MPEP § 2411 — MPEP § 2411
Current through: 2022-07-01

2411-Examination Procedures 
 
 

 
 
 
 
 
 
 
 

 

 
 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
 
 

 
 
 
 
 
 
 
 
 
 
 

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 Manual of Patent Examining Procedure 

 Chapter 2400 

 Section 2411 
 

 
 
 
 
 
 2411 Examination Procedures [R-07.2015]

 
 37 CFR 1.809 Examination procedures. 

 
 (a) The examiner shall determine pursuant to § 1.104 in
 each application for patent, application for reissue patent or reexamination
 proceeding if a deposit is needed, and if needed, if a deposit actually made is
 acceptable for patent purposes. If a deposit is needed and has not been made or
 replaced or supplemented in accordance with these regulations, the examiner, where
 appropriate, shall reject the affected claims under the appropriate provision of
 35 U.S.C.
 112 , explaining why a deposit is needed and/or why a deposit
 actually made cannot be accepted.
 

 (b) The applicant for patent or patent owner shall reply to a
 rejection under paragraph (a) of this section by—
 
 (1) In the case of an applicant for patent, either making an
 acceptable original, replacement, or supplemental deposit, or assuring the
 Office in writing that an acceptable deposit will be made; or, in the case
 of a patent owner, requesting a certificate of correction of the patent
 which meets the terms of paragraphs (b) and (c) of §
 1.805 , or
 

 (2) Arguing why a deposit is not needed under the circumstances
 of the application or patent considered and/or why a deposit actually made
 should be accepted. Other replies to the examiner’s action shall be
 considered nonresponsive. The rejection will be repeated until either
 paragraph (b)(1) of this section is satisfied or the examiner is convinced
 that a deposit is not needed.
 

 
 

 (c) If an application for patent is otherwise in condition for
 allowance except for a needed deposit and the Office has received a written
 assurance that an acceptable deposit will be made, the Office may notify the
 applicant in a notice of allowability and set a three month period of time from
 the mailing date of the notice of allowability within which the deposit must be
 made in order to avoid abandonment. This time period is not extendable under
 §
 1.136 (see § 1.136(c) ). 
 

 (d) For each deposit made pursuant to these regulations, the
 specification shall contain:
 
 (1) The accession number for the deposit;

 (2) The date of the deposit;

 (3) A description of the deposited biological material
 sufficient to specifically identify it and to permit examination; and
 

 (4) The name and address of the depository.

 
 

 (e) Any amendment required by paragraphs (d)(1), (d)(2) or (d)(4) of
 this section must be filed before or with the payment of the issue fee (see
 § 1.312 ).
 

 
 

 37 CFR
 1.809 sets forth procedures that will be used by the examiner to
 address a deposit issue. The burden is initially on the Office to establish that access to
 a biological material is necessary for the satisfaction of the statutory requirements for
 patentability under 35
 U.S.C. 112 . Once the Office has met this burden, the burden shifts to
 the applicant or patent owner to demonstrate that access to such biological material either
 is not necessary, or is already available, or that a deposit of such material will be made
 in accordance with these regulations.
 

 
 2411.01 Rejections Based on Deposit Issue [R-07.2015]

 Under 37 CFR 1.809(a) , once the examiner has determined that access to
 a biological material is necessary, and there is no information that would support the
 conclusion that access is currently available in accordance with these regulations, the
 examiner should make an appropriate rejection under 35 U.S.C. 112 until such time as a
 deposit in accordance with these regulations is actually made or a written assurance is
 received in the patent application that such a deposit will be made upon an indication
 of allowability of the application. The examiner should clearly indicate the statutory
 basis for the rejection and the reasons that are relied upon by the examiner to conclude
 that the application does not comply with some requirement of 35 U.S.C. 112 .
 Although not exhaustive, the following grounds of rejection may be applicable in
 appropriate circumstances:
 

 
 (A) 35
 U.S.C. 112(a) , enablement requirement. 
 Rejection for lack of an enabling disclosure without access to a specific
 biological material. This ground of rejection should be accompanied by evidence of
 scientific reasoning to support the conclusion that a person skilled in the art
 could not make or use the invention defined in and commensurate with the claims
 without access to the specific biological material. See MPEP §
 2164.06(a) . 
 

 (B) 35
 U.S.C. 112(a) , written description requirement. 
 A rejection for lack of written description typically arises in the context that
 the application as filed does not contain a description to support an amendment to
 the specification or claims, although it can arise in the context of original
 claims. See MPEP §
 2163 et seq. An amendment to the claims that is not described in the
 application as filed would justify a rejection of the affected claims under
 35
 U.S.C. 112(a) . If an amendment is made to the application,
 other than the claims, that is not described in the application as filed, this
 would justify a rejection under 35 U.S.C. 112(a) and/or an
 objection under 35 U.S.C. 132 (prohibition against the introduction of new
 matter) and a requirement that the amendment be canceled.
 

 (C) 35
 U.S.C. 112(a) , best mode requirement. A
 rejection for lack of a best mode will be rare in the ex parte 
 examination process because it requires (1) a finding by the examiner that, at the
 time the application was filed, the inventor(s) knew of a specific material that
 was considered by the inventor(s) to be better than any other, and (2) if a best
 mode was contemplated at that time, that the inventor(s) concealed the best mode
 (accidentally or intentionally) by failing to adequately describe that best mode.
 See Chemcast Corp. v. Arco Industries Corp., 913 F.2d 923, 16
 USPQ2d 1033 (Fed. Cir. 1990). See also MPEP § 2165 et seq. 

 (D) 35
 U.S.C. 112(b) , requirement to particularly point out and
 distinctly claim invention. A rejection for indefiniteness, as
 applied to a deposit issue, requires the examiner to provide reasons why the terms
 in the claims and/or scope of the invention are unclear because of an incomplete
 or inaccurate description or the absence of a reference to a biological
 material.
 

 (E) 35
 U.S.C. 112(b) , requirement to claim what the inventor or
 a joint inventor regards as the invention. A rejection on the basis
 that the claims do not set forth the subject matter that the inventor or a joint
 inventor regards as the invention requires the citation of some evidence, not
 contained in the application as filed, to support the rejection. In re
 Prater, 415 F.2d 1393, 162 USPQ 541 (CCPA 1969). Any disagreement
 between the content of the application disclosure and the scope of the claims
 should be addressed under 35 U.S.C. 112(a) . See
 In re Ehrreich, 590 F.2d 902, 200 USPQ 504 (CCPA 1979). 
 

 
 Where a deposit is required to satisfy 35 U.S.C. 112 , a
 deposit must be made in accordance with these regulations. See 37 CFR 1.802 . A
 deposit accepted in any International Depositary Authority (IDA) under the Budapest
 Treaty shall be accepted for patent purposes if made under conditions which comply with
 37 CFR
 1.806 and 37 CFR 1.808(a) concerning term of
 deposit and permissible conditions on access once the patent is granted. 
 

 

 
 2411.02 Replies to Rejections Based on Deposit Issue [R-07.2015]

 Once a rejection under 35 U.S.C. 112 has been made by the
 examiner directed to the absence of access to a biological material, applicant may
 reply, pursuant to 37
 CFR 1.809(b)(1) , by either making an acceptable original,
 replacement, or supplemental deposit in accordance with these regulations, or assuring
 the Office in writing that an acceptable deposit will be made on or before the date of
 payment of the issue fee, or by submitting an argument of why a deposit is not required
 under the circumstances of the application being considered. Other replies to such a
 rejection by the examiner shall be considered nonresponsive and may result in
 abandonment of the application. The rejection will be repeated and made final until the
 requirements of 37 CFR
 1.809(b)(1) are satisfied or the examiner is convinced that a
 deposit is not required for the claimed subject matter. Once the rejection is made
 final, the requirements of 37 CFR 1.116 apply to further
 submissions. The written assurance will be accepted by the Office if it clearly states
 that an acceptable deposit will be made within the required time and under conditions
 which satisfy these rules. In the case that an acceptable written assurance has been
 made by the applicant, the rejection under 35 U.S.C. 112 directed to the
 absence of access to the biological material should be removed. 
 

 

 
 2411.03 Application in Condition for Allowance Except for Deposit [R-07.2015]

 As set forth in 37 CFR 1.809(c) , in the event that
 an application for patent is otherwise in condition for allowance except for a required
 deposit and the Office has received a written assurance that an acceptable deposit will
 be made, the Office may notify the applicant in a notice of allowability and set a three
 month period of time from the mailing date of the notice of allowability within which
 the deposit must be made in order to avoid abandonment. This time period is not
 extendable under 37
 CFR 1.136 (see 37 CFR 1.136(c) ). Failure to make
 the needed deposit in accordance with this requirement will be considered a failure to
 prosecute the application under 35 U.S.C. 133 and result in
 abandonment of the application. 
 

 Once the deposit has been made, information regarding the deposit, such
 as the name and address of the depository, the accession number and the date of the
 deposit, that is to be added to the specification must be added by means of filing an
 amendment under the provisions of 37 CFR 1.312 . Such an amendment must
 be filed before or with the payment of the issue fee. Therefore, applicants need to make
 any necessary deposit of biological material well prior to payment of the issue fee such
 that the accession number is received with sufficient time remaining to amend the
 specification as required by 37 CFR 1.809(d) on or before the
 date the issue fee is paid. See 37 CFR 1.809(e) .
 

 

 
 2411.04 [Reserved]

 

 
 2411.05 Content of Application with Respect to Deposited Material [R-08.2012]

 37 CFR
 1.809(d) sets forth the requirements for the content of the
 specification with respect to a deposited biological material. Specifically, the
 specification shall contain the accession number for the deposit, the date of the
 deposit, the name and address of the depository, and a description of the deposited
 biological material sufficient to specifically identify it and to permit examination.
 The description also must be sufficient to permit verification that the deposited
 biological material is in fact that disclosed. Once the patent issues, the description
 must be sufficient to aid in the resolution of questions of infringement. As a general
 rule, the more information that is provided about a particular deposited biological
 material, the better the examiner will be able to compare the identity and
 characteristics of the deposited biological material with the prior art.
 

 

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 2401-Introduction 

 2402-The Deposit Rules 

 2403-Deposit of Biological Material 
 2403.01-Material Capable of Self- Replication 

 2403.02-Plant Material 

 
 

 2404-Need or Opportunity to Make a Deposit 
 2404.01-Biological Material That Is Known and Readily Available to the Public 

 2404.02-Biological Material That Can Be Made or Isolated Without Undue Experimentation 

 2404.03-Reference to a Deposit in the Specification 

 
 

 2405-Acceptable Depository 

 2406-Time of Making an Original Deposit 
 2406.01-Description in Application Specification 

 2406.02-Deposit After Filing Date - Corroboration 

 2406.03-Possible Loss of U.S. Filing Date in Other Countries 

 
 

 2407-Replacement or Supplement of Deposit 
 2407.01-In a Pending Application 

 2407.02-After a Patent Has Issued 

 2407.03-Failure to Replace 

 2407.04-Treatment of Replacement 

 2407.05-Exemption From Replacement 

 2407.06-Replacement May Not Be Recognized 

 
 

 2408-Term of Deposit 

 2409-Viability of Deposit 

 2410-Furnishing of Samples 
 2410.01-Conditions of Deposit 

 2410.02-Certification of Statement of Availability of Deposit 

 
 

 2411-Examination Procedures 
 2411.01-Rejections Based on Deposit Issue 

 2411.02-Replies to Rejections Based on Deposit Issue 

 2411.03-Application in Condition for Allowance Except for Deposit 

 2411.04-[Reserved] 

 2411.05-Content of Application with Respect to Deposited Material 

 
 

 2412-The Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence Disclosures to Include
 a Sequence Listing in XML file format 
 2412.01-Overview of the Sequence Rules 

 2412.02-Definition of “Sequence Listing XML” 
 2412.02(a)-“Enumeration of its residues” 

 
 

 2412.03-Nucleotides and Amino Acids Included and Excluded From a “Sequence Listing XML” 
 2412.03(a)-“Specifically Defined” 

 2412.03(b)-“Amino Acid” 

 2412.03(c)-“Modified Amino Acid” 

 2412.03(d)-“Nucleotide” 

 2412.03(e)-“Modified Nucleotide” 

 
 

 2412.04-Use of Sequence Identifiers to Denote Sequences Disclosed in the Description, Drawings or Claims 

 2412.05-Representation and Symbols for Nucleotide and/or Amino Acid Sequences 
 2412.05(a)-Use of Sequentially Numbered Sequence Identifiers in the “Sequence Listing XML” 

 2412.05(b)-Representation and Symbols of Nucleotide Sequence Data 

 2412.05(c)-Representation and Inclusion of Variants 

 2412.05(d)-Representation and Symbols of Amino Acid Sequence Data 

 2412.05(e)-Presentation of Special Situations 

 
 

 2412.06-The Requirement for Exclusive Conformance; Sequences Presented in Drawing Figures 

 2412.07-Examination of Patent Applications Claiming Large Numbers of Nucleotide Sequences 

 
 

 2413-Content of a “Sequence Listing XML” and Form and Format of the “Sequence Listing XML” File 
 2413.01-Parts of the “Sequence Listing XML” 
 2413.01(a)-The “Sequence Listing XML” is a Single File Encoded Using Unicode UTF-8 

 2413.01(b)-The “Sequence Listing XML” Must Be Valid According To the DTD 

 2413.01(c)-The “Sequence Listing XML” Must Contain an XML Declaration 

 2413.01(d)-The “Sequence Listing XML” Must Contain a DOCTYPE Declaration 

 2413.01(e)-The “Sequence Listing XML” Must Contain a Root Element 

 2413.01(f)-The “Sequence Listing XML” Must Contain a General Information Part 

 2413.01(g)-The “Sequence Listing XML” Must Contain a Sequence Data Part 

 2413.01(h)-Language Dependent Free Text Qualifier Values in the English Language 

 2413.01(i)-Title Element in “Sequence Listing XML” 

 
 

 2413.02-Form and Format of the XML file containing the “Sequence Listing XML” 

 2413.03-How to Submit the “Sequence Listing XML” 

 2413.04-Requirements Regarding Incorporation By Reference of the “Sequence Listing XML” 

 2413.05-Presumptions Regarding Compliance 

 
 

 2414-Notification of a Failure to Comply with Sequence Listing Requirements and Amendments Relating to “Sequence Listing XML” Files
 Under 37 CFR 1.835 
 2414.01-Issuance of a Notice Relating to the Requirements For Patent Applications Containing Nucleotide and/or Amino Acid Sequence
 Disclosures 

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

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

 2414.04-Translation of “Sequence Listing XML” is Not an Amended “Sequence Listing XML” under 37 CFR 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 

 2414.06-Amendment of a “Sequence Listing XML” in a Patent 

 
 

 2415-Applicability date of “Sequence Listing XML” Requirements to Applications Based on Filing Date of Application and Procedures
 for Failure to Submit Correct Format of Sequence Listing 
 2415.01-Determining if a “Sequence Listing XML” Must be Submitted 

 2415.02-Provisional Applications Containing Disclosures of Nucleotides and/or Amino Acids, Compliance with 37 CFR 1.831-1.834 

 2415.03-Improper Submissions of “Sequence Listing” under 1.821(c) When a “Sequence Listing XML” was Required 

 
 

 2416-Form Paragraphs 

 2417-Helpful Hints for Sequence Rules Compliance under WIPO Standard ST.26 

 2418-WIPO Sequence Tool 

 2419-Publishing of Patent Grants and Patent Application Publications with a “Sequence Listing XML” 
 2419.01-Patent Grants and Patent Application Publications Containing a Non-Lengthy “Sequence Listing XML” 

 2419.02-Patent Grants and Patent Application Publications Containing a Lengthy “Sequence Listing XML” 

 2419.03-Patent Grants and Patent Application Publications Containing a “Sequence Listing XML” of 1GB or Larger 

 
 

 2420-The Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence Disclosures under World
 Intellectual Property Office Standard ST.25 (WIPO ST.25) - the Sequence Rules 

 2421-Overview of the Sequence Rules under WIPO ST.25 
 2421.01-Definition of “Sequence Listing” and Computer Readable Form (CRF) 

 2421.02-Summary of the Requirements of the Sequence Rules 

 2421.03-Notification of a Failure to Comply 

 2421.04-[Reserved] 

 
 

 2422-Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications Subject to WIPO ST.25 
 2422.01-Nucleotide and/or Amino Acids Disclosures Requiring a “Sequence Listing” 

 2422.02-The Requirement for Exclusive Conformance; Sequences Presented in Drawing Figures 

 2422.03-Sequence Listing Submission 

 2422.03(a)-“Sequence Listing” Submitted as ASCII Plain Text Files 

 2422.04-The Requirement for a Computer Readable Copy of the “Sequence Listing” 

 2422.05-[Reserved] 

 2422.06-Requirement for Statement Regarding Information Contained in the “Sequence Listing” and Separate Computer Readable Form 

 2422.07-Requirements for Compliance and Consequences of Non-Compliance 

 2422.08-Presumptions Regarding Compliance 

 2422.09-[Reserved] 

 
 

 2423-Symbols and Format To Be Used for Nucleotide and/or Amino Acid Sequence Data for WIPO ST.25 
 2423.01-Format and Symbols To Be Used in a “Sequence Listing” 

 2423.02-Depiction of Coding Regions 

 2423.03-Presentation and Numbering of Sequences 

 
 

 2424-Requirements for Content of a “Sequence Listing” Part of the Specification under WIPO ST.25. 
 2424.01-Informational Requirements for the “Sequence Listing” 

 2424.02-“Sequence Listing” Numeric Identifiers 

 2424.03-Additional Miscellaneous Requirements 

 
 

 2425-Form and Format for a Nucleotide and/or Amino Acid Sequence Submission as an ASCII Plain Text File under WIPO ST.25 

 2426-Amendments to Add or Replace a “Sequence Listing” and CRF Copy Thereof Subject to WIPO ST. 25 

 2427-Form Paragraphs for Applications Subject to WIPO ST.25 

 2428-Sample Statements under WIPO ST.25 

 2429-Helpful Hints for Sequence Rules Compliance under WIPO ST.25 

 2430-PatentIn Information 

 2431-Sample “Sequence Listing” under WIPO ST.25 

 2432-[Reserved] 

 2433-Box Sequence; Hand Delivery of a “Sequence Listing” and Computer Readable Forms 

 2434-Examination of Patent Applications Claiming Large Numbers of Nucleotide Sequences 

 2435-Publishing of Patents and Patent Application Publications with a Lengthy “Sequence Listing” 

 

 

 
 

 
 
 

 
 

 

 
 
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 Last Modified: 
 
 03/09/2026 20:49:35