ST.26 Sequence Listing With Effect From July 01, 2022 – The Big Bang Date For Harmonizing The Submission Of Sequence Listing. – Patent

Biotechnology Patent Applications often contains biological
molecules, whether naturally occurring or synthesized, such as
nucleotides (DNA/RNA), amino acids, primers and other artificial
constructs. In fact, it is a mandate for the Patent Applicant to
submit the sequences of any such biological construct/molecule to
sufficiently disclose the biological sequences in the
specification. Usually such disclosure of sequences is provided in
the form of sequence listing. A sequence listing is a list of
sequences submitted in a patent application in a globally
acceptable standardized format prescribed by World Intellectual
Property Organization (WIPO). The sequence listing is then used by
the patent office to search and examine the submitted sequences to
test its patentability.

These sequence listing forms the part of searchable database for
the public once the patent application is published, thereby
serving as prior arts and future reference for further research and
development.

Need for the new standard

Till July 1st 2022, the prescribed format for submitting
sequence listing in a patent application was in compliance with the
WIPO Standard ST.25. The sequences were submitted in electronic
format, specifically TXT format. In the absence of clear rules,
each patent office had comprehended and imposed the rules
differently.

The existing ST.25 format did not meet the requirements of
International Nucleotide Sequence Database Collaboration, as a
result of which few data was missed out while transferring
sequences to the public database such as GenBank. Further, ST.25
fails to recognize certain diverse sequences such as branched
sequences, D-amino acids and nucleotide analogs. The data in ST.25
was unstructured, making it difficult to validate.

In order to counteract the above issue and to harmonise the
procedure in all patent offices, the WIPO has made it mandatory for
all Patent office to switch to ST.26 format, with effect from July
01, 2022 for international applications, wherein the filing
date of the applications fall on or after July 01, 2022.
However, sequence listing furnished in respect of applications
before July 01, 2022 should comply with ST.25 standard even if the
sequence listing is submitted at later stage.

The major difference between ST.25 and ST.26 format is
highlighted below:

1. The electronic format of sequence listing has been changed from
   TXT to XML format.




2. Annotation of D-amino acids, nucleotide analogs and branched
   sequences




3. The alphabet “t” is used in the new format to
   represent uracil of RNA instead of “u”




4. One letter code for representing amino acids instead of three
   letters.




5. Sequence listing must not include any sequences having fewer
   than ten specifically defined nucleotides, or fewer than four
   specifically defined amino acids.




6. Standardization of feature keys, feature locations, qualifiers,
   qualifier values, and sequence variant presentation.




7. Unlike ST.25 where all the priority application information can
   be included along with the name of all the applicants and
   inventors, in ST.26 only the earliest priority application can be
   included along with one applicant and optionally one inventor.




8. ST.25 format identified the Sequence identifiers as DNA, RNA or
   PRT(protein), however in ST.26, the sequences are identified as
   DNA, RNA or AA (amino acids) along with mandatory mol_type
   qualified to further describe the type of molecule.




9. For generated contrast sequences, the organism name has been
   changed from “artificial sequence” in ST.25 to
   “synthetic construct” in ST.26.




10. Mixed mode was allowed in ST.25 such as representing the
    nucleotide sequences with the amino acid translation at the bottom,
    however such mixed mode is not allowed in ST.26.

Generating ST.26 compliant sequence listing:

WIPO sequence, as free desktop based software assist the
Applicants in generating sequences compliant with the new standard.
Additionally, there exists an option of Sequence validator to
validate the sequences generated against the ST.26 requirements.
The database can work without internet as it is a standalone
desktop tool as opposed to web application. The desktop software
can be accessed here

https://www.wipo.int/standards/en/sequence/index.html

Readability of XML format

Based on our experience with the new standards, Applicants are
encountering difficulty in reading the XML format as compared to
TXT format. The TXT format appeared to be more compact and
comprehensive. The XML format has too many coding tags.

WIPO has allowed stripping off of the XML tags and leaving
behind only the sequences listing content to be published subject
to the decision of the national patent office.

For PCT applications, the sequence listing as filed by the
Applicant in XML format will be published.

Where the Indian Patent Office stands

The Indian Patent Office vide its public notice dated June 17,
2022 has stated that all sequence listing that are part of an
international application filed on or after the July 01, 2022 under
the PCT shall comply with WIPO standard ST.26. Sequence listing
compliant with the WIPO standard ST.26 will be accepted by Indian
Patent Applications in case or ordinary applications as well.

Below are the details for submission of sequence listing:

***

References:
https://www.wipo.int/standards/en/sequence/faq.html#FAQ:OfficeImplementationofWIPOST.26-WIPOSequencesuite

https://www.wipo.int/export/sites/www/standards/en/pdf/03-26-01.pdf

The content of this article is intended to provide a general
guide to the subject matter. Specialist advice should be sought
about your specific circumstances.