ST.26 – A new standard for sequence listings

A new global sequence listing standard came recently came into force, replacing the existing WIPO ST.25. As of 1 July 2022, sequence listings in all new PCT and national/regional applications must comply with ST.26.

Most patent offices require patent applications disclosing nucleotide or amino acid sequences to be filed with a formal sequence listing. A sequence listing is a list of all disclosed biological sequences in a standardised electronic format that allows for easier processing and searching by patent offices worldwide.

The aim of ST.26 is to harmonize sequence listing practice across all patent offices, reflect advances in biotechnology, and meet international sequence database requirements. The full text of ST.26 can be found here.

What are the key changes from ST.25 to ST.26?

The major change between the two formats is that ST.26 requires sequence listings to be in electronic XML format rather than the “plain text” TXT format required by ST.25. The use of XML format is intended to facilitate searching and transfer of the sequences to international sequence databases.

WIPO has developed its own software (WIPO Sequence) for the generation and editing of ST.26 compliant sequence listings. The new software may also be used to convert old ST.25 sequence listing into the new ST.26 XML format.

Other key changes are summarised below:

• Sequences having fewer than 10 specifically defined nucleotides or fewer than four specifically defined amino acids are not permitted. Undefined residues (place holder residues ‘Xaa’ for amino acids, ‘n’ for nucleic acids) do not count towards the new minimum length requirement.
• It is now mandatory to include and annotate D-amino acids, linear portions of branched sequences and nucleotide analogues (e.g. PNA or GNA) in sequence listings.
• Each sequence must have not only a “moltype” indication (e.g. DNA, RNA, AA), but must also include a “moltype” qualifier to further define the molecule (e.g. “genomic DNA”, “other DNA”, “genomic RNA”, “mRNA”, “viral RNA”, “transcribed RNA”).
• Amino acids must be represented by their one letter code, instead of their three letter code.
• Both uracil and thymine must be represented by “t”, rather than “u” for uracil and ‘t’ for thymine.
• Further options/qualifiers for the annotation of sequences are available.

Key Considerations

It is important to note that the patent application filing date (and not the priority date) will be the reference date that determines if an application falls under ST.25 or ST.26 sequence rules. There is no transition period between the standards so all new applications comprising sequence listing must now comply with the ST.26 standards.
With regard to PCT applications, the relevant date is the international filing date. Therefore, if a PCT application filed before 1 July 2022 enters the EP regional or GB national phase after that date, the relevant standard is ST.25.

As regards divisional applications, implementation of the new standard may vary between patent offices. For example, the UKIPO does not require ST.26 compliant sequence listings for divisional applications if the parent application has a filing date before 1 July 2022, whereas the EPO requires conversion of the parent ST.25 sequence listing into ST.26 format.

The EPO recently came under fire from the Institute of Professional Representatives before the European Patent Office (epi) for its approach to implementing the new sequence listing rules. The main concern was in relation to divisional applications and the risk of added matter problems since the ST.26 standard requires more information than ST.25. In its response to epi, the EPO provided the following advice to avoid added matter:

“The applicant may choose to file a sequence listing in PDF on the filing date, or to file the divisional application by reference to the description of the parent application, and thus to file the ST.26 sequence listing only for search purposes under Rule 30(3) EPC. This prevents added subject matter issues from arising but an additional fee may fall due, reflecting the additional burden on the side of the EPO.”

The EPO’s response also confirmed that its approach for divisional applications is in-line with that of the USA, Japan, Germany, Denmark and Norway. This divergence in practice between jurisdictions means that clients should provide instructions with sufficient time to allow for the potential conversion into the new format prior to filing a divisional application.