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.
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| Novel nucleotide residues |
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)
Reviewed by Rose Hughes
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Monday, August 01, 2022
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Posts
Unfortunately, you can only import one sequence at a time using FASTA format and WIPO have no plans on expanding that to bulk import according to webinars.
ReplyDeleteBy all means change the sequence listing standard if you must, it does seem to be more comprehensive, more versatile, and the new software does seem to be less of a headache than Bissap (an admittedly low bar).
ReplyDeleteBut I just don't understand why - why? - it makes any conceivable sense to apply it to divisional applications? Any thoughts on this would be welcome, I'm entirely willing to accept there's something terribly important I am missing.
But I am less convinced any reasons would out weigh the following:
There's a non-zero risk of added matter which in itself should be a reason to avoid it at almost any cost, especially at the EPO.
The filing date is by definition before the implementation date.
There's a very good chance some or all of the search of the sequences has already occurred, what with it being a divisional application.
Even if more searches are required they won't be comparing them to other ST.26 listings, because (again) the filing date is by definition before the implementation date.
The obvious safety net around adding or losing matter matter (including the old ST.25 as part of the description) is likely to add hundreds or thousands to page fees, especially in the cases where it would most be needed (i.e. applications with loads of sequences, where such an approach would likely be most needed).
This is another one of those times where I just don't understand the EPO's approach - where they just seem to be throwing out bureaucratic hurdles for no reason. No use blaming WIPO, they explicitly gave the choice and gave no reasoning for why ST.26 is necessary for divisionals either. Most of the above are headaches for the applicant rather than the EPO, but at least some have the capacity to create years of irritation on both sides.
Seriously, does anyone have any explanation? Is it just because they don't want to run two systems for however long? In that case why aren't ST.26 listings required for regional phase entries filed before the implementation date? Perhaps I should shut up before I give them any ideas.
In recent years, it has become hard to escape the conclusion that the EPO is being run solely for the benefit of those in charge (the management and the AC delegates / delegations), and that any concessions to the needs or wants of the EPO's users are the exception rather than the rule ... and even then those concessions are often only made either for the sake of appearances or for the sake of securing a continued flow of funds (from official fees).
ReplyDeleteThe handling of ST.26 is a perfect illustration of this approach.
Harm to applicants from the EPO's decision regarding divisionals: very significant, at least for the cost for preparing a converted listing, and also (potentially unavoidable) legal risks stemming from the addition of new matter from the conversion.
Harm to the EPO if they had instead adopted the same (common-sense) approach to divisionals as the UK IPO: none ... perhaps other than a slight tarnishing of the EPO's crown as the true standard-bearer of transition to ST.26 and/or a slight delay to their plans to retire the software used to search ST.25 listings.
It is hard to imagine a decision being taken by the EPO that had any flimsier excuse for imposing such a (potentially impossible) burden onto applicants. And that is before we even consider the shortcomings of the conversion software and the fact that, if the EPO were so keen on ensuring that ST.26 listings are made publicly available for divisionals of "old" applications, they could have requested them as an "added extra" ... to be added to the public file for information purposes only. (Or, perish the thought, the EPO could themselves have produced "information only", converted ST.26 listings.)
One might have thought that being the standard bearer for common sense would also be a worthy aim.
DeleteLooking forward to the paid online training which 'confirms the EPO practice' on ST.26 for divisionals, reports a curated selection of views, and declares it as a roaring success.
An interesting dilema. According to the December 2021 Notice, the sequence listing is part of the description but under Rule 40(2), a reference to an earlier application replaces the description, so no listing would then have to be filed.
ReplyDeleteI have no idea if it can be done, but can one file both formats in a divisional application, so giving wiggle room later if added subject matter becomes an issue with the new format one?
ReplyDeleteThat all depends upon whether you can persuade the EPO to accept a sequence listing in ST.25 format. As far as I am aware, there is now no (electronic) method of filing that will accept a listing in ST.25 format.
DeleteTransfoming an ST25 file to an ST26 file can be done in most cases with about a dozen clicks, BUT you will get an enormous "Import Report" with "Change Data" in many many cases. If the ST25 file had some "special features", these will all be stuffed into a "note" irrespective of whether they would need to be described properly in line with ST26. Short sequences (e.g. some CDR regions, become skipped autmatically and their sequence information will be lost in the new ST26 file. Then, you need make mol_type definitions for sequences where you just don't know what type they really are. Finally, you have to go through the appliciton and check for sequences that under the NEW ST26 need to be adopted into the ST26 file (like, e.g. consensus sequence strings, or aa containing D-aminoacids). Then there are the few cases that throw up errors and if you have a Sequence Listing like that you likely have a TON of errors, none of which you will be able to bulk edit. E.g. if you have DNA/RNA hybrid sequences, oyu will have to define every single occurrence of uracil manually in each sequence. If you have about hundred mixed RNA/DNA sequences ... you get hundreds of pages of import report with thousands of errors that you need to fix manually ...
ReplyDeleteI have converted a few Sequence Listings and literally none of the conversions was such that I would not have wanted to inform the applicant about some possible issues.
Then the WIPO Sequence tool has bugs, some make it difficult to add features, some other lead to problems on the patent offices verification side I heard.
Now the question: WHAT FOR? Have applicants asked for a new standard 7x more complex than the old one? Did the public ask for XML files rather then TXT files? Couldn't ST25 be revised to adopt branched sequences and D-aminoacid containing sequences, etc.? The ONLY reason for this standard is INSDC, the file format of public databases and the ease for the patent office to feed their search engines.
--> So the applicants have more burden, more costs and an error-prone and legally uncertain conversion task, the public has non-human readable files and less legal certainty than before, and the only beneficiaries are the patent offices ... they get the conversion job done by the applicants (and may force them with legal consequendes of refusals of patent applications), have less own conversions to do and easy searching.
There seems to be a rather straightforward solution to this issue: allow applicants to choose which standard they adopt for filing divisional applications that have an effective filing date of before the transition, but mandate that, if they choose ST.25, they also file a conversion to ST.26 that is also published alongside the application and patent. Applicants and representatives could then file divisional applications with confidence that they are not introducing new subject matter, and the EPO and the public would get the benefit of an ST.26-compliant sequence listing.
ReplyDeleteThis would be similar to how the EPO handles divisional applications where the earlier filing was in a non-EPO language, whereby applicants can choose whether to file in the EPO language of proceedings or in the original non-EPO language, provided it is accompanied or followed by a translation.
I believe that epi's discussions with the EPO covered various (more applicant-friendly) options that the EPO could adopt. However, it seems that the EPO never had any intention of retreating from the position outlined in the Decision of the President that was issued without anything approaching a sensible level of prior consultation.
DeleteFor some reason, the EPO could not see the problems with (and unfairness to applicants stemming from) their proposed approach to divisionals ... despite the fact that those problems were always self-evident to virtually everyone else in the European patent ecosystem, including the UK IPO. My guess is that this is because the person or persons who had the relevant decision-making power were never in the room with epi. Whatever the reason, it is hard to interpret the outcome as anything other than the EPO raising a middle digit to the whole life sciences section of the European patent profession (and to essentially the whole life sciences industry).
Concerning filing of divisionals, there has already been a reasoned proposal including a draft for an amended Rule 36 EPC published in epi information 2020, 14 (https://information.patentepi.org/uploads/pdf/epi-Information-02-2020.pdf), which would also reduce the risk for applicants with respect to sequence listings. Unfortunately, it seems not to have been considered by the EPO.
ReplyDelete