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Federal Register / Vol. 86, No. 126 / Tuesday, July 6, 2021 / Proposed Rules
jbell on DSKJLSW7X2PROD with PROPOSALS

the associated biological sequence data in a standardized electronic format a Sequence Listing XML as a separate part of the specification. Under the proposed rules, in international applications filed under the Patent Cooperation Treaty PCT and in national and regional applications in Intellectual Property Offices IPOs of WIPO member states, an applicant will have to submit a single internationally acceptable sequence listing in a language neutral format using specified International Nucleotide Sequence Database Collaboration INSDC
identifiers, such that a single sequence listing can be prepared for worldwide use.
The proposed rule changes include:
1 Creation of new rules 1.831
through 1.835 to incorporate by reference Standard ST.26; 2 use of INSDC sequence data elements to replace numeric identifiers from the previous standard; 3 modification of rules of practice to include reference to Sequence Listing XML; 4
elimination of a paper or PDF copy of the sequence listing; 5 elimination of the option to include within a sequence listing sequences with fewer than 4
amino acids and fewer than 10
nucleotides; and 6 clarification and simplification of the rules to aid in understanding of the requirements that they set forth.
b. Introduction The sequence rules 37 CFR 1.821
through 1.825 provide a standardized format for description of nucleotide and amino acid sequence data in patent applications and require the submission of such sequences in computer readable form CRF. The current USPTO rules are based on WIPO Standard ST.25, which became effective in 1998, and use a flat file structure of numeric identifiers using a limited set of character codes. A new international standard, ST.26, was agreed upon by WIPO member states, and would apply to international and national applications filed on or after January 1, 2022. Applications pending prior to January 1, 2022, would not have to comply with Standard ST.26.
In an effort to streamline and reduce the procedural requirements found in the existing rules, and to respond to the needs of our customers to conform to Standard ST.26, the USPTO is proposing to amend its rules of practice for submitting biological sequence data associated with disclosures of nucleotide and amino acid sequences in patent applications filed on or after January 1, 2022, to comply with Standard ST.26.

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To decrease the burden on applicants who file applications containing nucleotide and amino acid sequence information internationally, the USPTO
has worked with other WIPO member states as part of the Committee on WIPO
Standards CWS to develop a single internationally acceptable sequence listing standard for use in patent applications filed in those states.
Beginning in October of 2010, the CWS
established a Task Force to propose a revised standard for the filing of nucleotide and/or amino acid sequence listings in XML file format hereinafter referred to as a Sequence Listing XML. In order to obtain public input on the content of Standard ST.26, the USPTO issued Requests for Comments in 2012 and 2016 Request for Comments on the Recommendation for the Disclosure of Sequence Listings Using XML Proposed ST.26. See 77
FR 28541 May 15, 2012 and Standard ST.26-Request for Comments on the Recommended Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings using XML
eXtensible Markup Language. See 81
FR 74775 October 27, 2016. The adopted version of Standard ST.26 takes those comments into account. To achieve the goals that WIPO and WIPO
member states including the United States set out by developing the sequence listing standard for presenting data consistently across all IPOs, all WIPO member states agreed to implement ST.26 for international and national applications filed on or after January 1, 2022. Therefore, upon finalizing the proposed rules, applications filed electronically in the United States on or after January 1, 2022, would need to conform to Standard ST.26, which requires submitting sequence listings in XML
format. The USPTO is further proposing that applications that claim benefit or priority to an earlier application, where the earlier application contained a sequence listing that complied with the Standard ST.25 sequence rules, comply with the new rules that incorporate by reference Standard ST.26. In order to facilitate compliance, WIPO Sequence, a sequence listing authoring and validating tool, has been developed by WIPO with input from WIPO member states so that applicants can use it to prepare and validate their sequence listings in XML format as discussed infra. The USPTO is proposing to add to the patent rules 37 CFR part 1 by incorporating by reference Standard ST.26, and providing conforming amendments to the current rules.

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To ensure that biological sequence data associated with the disclosures of nucleotides and/or amino acid sequences in patent applications can be widely disseminated and searchable by the public and IPOs, the USPTO
works with the National Center for Biotechnology Information NCBI for inclusion of patent sequence data in the GenBank searchable database. For NCBI
to include all sequence data from the USPTO, the data must be provided in INSDC format so that it is compatible with GenBank. The Standard ST.25
format sequence listings cannot be readily converted to INSDC format, resulting in only a fraction of patent sequence information appearing in GenBank. This data loss limits the sequence information provided to the public and exchanged with other sequence database providers, e.g., the National Institute of Genetics NIG in Japan, the DNA Data Bank of Japan DDBJ and European Molecular Biology Laboratory, European Bioinformatics Institute EMBLEBI. WIPO has been working with the WIPO member states to create, adopt, and implement Standard ST.26 for sequence listing submissions in XML file format having the INSDC data elements to address the data loss. Standard ST.26 aims to enhance the accuracy and quality of biological sequence data that is publicly disseminated. In adopting and implementing Standard ST.26, more complete biological sequence data from patents and patent applications will be included in GenBank and thus be accessible by the public. The change from ASCII format to XML format will result in sequence data having computer tags that facilitate sorting and retrieving, and permit ease of access to the data.
Additionally, NCBI is planning to stop accepting data in Standard ST.25 format for inclusion in GenBank in about 35
years after January 1, 2022 the Standard ST.26 transition date.
c. Standard ST.26
The WIPO Handbook on Industrial Property Information and Documentation sets forth standards for the presentation of data in many contexts. Standard ST.26 is titled Recommended Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings Using XML
eXtensible Markup Language.
Adoption of the current version, version 1.4, by the CWS, occurred in December of 2020 and reaffirms that January 1, 2022, is expected to be the implementation date for all WIPO
member states. The proposed USPTO
rules incorporate by reference Standard ST.26.

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