.
ST.26 sequence listings have to be generated and validated using the free WIPO software, WIPO sequence. From the patent applicant’s perspective, WIPO Sequence is orders of magnitude more efficient than previous software for preparing sequence listings (such as the USPTO’s infamously clunky PatentIn). In contrast to previous sequence listing tools, WIPO sequence allows users to input multiple sequences at once (e.g. in FASTA format) and to then edit sequences in bulk. WIPO sequence therefore not only saves time but reduces the risk of copy and paste errors. It always felt bizarre to this Kat that such an important document as a sequence listings had to be prepared by copying, pasting and naming each individual sequence, especially when there can be hundreds (if not thousands) of sequences in an application.
| Novel nucleotide residues |
One crucial difference between the ST.25 and ST.26 formats is that ST.25 sequence listings are in TXT, whilst ST.26 sequence listings are in XML. Unlike the TXT file, the ST.26 XML files themselves are difficult to decipher without WIPO sequence or other XML reading software (IPKat). However, there have been assurances from WIPO that the XML file will, at least, not be converted to an even more unreadable PDF when it is published by WIPO on Patentscope.
In a communication to IPKat, the WIPO have also indicated their intention to provide a sequence viewer integrated into Patentscope itself. As an alternative to downloading the XML file, a third party will be able to use this tool to view one or more sequences from the sequence listing. The third party would simply be able to type a sequence ID into the sequence selection box and be shown that sequence and its associated qualifiers in a human-friendly format. This functionality would be welcome. This Kat hopes that the national and regional patent offices will follow suit in providing similar tools for easy viewing of ST.26 sequence listings. Notably, the EP register currently publishes sequence listings as PDFs.
Problems with ST.26
epi has submitted a paper to the EPO legal department in which it criticises the approach the EPO has taken to the implementation of ST.26, as well as the EPO’s persistent refusal to engage with users’ concerns.
epi’s main issue with the EPO, is the EPO’s decision to require ST.26 sequence listings to be filed for divisional applications, even when the parent application was filed with a ST.25 sequence listing. It is an international requirement that the ST.26 format applies to any new applications filed on or after 1 July 2022 (regardless of priority date). However, it has been left at the discretion of the patent offices as to whether this applies to divisional applications. The WIPO merely recommends that, “in the spirit of an effective transition”, the ST.26 format should be required for divisionals (FAQ: Implementation of WIPO ST.26, 31). The EPO has chosen to follow this recommendation (OJ 2021, A97).
epi argues that the effective filing date of a divisional application is the filing date of the parent. As such, says epi, it should be the filing date of the parent that determines whether a ST.26 or ST.25 sequence listing is required. epi further argues that converting a ST.25 to ST.26 for a divisional application runs the risk of adding matter (Article 76 EPC), given that a ST.26 sequence listings include more information than a ST.25 sequence listing. The handbook for ST.26 itself highlights scenarios in which particular care must be taken not to add matter when converting sequence listings from ST.25 to ST.26 format (Annex VII). In cases where the original ST.25 sequence listing was itself vague or unclear, the handbook notes that “compliance with ST.26, without introduction of added subject matter, is not possible” (ST.26, Annex VII, Scenario 7). epi’s arguments raise the question of whether granted European patents could be successfully challenged on the basis that a ST.26 sequence listing added matter over the originally filed ST.25 sequence listing.
epi also complains about the burden on users of converting sequences to ST.25 to ST.26. The WIPO sequence software allows users to directly convert an ST.25 sequence listing into the ST.26 format. ST.25 to ST.26 conversion is fairly straightforward and painless for cases with a moderate number of sequences and takes only a few minutes. As previously mentioned, WIPO sequence is a far easier and more efficient tool for preparing sequence listings than previous sequence listing software. epi argues, however, that there is a considerable burden for applicants of cases having hundreds of sequence listings (e.g. for the 2.5% of cases with over 1000 sequences). This burden is even greater considering the extra checks needed to ensure that there is no added matter , particularly for sequence listings containing many features and qualifiers.
Final thoughts
The letter from epi reveals its considerable frustration with the EPO:
“epi has tried to engage with the EPO on several levels, and with different people and different departments, regarding the new ST.26 standard. However, we are becoming increasingly concerned that the EPO is not sharing users’ concerns and any issues raised are dismissed by summarily reference to the guidance provided by WIPO . It appears that the EPO has decided that it will implement ST.26 irrespective of the potential consequences for the EPO, practitioners, and applicants alike.”
The willingness of epi to now raise the issue publicly and directly with the EPO will at least mean that the EPO will find it difficult to sweep the issue under the carpet, in the manner it appears to be trying to do with controversial topic of description amendments (IPKat). Notably, the UK IPO had a change of heart with regards to whether ST.26 sequence listings are required for divisional. For UK patent applications, the sequence listing should be in the same format as that required for the parent application. It remains to be seen whether the EPO will have a similar change of mind. At the moment, all evidence would appear to point to the contrary.
Further reading
ST. 26 sequence listings: A forward or backward step for ease of access to patent sequence data? (20 Feb 2022)
Content reproduced from The IPKat as permitted under the Creative Commons Licence (UK).