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

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.