2414.01 Issuance of a Notice Relating to the Requirements For Patent Applications Containing Nucleotide and/or Amino Acid Sequence Disclosures [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]

Initial review by the pre-examination staff at the USPTO checks for compliance with formal matters. In order to ensure that an application is ready for examination, pre-examination staff check that applications containing disclosures of nucleotides and/or amino acid sequences have complied with the sequence listing rules. This means that for applications having a filing date on or after July 1, 2022, containing such sequence disclosures, a “Sequence Listing XML” must be of record and if not, applicant will be notified of such deficiency and provided instructions for responding. Adding a “Sequence Listing XML” where one was not previously filed must conform with the requirements of 37 CFR 1.835(a). See MPEP § 2414.02 for details. To amend a “Sequence Listing XML” due to errors or omissions, the procedure is outlined in 37 CFR 1.835(b). See MPEP § 2414.03 for details.

2414.02 Amendment to Add an Initial “Sequence Listing XML” under 37 CFR 1.835(a) [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]

Part of the pre-examination process as well as initial review by the examiner involves identifying whether an application that discloses nucleotide and/or amino acid sequences requires submission of a “Sequence Listing XML,” and if so, if it contains a compliant “Sequence Listing XML.” If pre-examination staff identifies that a “Sequence Listing XML” is required but missing or that compliance with 37 CFR 1.831 - 1.835 is lacking, a notice indicating the deficiencies will be issued to the applicant. Similarly, upon having a new application placed on the examiner’s docket, the examiner can assess whether a disclosure of nucleotide and/or amino acid sequences in the application requires a “Sequence Listing XML” to be submitted where one has not been submitted. The examiner can identify the requirement for a “Sequence Listing XML” on an “OPAP Routing Sheet” (Document Code “SEQREQ”) and return the application to pre-examination for the mailing of a notice indicating the deficiencies.

Applicant's response to a notice or an Office Action requiring an initial “Sequence Listing XML” would involve providing the following:

• (1) A compliant “Sequence Listing XML” submitted as an XML file using either the USPTO patent electronic filing system (currently, XML files can only be submitted via Patent Center) or a read-only optical disc that is mailed or hand-delivered into the Office. If the size of “Sequence Listing XML” file exceeds the upload limit of Patent Center, then it must be submitted on read-only optical disc. (37 CFR 1.835(a)(1));
• (2) An amendment to the specification to incorporate by reference the material in the “Sequence Listing XML” by reciting in a separate paragraph of the specification the name of the file, the date of creation, and the size of the file in bytes (37 CFR 1.835(a)(2) and 37 CFR 1.835(c));
• (3) A statement identifying the basis for the added “Sequence Listing XML,” which would include, e.g., paragraphs of the originally filed specification or sheets of the drawings where a sequence is disclosed, identifying each sequence that is part of the “Sequence Listing XML” (37 CFR 1.835(a)(3)); and
• (4) A statement that no new matter is introduced by the content of the “Sequence Listing XML” (37 CFR 1.835(a)(4)).

2414.03 Amendment Adding to, Deleting from, or Replacing Sequence Information in a “Sequence Listing XML” under 37 CFR 1.835(b) [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]

Part of the pre-examination process as well as initial review by the examiner involves identifying whether an application that discloses nucleotide and/or amino acid sequences contains a compliant “Sequence Listing XML.” If pre-examination staff identifies that a previously submitted “Sequence Listing XML” contains errors and/or the application fails to comply with 37 CFR 1.831 - 1.834, a notice indicating the deficiencies will be issued to the applicant. Similarly, upon having a new application placed on the examiner’s docket, the examiner can identify errors in any “Sequence Listing XML” and/or instances of noncompliance with 37 CFR 1.831 - 1.834 that might not have been identified by pre-examination staff. The examiner can identify the outstanding requirements on a “OPAP Routing Sheet” (Document Code “SEQREQ”) and return the application to pre-examination status for the mailing of a notice indicating the deficiencies.

Applicant response to a notice or an Office action requiring a replacement “Sequence Listing XML” would involve submitting the following:

• (1) A compliant replacement “Sequence Listing XML” submitted as an XML file containing the entire “Sequence Listing XML,” including any additions, deletions, or replacements of sequence information, using either the USPTO patent electronic filing system (currently, XML files can only be submitted via Patent Center) or a read-only optical disc that is mailed or hand-delivered into the Office. If the size of “Sequence Listing XML” file exceeds the upload limit of Patent Center, then it must be submitted on read-only optical disc (37 CFR 1.835(b)(1));
• (2) An amendment to the specification to incorporate by reference the material in the replacement “Sequence Listing XML” by reciting in a separate paragraph of the specification the name of the file, the date of creation, and the size of the file in bytes (37 CFR 1.835(b)(1) and 37 CFR 1.835(c));
• (3) A statement that identifies the location of all additions, deletions, or replacements of sequence information relative to the replaced “Sequence Listing XML” (37 CFR 1.835(b)(3));
• (4) A statement identifying the basis for the additions, deletions, or replacements of the sequence information in the application as originally filed for all amended sequence data in the replacement “Sequence Listing XML,” which would include, e.g., paragraphs of specification or sheets of the drawings where a sequence is disclosed, identifying the sequence which is part of the replacement “Sequence Listing XML” (37 CFR 1.835(b)(4)); and
• (5) A statement that no new matter is introduced by the content of the replacement “Sequence Listing XML” (37 CFR 1.835(b)(5)).

If applicant recognizes a deficiency in a previously submitted “Sequence Listing XML” or otherwise chooses to amend a previously submitted “Sequence Listing XML,” a replacement “Sequence Listing XML” must be filed including all of the above-described items.

2414.04 Translation of “Sequence Listing XML” is Not an Amended “Sequence Listing XML” under 37 CFR 1.835(b) [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]

In accordance with 37 CFR 1.52(b)(1)(ii), any:

“application or proceeding and any amendments or corrections to the application (including any translation submitted pursuant to paragraph (d) of this section) or proceeding, except as provided for in § 1.69 and paragraph (d) of this section, must:

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(ii) Be in the English language or be accompanied by a translation of the application and a translation of any corrections or amendments into the English language together with a statement that the translation is accurate.”

Thus, any “Sequence Listing XML” that contains one or more qualifiers having a free text value that is language-dependent must comprise an “INSDQualifier_value” element containing text in the English language, otherwise a translation of the “Sequence Listing XML” is required.

The provisions of 37 CFR 1.835(d)(2) indicate that providing a translation of such language-dependent free text values into English in a new “Sequence Listing XML” does not constitute an added or amended “Sequence Listing XML” under 37 CFR 1.835(a) or 1.835(b).

2414.05 Notifications for Failure to Submit a “Sequence Listing XML” in an International Application under the PCT to be Searched by the United States International Searching Authority or Examined by International Preliminary Examination Authority [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]

Where an international application, filed under the PCT, contains a disclosure of nucleotide and/or amino acid sequences, PCT Rule 5.2 requires that the description shall include a sequence listing part of the description complying with the standard provided for in the Administrative Instructions (AI). In accordance with Section 208, any sequence listing, whether forming part of the international application or not forming part of the international application, shall comply with Annex C of the AI. Where applicant has not provided a sequence listing in accordance with Annex C of the AI and the USPTO acts as International Searching Authority (ISA) or International Preliminary Examining Authority (IPEA), the ISA/IPEA may invite applicant to furnish a sequence listing, with a late furnishing fee, under PCT Rule 13ter . This invitation will specify a time limit for a proper response. A proper response to such an invitation would include, the submission of a sequence listing accordance with Annex C of the AI, the late furnishing fee specified in 37 CFR 1.445(a)(5), and a statement to the effect that the sequence listing does not go beyond the disclosure of the international application as filed. If a sequence listing compliant with WIPO Standard ST.26 has not been furnished to the ISA/IPEA within the time limit set forth in the invitation, the ISA/IPEA will only search/examine the international application to the extent that a meaningful search or examination can be performed without the sequence listing.

See MPEP §§ 1823.02 and 1848.

2414.06 Amendment of a “Sequence Listing XML” in a Patent [R-01.2024]

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]

Where an amendment is made to a “Sequence Listing XML” contained in a patent, the correction must be made by way of an amendment to the “Sequence Listing XML” contained in a patent, pursuant to 1.835(b).