Sequence Listings Webinar Suzannah K. Sundby Carl Oppedahl

Suzannah K. Sundby Canady + Lortz LLP Sequence Listings Webinar January 9, 2018 – Updated Version Carl Oppedahl Oppedahl Patent Law Firm LLC DISCLAIMER These materials and views expressed today reflect only the personal views of the author and do not necessarily represent the views of other members and clients of the author’s organizations. These materials are public information and have been prepared solely for educational purposes to contribute to the understanding of U.S. intellectual property law. While every attempt was made to ensure that these materials are accurate, errors or omissions may be contained therein, for which any liability is disclaimed. These materials and views are not a source of legal advice and do not establish any form of attorney-client relationship with the authors and their law firms. Why are some sequence errors not identified by Checker? Is “SEQ ID NO” required before sequences in Specifications? Do you recommend using the PatentIn Software? How do you correct sequence listing errors in PCTs? What about the new WIPO ST.26 Standard? Is Checker worthwhile? How can I easily edit sequence listings generated by others? Can I use other software to generate sequence listings? How do I file sequence listings using EFS-Web and ePCT? How long does it take the USPTO to review and approve? Any risk TYFNIL of using certain sequence descriptors? Help! IT locked down my computer… what do I do? Any sequence listing tips? Why Practitioners Should Know and Do Usually lack of time to send to outside vendors Last minute changes to applications (apps) containing sequences (seqs) Particularly, changes to claims Not hostage to staff/vendors, overtime, etc. Ultimate responsibility/review More time efficient and less expensive to clients Will need to understand minimum requirements, and differences when new ST.26 and how such is automatically converted (what is, what isn’t) Avoid looking really stupid and incompetent Text file (SL as text file and CRF) = ASCII format ASCII ANSI = Plain Text (*.txt) 4 Agenda Sequence Listing (SL) Rules and Requirements Generating a SL using PatentIn Checking with Checker Modifying an existing SL Using a PatentIn Project File Downloading from WIPO and modifying the text file Submitting a SL EFS-Web, ePCT, and digital media Responding to Notices Tips and Tricks 5 Sequence Listing Rules 37 CFR 1.821-1.825 US Applications – Utility and 371s PCT Applications 37 CFR 1.821 1.821(b) – Apps that have seqs as defined in (a) must conform with 1.821-1.825 1.821(a) (MPEP 2421.02) Unbranched amino acid (aa) seqs of ≥4 aa Unbranched nucleotide (nt) seqs of ≥10 nt Excluded sequences = branched seqs and seqs <4 specifically defined aa or <10 specifically defined nt "Specifically defined" means aa other than "Xaa" and nt bases other than "n" as defined in the WIPO Standard ST.25, including Tables 1-6 in Appendix 2 (MPEP 2422) 7 37 CFR 1.821(a) Nucleotides = those that can be represented using the symbols set forth in Table 1 Modified nts may be described as set forth Table 2, but not explicitly shown in the seq itself Amino acids = L-amino acids listed in Table 3 D-amino acids are not intended to be embraced by the aa defn Seqs containing post-translationally modified aa’s may be described as the aa seq that is initially translated using symbols of Table 3 with the modified positions described (see Table 4) Any peptide or protein (p/p) that can be expressed as a seq using the symbols in Table 3 + description in the Feature section for, e.g., modified linkages, cross links and end caps, non-peptidyl bonds, etc. 8 D-Amino Acids PPT by Bob Wax entitled “Sequence Compliance Soup to Nuts” states: Not according to USPTO’s current “Amino acid sequences unwritten policy containing even one D- amino acid are excluded Save your breath and time from the sequence rules (37 Include seqs containing D-amino acids CFR 1.821(a)(2))”. See Slide 17. in SLs with Feature Data/Name “MISC_FEATURE” indicating the D- amino acid residues 9 37 CFR 1.821(c) Such apps must contain, as a separate part of the disclosure, a paper copy or CD copy (aka SL*) in accordance with 1.822-1.823 * Some parts of MPEP are confusing due to the EFS-Web Legal Framework, so careful of term usage in MPEP and elsewhere. See, e.g., MPEP 2421.01. MPEP 2422.03(a) states that the text file submitted via EFS-Web may serve as both the “paper copy” and the “CRF” For the purposes of this webinar: Sequence Listing (SL) The “Official” SL, i.e., legally recognized SL, whether a text copy or a paper copy Assume SL is text copy, unless indicated otherwise Paper copy = Actual paper or PDF file of SL CRF = Computer Readable Form of the paper copy as the SL Text copy = SL as ASCII text filed via EFS-Web CD copy = SL submitted on physical media, e.g., CDRom. This is NOT a “text copy”. Difference from “text copy” must submit 3 physical carriers labeled “Copy 1”, “Copy 2”, and “CRF” 10 37 CFR 1.821(d) Where spec, claims, or drawings discuss a seq provided in an SL, “reference must be made to the sequence by use of the sequence identifier, preceded by "SEQ ID NO:" in the text of the description or claims, even if the sequence is also embedded in the text of the description or claims of the patent application” Sequence identifier = sequence number “preceded by” refers to placing “SEQ ID NO:” before the seq #, e.g., SEQ ID NO: 2. Important to use “NO” instead of “No” and a colon instead of a period, i.e., use “NO:” not “No:”, “No.”, or “NO.” If seq is in a figure, can provide SEQ ID in description of the drawings or the figure itself (MPEP 2422.02) I put SEQ IDs in parentheticals after the given seq when embedded in the spec and in the description of the drawings when in the figures 11 37 CFR 1.821(e) If the SL is a paper copy or a CD copy, then a CRF in accordance with 1.824 must be submitted Again, note difference between “CD copy” and “text copy” The CRF will not form a legally recognized part of the patent application itself If the CRF is to be identical to a prior CRF of another app of the applicant on file in the USPTO, one can submit a Transfer Request (more later) Recall, if a CRF, then the SL is a paper copy (or CD copy); if SL is a paper copy (or CD copy), then must submit a CRF 12 37 CFR 1.821(f) When submitting a CRF, must submit a Sequence Listing Statement that "the sequence listing information recorded in computer readable form is identical to the written (paper copy or CD copy) sequence listing“ I’ve always said: In accordance with 37 C.F.R. 1.821, the undersigned hereby states that the content of the paper copy of the Sequence Listing and the Computer Readable Form submitted herewith are the same. But don’t use anymore because I submit “text copy” SLs via EFS-Web See 1.824 for form and format of submitting CRFs and SLs as text files on physical data carriers rather than via EFS-Web 13 If 1.821(b)-(f) not satisfied at app filing… 1.821(g) – Provides time to comply upon receipt of a Notice for US utility apps and US 371 national phase entries 1.821(h) – For PCT apps, where US is the ISA or IPEA, provides time to provide CRF for search purposes Usually receive a Notice If CRF is not provided timely, then search/exam will proceed without to the extent possible Note: New Fee for Late Furnishing Fee under PCT Rule 13ter ($300) 14 37 CFR 1.822 – Symbols and Format 1.822(a) – Must use symbols and format set forth in ¶¶ (b)-(e) 1.822(b) For nt and aa, must use codes according to Tables 1 and 3 Can show modified nt and aa in seqs of SL if provided in Tables 2 and 4 Otherwise, must use “n” or “Xaa” with a description in the Feature section Preferably using feature keys listed in Tables 5 or 6 1.822(e) Seqs w gaps must be provided as separate seqs A seq comprising noncontiguous segments of a larger seq or segments from different seqs shall be presented as a separate seq 15 37 CFR 1.822(c) - Nucleotides Lower case letters One letter code (Table 1) Bases of a seq (including introns) provided in groups of 10 except designated coding regions, which are then provided as groups of 3 (i.e., codons) AAs encoded by codons are provided immediately below Max of 16 codons or 60 bases per line, with a space provided between each codon or group of 10 bases Presented, only by a single strand, in the 5’ to 3’ direction, from left to right Except for circular seqs, nts are enumerated beginning with the first base of the seq as number 1 If circular seq, first nt is applicant’s option 16 37 CFR 1.822(d) – Amino Acids Three letter abbreviations, with first letter capitalized Max of 16 aa per line, with a space provided between each aa N-terminal to C-terminal direction, from left to right, without providing the amino and carboxy groups Enumeration may start at the first aa of the first mature protein, with the number 1 If pre-, pro-, prepro-, or signal seq, provided before the mature protein, then enumerate w negative numbers, counting backwards starting with the aa next to number 1 Otherwise, enumerate w first aa as number 1 and marking below the seq every 5 aa If circular seq, first aa is applicant’s option If internal terminator symbols, e.g., “Ter”, “*”, or “.”, must provide as separate seqs 17 37 CFR 1.823 – Paper Copy as SL Must start on a new page and be titled "Sequence Listing" Pages are numbered independently of the other parts of the app No more than 66 lines per page No more than 72 characters per line May not include other material that is not part of SL Should use a

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