And it all Started with a Big Bang! – The New WIPO Standard for Sequence Listings (ST.26)

By Erin O'Connor, Trainee Patent Attorney

There is a requirement that biological sequences (e.g., DNA, RNA, peptides) disclosed in patent applications be provided in a sequence listing, which conforms with the applicable WIPO standard. The international standardisation of this information is intended to facilitate searching by IPOs, simplify filing for applicants and allow sequences to be shared with the public.

The current standard, ST.25, was adopted in 1998 and has been in force ever since. However, this standard is not compliant with the International Nucleotide Sequence Database Collaboration (INSDC) requirements meaning that data may be lost when entered into public databases. Further, sequence types that are common today (such as nucleotide analogs, D-amino acids, branched sequences) are also not covered by ST.25 and therefore are not present in searchable databases.

The new standard, ST.26, will remedy these issues.

The Big Bang Date

From 1 July 2022, denoted the “Big Bang” date, ST.25 will be replaced with new standard ST.26, which can be found here.

There is no transition period between the standards, so new applications comprising sequence information filed on or after 1 July 2022 will need to comply with the ST.26 format.

Priority-claiming applications will also require ST.26 compliant sequence listings filed after 1 July 2022, even if the priority application has a filing date prior to 1 July 2022.

For divisional applications and regional/national phase entry, implementation of the new standard may vary between patent offices. For example:

The EPO has indicated that they WILL require ST.26 compliant sequence listings for divisional applications filed after 1 July 2022, even if the parent application has a filing date before 1 July 2022.

The UKIPO however, has indicated that they WILL NOT require ST.26 compliant sequence listings for divisional applications if the parent application has a filing date before 1 July 2022.

Both the EPO and UKIPO have indicated that they WILL NOT require a ST.26 compliant sequence listing at regional/national phase entry, if the PCT application has a filing date before 1 July 2022.

Out with the old and in with the new

In addition to compatibility with INSDC requirements and inclusion of additional sequence types, many other updates have been made. Some key changes include:

  • The requirement of an XML format as opposed to the TXT format required for ST.25
  • Sequences with < 10 nucleotides or < 4 amino acids can no longer be included
  • Sequence identifiers can now be more precisely defined with the mandatory mol_type qualifier (e.g., RNA can now be annotated as mRNA, tRNA etc.)
  • Some changes made to the nomenclature for the mandatory “organism” qualifier (“artificial sequence” renamed “synthetic construct”, “unknown” renamed “unidentified”)
  • “T” to be used to represent both uracil in RNA and thymine in DNA
  • Amino acid sequences will now be represented by one letter abbreviations
  • Mixed mode sequences are no longer allowed (i.e. separated sequences must be submitted for an amino acid sequence and the corresponding nucleotide sequence)
  • Further options/qualifiers for annotation of sequences are available
  • “x” or “n” no longer need to be defined and have a default value (e.g., n is T, A, G, C and x is any natural amino acid)
  • The sequence listing can now only include details of one applicant and details of the earliest claimed priority.

ST.26 also has a number of Annexes that provide guidance on the new standard.

For example, Annex IV provides an extensive list of sequence examples with detailed comments on their representation in an ST.26 compliant sequence listing. Annex VII provides useful information on the conversion of ST.25 sequence listings to ST.26 compliant sequence listings.

WIPO Sequence

In conjunction with the implementation of ST.26, WIPO has released a new software, WIPO Sequence, which is the only software that can be used to compile sequence listings and generate XML files that are ST.26 compliant. The software also provides a conversion feature, which converts an ST.25 TXT file into a ST.26 XML file (however, manual checking is strongly recommended, as there are some incompatibilities between the two formats).

The new software can be downloaded from the WIPO website. A detailed user manual and test sequences are also provided (see here). An online webinar, available in multiple languages, on the new software has also been released by WIPO, in addition to further webinars on the new standard. A link to this webinar can be found here, if you require further information.

For further information and advice about sequence listings, please get in touch with your usual Haseltine Lake Kempner advisor.

This is for general information only and does not constitute legal advice. Should you require advice on this or any other topic then please contact hlk@hlk-ip.com or your usual Haseltine Lake Kempner advisor.