Biotech patent attorneys evolving just fine in the aftermath of the sequence listing Big Bang

02 Feb 2024 | Newsletter

Noel CouragePCT Committee, Bereskin & Parr LLP

WIPO recently switched all patent application sequence listings over to a new, more modern format. For those not familiar with sequence listings, they are an electronic document that sets out DNA and amino acids in a standardized format. The sequences in the listing may be prior art, support for an invention, or the invention itself.

There was a tremendous amount of interest among biotechnology attorneys and a little reticence when on July 1, 2022, the new system (called “ST.26”) went live after decades since the last major, substantive update. The old standard (called “ST.25”) was no longer acceptable, and all international and national offices were required to switch over at the same time (the “big bang” date). An updated version of ST.26 was created one year later.

The AIPPI PCT Committee held a well-attended and successful webinar on the state of affairs since the launch of ST.26. Hannah Kang of WIPO provided an overview of the importance of sequence listings and the goals of the new standard. The consistent presentation of information facilitates data transfer to public databases and searching, and the old format was not keeping up well enough with these objectives anymore. In particular, there was a need for improved alignment with the current scientific standard for sequence databases, called INSDC. Using the old standard meant that some sequence data would likely be lost from patent application sequence listings when transferred to other public sequence databases, which reduces searchability. This undermines the public notice function of the patent system. The old standard also did not require identification of some less common sequence types, such as branched amino acids, nucleotide analogs and D-amino acids. It was not just the sequence content that got a boost from the update, it was also the technology itself. The old standard was in text only format, unlike the new standard, which is in XML, a computer language that better facilitates data validation and exchange.

Emma Francis of WIPO discussed the new ST.26 standard in detail. There are many new nuances that patent attorneys must learn, such as the strict ways of defining features and their location. Some of these aspects are already familiar to those that have worked with the INSDC standard, but there is, of course, a learning curve to adapt to providing information in a patent office software environment. Tips for complying and remediating issues were also provided. For example, in the rare event that a sequence listing is not properly provided on filing, the sequence listing may be subsequently provided and designated as for search purposes only (i.e., not forming part of the application), if the applicant doesn’t want its filing date changed (potentially useful where inventive sequences are already somewhere else in the patent application). WIPO has created a FAQ section on its web site to address many other common questions.

Learning the new sequence standard involves learning new software. The ST.26 software for preparing listings, called WIPO Sequence, is a stand-alone desktop tool, not a web application. The advantage is that sequences can be prepared without connecting to the internet. Patent attorneys, particularly those that cannot install software on their desktop without groveling before their tech department, are hopeful for an eventual web application. There is also a companion software, called WIPO Sequence Validator, because we could all use a little validation. The WIPO patent database, Patentscope, has tools embedded in it to read and display sequences.

Although there are complications in learning and complying with ST.26, there are efficiency gains at patent offices. If all the new requirements are satisfied, no national office should ask for the sequence listing to be provided again on national entry (subject to language translation requirements). This should avoid unnecessary costs and duplication of effort.

A patent attorney perspective was provided by Rose Hughes of AstraZeneca, a drug company. Rose discussed the importance of sequence listings to company IP. There is a burden on companies in the logistics of compiling sequence listings, and the consequences of error can be grave. Rose advocated for advancement of sequence listing technology to support and simplify sequence listing preparation. For example, AI and other technology may eventually be able to pull sequence listing information together from relatively raw research data.

The private firm patent attorneys were represented by the webinar moderators, Catherine Bonner and Noel Courage of the AIPPI PCT Committee, who fielded many questions from webinar attendees. The ST.26 standard appears to have been implemented without significant controversy, which has been taken as a sign that it was a useful update.