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2422.03 The Requirements for a Sequence Listing and Sequence Identifiers; Sequences Embed- ded in Application Text; Vari- ants of a Presented Sequence - 2400 Biotechnology
2422.03 The Requirements for a Sequence Listing and Sequence Identifiers; Sequences Embed- ded in Application Text; Vari- ants of a Presented Sequence
37 CFR 1.821(c) requires that applications containing nucleotide and/or amino acid sequences that fall within the above definitions, contain, as a separate part of the disclosure on paper or compact disc, a disclosure of the nucleotide and/or amino acid sequences, and associated information, using the format and symbols that are set forth in 37 CFR 1.822 and 37 CFR 1.823. This separate part of the disclosure is referred to as the "Sequence Listing." The "Sequence Listing" submitted pursuant to 37 CFR 1.821(c), whether on paper or compact disc, is the official copy of the "Sequence Listing."
37 CFR 1.821(c) requires that each sequence disclosed in the application appear separately in the "Sequence Listing," with each sequence further being assigned a sequence identification number, referred to as "SEQ ID NO." The sequence identifiers must begin with 1 and increase sequentially by integers. The requirement for sequence identification numbers, at a minimum, requires that each sequence be assigned a different number for purposes of identification. However, where practical and for ease of reference, sequences should be presented in the separate part of the application in numerical order and in the order in which they are discussed in the application.
If submitted on paper, the "Sequence Listing" is a separate part of the disclosure which must begin on a new page within the specification. A plurality of sequences may, if feasible, be presented on a single page; the separate presentation of both nucleotide and amino acid sequences on the same page is also permitted.
If the "Sequence Listing" is submitted on compact disc, the specification must contain an incorporation by reference of the material on the compact disc in a separate paragraph, identifying each compact disc by the names of the files contained on each of the compact discs, their date of creation and their sizes in bytes ( 37 CFR 1.52(e)). The total number of compact discs including duplicates and the files on each compact disc shall be specified ( 37 CFR 1.77(b)(4)). The compact disc used to submit the sequence listing may also contain table information if the table has more than 50 pages of text. See 37 CFR 1.823(a)(2) and 1.52(e)(1)(iii). The compact disc and duplicate copy must be labeled "Copy 1" and "Copy 2," respectively, and a statement stating that the copies are identical must be included. If the two compact discs are not identical, the Office will use the disc labeled "Copy 1" for further processing ( 37 CFR 1.52(e)(4)). See also MPEP § 608.05.
The compact disc submitted under 37 CFR 1.821(c) may, if it contains no tables, be identical to the computer readable form (CRF) submitted under 37 CFR 1.821(e) and 37 CFR 1.824, if that CRF is submitted on a compact disc. Even if the compact discs submitted under both 37 CFR 1.821(c) and (e) are identical, each compact disc submitted under 37 CFR 1.821(c) must be submitted in duplicate, in addition to the CRF under 37 CFR 1.821(e).
The requirement for compliance in 37 CFR 1.821(c) is directed to "disclosures of nucleotide and/or amino acid sequences." (Emphasis added.) All sequence information, whether claimed or not, that meets the length thresholds in 37 CFR 1.821(a) is subject to the rules. The goal of the Office is to build a comprehensive database that can be used for, inter alia, the purpose of assessing the prior art. It is therefore essential that all sequence information, whether only disclosed or also claimed, be included in the database. In those instances in which prior art sequences are only referred to in a given application by name and a publication or accession reference, they need not be included as part of the "Sequence Listing," unless an examiner considers the referred- to sequence to be "essential material," per MPEP § 608.01(p). However, if the applicant presents the sequence as a string of particular bases or amino acids, it is necessary to include the sequence in the "Sequence Listing," regardless of whether the applicant considers the sequence to be prior art. In general, any sequence that is disclosed and/or claimed as a sequence, i.e., as a string of particular bases or amino acids, and that otherwise meets the criteria of 37 CFR 1.821(a), must be set forth in the "Sequence Listing."
It is generally acceptable to present a single, general sequence in accordance with the sequence rules and to discuss and/or claim variants of that general sequence without presenting each variant as a separate sequence in the "Sequence Listing." By way of example only, the following types of sequence disclosures would be treated as noted herein by the Office. With respect to "conservatively modified variants thereof" of a sequence, the sequences may be described as SEQ ID NO:X and "conservatively modified variants thereof," if desired. With respect to a sequence that "may be deleted at the C-terminus by 1, 2, 3, 4, or 5 residues," all of the implied variations do not need to be included in the "Sequence Listing." If such a situation were encompassed by the rules, it would introduce far too much complexity into the "Sequence Listing" and the Office's database. The possible mathematical variations that could result from this type of language could reasonably require a "Sequence Listing" that would be thousands of pages in length. In this latter example, only the undeleted sequence needs to be included in the "Sequence Listing," and the sequences may be described as SEQ ID NO:X from which deletions have been made at the C-terminus by 1, 2, 3, 4, or 5 residues. The Office's database will only contain the undeleted sequence.
37 CFR 1.821(d) requires the use of the assigned sequence identifier in all instances where the description or claims of a patent application discuss sequences regardless of whether a given sequence is also embedded in the text of the description or claims of an application. This requirement is also intended to permit references, in both the description and claims, to sequences set forth in the "Sequence Listing" by the use of assigned sequence identifiers without repeating the sequence in the text of the description or claims. Sequence identifiers can also be used to discuss and/or claim parts or fragments of a properly presented sequence. For example, language such as "residues 14 to 243 of SEQ ID NO:23" is permissible and the fragment need not be separately presented in the "Sequence Listing." Where a sequence is embedded in the text of an application, it must be presented in a manner that complies with the requirements of the sequence rules.
The rules do not alter, in any way, the requirements of 35 U.S.C. 112. The implementation of the rules has had no effect on disclosure and/or claiming requirements. The rules, in general, or the use of sequence identifiers throughout the specification and claims, specifically, should not raise any issues under 35 U.S.C. 112, first or second paragraphs. The use of sequence identification numbers (SEQ ID NO:X) only provides a shorthand way for applicants to discuss and claim their inventions. These identification numbers do not in any way restrict the manner in which an invention can be claimed.
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