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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

Current Sequence Listing Process for Nucleic Acids and Polypeptides

Dave Nguyen

Technology Center 1600

current sequence listing process
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.
electronic sequence listing supply chain
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

opap office of patent application processing process map
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

slide5

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

slide6

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

sequence listing data flow processing on abss
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

guidance on common issues

Guidance on Common Issues

Joseph Woitach

Technology Center 1600

what sequence rules apply
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
common compliance issues
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>
common compliance issues1
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

common compliance issues2
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
slide15

Sequence Listing Examples

Example 1

Example 2

common compliance issues3
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))
common compliance issues4
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
filing option
Filing option
  • Electronic Filing System (EFS) - Legal Framework:

http://www.uspto.gov/patents/process/file/efs/guidance/New_legal_framework.jsp

filing option1
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)
slide20
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”

slide21
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.

slide22
FAQs
  • Do genes identified by gene accession numbers in the specification need to comply with the sequence rule requirements?
slide23
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.

slide24
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.

q and a
Q and A

Thank You!

Dave Nguyen

TC 1600 Management

Dave.Nguyen@uspto.gov

571-272-0731

Joseph Woitach

TC 1600 Management

Joseph.Woitach@uspto.gov

571-272-0739