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Current Sequence Listing Process for Nucleic Acids and Polypeptides

Current Sequence Listing Process for Nucleic Acids and Polypeptides. Dave Nguyen Technology Center 1600. Current Sequence Listing Process. Technology Center 1600 (TC 1600) is a primary stakeholder in the current sequence listing process and is taking a major role in

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Current Sequence Listing Process for Nucleic Acids and Polypeptides

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  1. Current Sequence Listing Process for Nucleic Acids and Polypeptides Dave Nguyen Technology Center 1600

  2. Current Sequence Listing Process Technology Center 1600 (TC 1600) is a primary stakeholder in the current sequence listing process and is taking a major role in • Conducting Automation Workgroup Meetings (AWG) on a biweekly basis to sustain the USPTO business function of performing quality searching of molecular sequences by TC 1600 • Sustaining the PTO's best business practices for processing genetic sequences claimed in patent applications • Continuing to improve our business process for maintaining the infrastructure for processing molecular sequence listings and searching genetic sequences from applicant submissions and commercial databases of published sequence listings.

  3. Electronic Sequence Listing Supply Chain EAST/WEST Search System Automatic load App FT/ Pat FT (Search System) Interface for public & applicants to access IFW & SCORE databases Scan the application including Sequence listing. PAIR 1. Paper --> TIF 2. CRF --> TXT and paper Manually load Sequence listing VALIDATION Manually try to fix formality errors Run the files through CRF or SCORE Yes CRF/SCORE passed? No fixable errors? Yes No Not in Compliance Search Environment Ask for Revalidation Automatically load Sequence listing Raw sequence listing Patent & PG PUB Can access Patent & PG Pub (Pre-Grant Publications) w/ sequence listings but cannot search sequence listing NCBI - COTS Converts pep & seq files to ASN.1 records CRF/SCORE creates up to 3 files: .raw (original data) .pep (protein data in IG format) .seq (nucleic data in IG format) Manually ftp the files to ABSS /crf/work/ Publication ASN.1 files

  4. OPAP (Office of Patent Application Processing) Process Map Mail/CRF Processing; Palm Initialization; Indexing and Scanning (OPAP) New Application Received (OPAP) Review (TC 1600) NO CRF, IFW (OPAP) CRF Needed RETURN to OPAP CRF Needed 2nd round of CRF 1st CRF accepted PLRC: Load CRF in SCORE STIC:CRF review (1st pass) CRF review (2nd pass) Export to ABSS TC1600 STIC: ABSS search 2nd CRF accepted 2nd CRF rejected CRF rejected Notice Mailed OPAP No reply to form No reply STIC:CRF review Export to ABSS 1st CRF accepted ABN

  5. Office records CRF (Good/Bad) statement as CRFE or CRFD Office (SCORE/STIC) processes New Sequence listing Applicant prepares New Sequence listing New Application Filed in OPAP New Pat. Application OPAP CRF Good Info. (CRFE) entered in System (PALM), Application sent for examination CRF Bad OPAP sends Sequence Compliance Letter and CRFD to applicant

  6. OPAP OPAP sends Sequence Compliance Letter and CRFD to applicant New Application in TC1600 (Status 20 or 25) New Pat. Application in TC1600 TC1600 Office records CRF (Good/Bad) statement as CRFE or CRFD CRF Good Info. (CRFE) entered in System (PALM), Application sent for examination Office (SCORE/STIC) processes New Sequence listing CRF Bad sequence disclosed but NO CRF Applicant prepares New Sequence listing

  7. SCORE (Supplemental Complex Repository for Examiners) Content Web App Internet Management Server Server 1 Edge ( LINUX ) HTTP ( LINUX ) (***) Server Server Load Balancers Web Servers DMZ SCORE AIS Oracle ` Database OIPE LOAD PTONET Private / Public PAIR Users Rhino 1 STIC Review Doc 1 Web App Edge ( LINUX ) HTTP ( LINUX ) Server Server Server (***) ScoreAccessWeb Load Balancers Web Servers z Duncan ScoreWSWeb ` eDAN Users ScoreXMLWeb Doc 3 Content Rhino 2 Management ` SCORE Imports / Exports Server 2 (***) WebSphere 6 . 1 . 0 . 5 STIC STIC examiners Export / Export Export Import Import ` SCORE ` OIPE Load users import / export server SCORE Tech ABSS SI - INTL Duncan RTIS NCBI System Architecture Diagram

  8. Sequence Listing Data Flow: Processing on ABSS ABSS (Automated Biotechnology Sequence Search System) Applicant mails in patent application documents and media with files Application docs are separated from the media with files • media with files Manually copy files from media to local storage Manually try to fix formality errors Manually run the files through CRF or SCORE yes CRF/SCORE passed? fixable errors? no yes no CRF/SCORE creates up to 3 files: .raw (original data) .pep (protein data in IG format) .seq (nucleic data in IG format) Not in Compliance Copy the .pep and .seq files to ABSS

  9. What Sequence Rules Apply? • US Rules - 37 CFR 1.821-825 • Original rules -- 55 Fed. Reg. 18230 (May 1, 1990) (effective October 1, 1990) • Amended rules -- 63 Fed. Reg. 29620 (June 1 1998) (effective July 1, 1998). • International Rules - WIPO Standard ST.25, effective July 1, 1998 • http://www.wipo.int/standards/en/pdf/03-25-01.pdf

  10. Common Compliance Issues • The organism of each sequence must be defined at heading <213> (Organism) (37 CFR 1.822(b)) • Genus/species or “artificial sequence” or “unknown” must be used at heading <213> • Use Genus/species if at all possible • If it is a human sequence, for example, use Homo sapiens • Depends on source of the actual sequence • If artificial sequence or unknown, further definition is required at headings <220> - <223>

  11. Common Compliance Issues Artificial Sequence at heading <213>? Explain why the sequence is artificial (not naturally-occurring) If a portion of the sequence was derived from a natural source, e.g., a bacterial gene, then provide the source and explain how the sequence differs from the naturally occurring source material

  12. Common Compliance Issues Unknown • Use if there is no scientific name disclosed or only a partial scientific name, e.g., Bacillus sp. • Use if only the source of the organism is disclosed, e.g., “soil sample from Pittsburgh” • Example sequence listing section: • <213> Unknown • <223> Bacillus species

  13. Sequence Listing Examples Example 1 Example 2

  14. Common compliance issues • Sequences having a gap or gaps must be displayed as separate sequences in the Sequence Listing. For example, if a chemical moiety has several strands of protein attached to it, each protein sequence should appear in the Sequence Listing separately. The chemical moiety should NOT be shown (37 CFR 1.822(e)) • Sequences made of fragments of other sequences must be displayed as separate sequences in the Sequence Listing (37 CFR 1.822(e))

  15. Common compliance issues • Sequence Listings are often non-compliant because of minor formatting issues- Use of PatentIn minimizes such occurrences • PatentIn’s “Copy to Disk” function results in loss of hard returns on the CRF - Regenerate the Sequence Listing and use Windows Explorer to copy the text file to the CRF

  16. Filing option • Electronic Filing System (EFS) - Legal Framework: http://www.uspto.gov/patents/process/file/efs/guidance/New_legal_framework.jsp

  17. Filing option • Electronic Filing System (EFS) • Learn about EFS at this website: http://www.uspto.gov/ebc/efs_help.html • Add the sequence listing to your EFS-Web submission • No paper copy or statement needed for initial filing • If filing in response to a Notice to Comply a statement that there is no new matter is needed. • Sequence listing is automatically processed by SCORE and immediately placed in ABSS (if compliant)

  18. FAQs Why does my CRF has an error on Field Code <213>? Numeric identifier <213> is something other than “Scientific name, i.e., Genus/species, Unknown or Artificial Sequence”

  19. FAQs Why does my CRF has an error on Field Code <223>? A major reason for noncompliance is that the information provided in field <223> to explain an artificial or unknown organism is improper. Solution: Indicating what the artificial sequences are is acceptable, e.g., primer, aptamer, linker, adapter, cloning vector, expression vector, siRNA, probe, expressed sequence tag, etc. Chimeric constructs should identify sources of the parts, etc.

  20. FAQs • Do genes identified by gene accession numbers in the specification need to comply with the sequence rule requirements?

  21. FAQs No, they are not considered disclosures of Sequences. When accession numbers appear in claims, they may raise an issue of improper incorporation of essential material by reference. If the sequences need to be brought into the disclosure then they must comply with the sequence rules.

  22. FAQs A sequence listing was prepared via PatentIn. Why did the sequence listing submission get rejected by the Patent Office? The USPTO uses an in-house verification software for validation. In addition, information provided in field <223> for artificial sequence or unknown organism must be manually verified.

  23. Q and A Thank You Dave Nguyen TC 1600 Management Dave.Nguyen@uspto.gov 571-272-0731

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