Administrative Instructions under the Patent Cooperation Treaty
ANNEX C32
INSTRUCTIONS RELATING TO THE PRESENTATION
OF NUCLEOTIDE AND AMINO ACID SEQUENCE LISTINGS IN INTERNATIONAL PATENT APPLICATIONS UNDER THE PCT
INTRODUCTION
1. In accordance with Rule 5.2(a), where the international application contains disclosure of nucleotide and/or amino acid sequences that, pursuant to the Administrative Instructions, are required to be included in a sequence listing, the description shall include a sequence listing part of the description complying with the standard provided for in the Administrative Instructions. In accordance with Section 208, any sequence listing, whether forming part of the international application or not forming part of the international application, shall comply with Annex C (this Annex).
2. This Annex provides the Instructions referred to above in relation to the filing and processing of sequence listings, whether forming part of an international applications or not forming part of an international application.
DEFINITIONS
3. For the purposes of these Instructions:
(a) the expressions "sequence listing", "nucleotide" and "amino acid" have the same meaning as in WIPO Standard ST.26;
(b) the expression "sequence listing forming part of the international application" means a sequence listing contained in the international application as filed, including any sequence listing which:
(i) is included in the international application under Rule 20.5(b) or (c) or Rule 20.5bis(b) or (c),
(ii) is considered to have been contained in the international application under Rule 20.6(b),
(iii) has been corrected under Rule 26, rectified under Rule 91 or amended under Article 34(2)(b), or
(iv) is included in the international application by way of an amendment under Article 34(2)(b) of the description in relation to sequences contained in the international application as filed but not originally included in a sequence listing;
(c) the expression "sequence listing not forming part of the international application" means a sequence listing that does not form part of the international application but is furnished for the purposes of the international search or international preliminary examination.
RELATIONSHIP WITH WIPO STANDARD ST.26
4. The sequence listing part of the description shall comply with WIPO Standard ST.26. Subject to the specific requirements set out in this Annex, that Standard shall apply to any nucleotide or amino acid sequence disclosure in an international application, notably with regard to:
(a) whether such disclosure is to be included in a sequence listing;
(b) the manner in which disclosures are to be presented;
(c) the qualifiers for which "free text" is permitted as a value and the identification of those qualifiers for which such free text is considered language-dependent33; and
(d) the Document Type Definition (DTD) for a sequence listing in XML (eXtensible Markup
Language).
5. Following any revision of WIPO Standard ST.26, the Director General shall decide a date from which the revised version of that Standard shall apply to international applications and publish that information in the Gazette, together with any transitional provisions concerning the furnishing on or after that date of sequence listings related to international applications filed prior to that date.
SEQUENCES REQUIRED TO BE PRESENTED IN A SEQUENCE LISTING
6. In accordance with WIPO Standard ST.26, a sequence required to be included in a sequence listing for the purposes of Rule 5.2 is one that is disclosed anywhere in an international application by enumeration of its residues and can be represented as:
(a) an unbranched sequence or a linear region of a branched sequence containing ten or more specifically defined nucleotides, wherein adjacent nucleotides are joined by:
(i) a 3' to 5' (or 5' to 3') phosphodiester linkage; or
(ii) any chemical bond that results in an arrangement of adjacent nucleobases that mimics the arrangement of nucleobases in naturally occurring nucleic acids; or
(b) an unbranched sequence or a linear region of a branched sequence containing four or more specifically defined amino acids, wherein the amino acids form a single peptide backbone, that is, adjacent amino acids are joined by peptide bonds.
7. In accordance with WIPO Standard ST.26, a sequence listing must not include, as a sequence assigned its own sequence identification number, any sequences having fewer than ten specifically defined nucleotides or fewer than four specifically defined amino acids.
PRESENTATION OF SEQUENCES IN THE INTERNATIONAL APPLICATION
8. Where sequences are included in a sequence listing, Offices may not require that the sequences also appear in the main part of the description. However, in specific cases, the applicant may have valid reasons for setting out some sequences from the sequence listing in the main part of the description, claims or drawings. Where any sequences are presented within the main part of description, claims or drawings, they may be set out in the manner considered most appropriate to present the information for the relevant purpose. In the description, claims or drawings of the application, the sequences included in the sequence listing shall be referred to by the sequence identifier preceded by "SEQ ID NO:", even if the sequence is also embedded in the description, claims or drawings. Similarly, sequences too short to be included in the sequence listing may be presented in the manner considered most appropriate by the applicant.
LANGUAGE-RELATED REQUIREMENTS
9. WIPO Standard ST.26 prescribes the use of "controlled vocabulary" that must be used when describing the features of a sequence, that is, annotations of regions or sites of interest as set out in Annex I to the Standard.
10. Under the Standard, "qualifiers" are used to supply certain information about features in addition to that conveyed by the feature key and feature location. There are several types of permitted "value formats" to accommodate different types of information conveyed by qualifiers, namely controlled vocabulary, enumerated values (for example, a number or date), "free text" and sequences.
11. The vocabulary set out in Annex I of the Standard that is not language-dependent shall be presented only in conformance with the requirements of WIPO Standard ST.26 and must not be translated. This includes:
(a) the nucleotide symbols set out in Section 1 and the amino acid symbols set out in Section 3;
(b) the abbreviations for modified nucleotides set out in Section 2 and the abbreviations for modified amino acids set out in Section 4 as the only permitted values for the certain qualifiers;
(c) the feature key names set out in Sections 5 and 7, and the qualifier names set out in Sections 6 and 8, notwithstanding that many of the allowed names of feature keys and qualifiers are in English or are English abbreviations (see, for example, feature keys 5.1 "C-region" and 7.18 "MOD_RES" (abbreviation of "modification of a residue"); and qualifiers 6.5 "cell_type" and 8.3 "organism");
(d) all "value formats" set out in Sections 6 and 8 allowed to be used to accommodate different types of information conveyed by qualifiers other than "free text" (that is, controlled vocabulary, enumerated values like a number or date, and sequences), notwithstanding that many of these allowed "value formats" contain elements in English or English abbreviations or are recognizably derived from English or Latin words (see, for example, qualifier 6.15 "direction", with the value format: "left", "right" or "both"); and
(e) "free text" qualifier values other than those identified in the Standard as language-dependent
12. The language-dependent free text must be provided in a language which the receiving Office accepts for that purpose. WIPO Standard ST.26 allows language-dependent free text to be provided in either one or two languages within the same sequence listing: English (in the INSDQualifier_value element) and/or another specified language (in the NonEnglishQualifier_value element). The language or languages permitted or required to be used in any particular case are considered in paragraphs 16 to 19.
13. The language of any free text included in the NonEnglishQualifier_value element shall be indicated in the nonEnglishFreeTextLanguageCode attribute. The same language shall be used for the contents of all NonEnglishQualifier_value elements in a sequence listing. Where language-dependent free text is provided for any INSDQualifier_value or NonEnglishQualifier_value element, it shall be provided in the relevant language for all such elements.
14. The language considered to be the original language of all of the language-dependent free text, being the language, or one of the languages, of the language-dependent free text in the sequence listing furnished at the time of filing, shall preferably be indicated using the originalFreeTextLanguageCode attribute of the ST26SequenceListing element. The indicated language may be used in the international phase to assist the assessment and, where relevant, rectification of discrepancies found between an INSDQualifier_value element and a NonEnglishQualifier_value element for a language-dependent free text qualifier included in the sequence listing as filed. For national phase processing, the relevance of the indicated original language in cases where more than one language version of free text was included on the international filing date shall be a matter of national law.
15. WIPO Standard ST.26 requires that the name of the first mentioned applicant be provided in the language of filing. Where the name of the first mentioned applicant is not provided in Latin characters, a transliteration or translation must also be provided in Latin characters, irrespective of the language of the sequence listing otherwise. The title of the invention must be provided in the language of filing and may also be provided in additional languages. In any sequence listing translation submitted to the receiving Office, the International Bureau, the International Searching Authority or the International Preliminary Examining Authority, the applicant may add these items in the language of the translation, but shall not be required to do so.
Languages of the Sequence Listing as Filed
16. Rule 12.1(d) allows receiving Offices to specify the language or languages that may be used for language-dependent free text in a sequence listing forming part of the international application as filed. The Office may allow or require the language-dependent free text to be submitted in a language either the same as or different to that of the main body of the international application. The receiving Office may also permit, but may not require the sequence listing as filed to include language-dependent free text in a second language in accordance with WIPO Standard ST.26. This allows the language-dependent free text to be submitted simultaneously in the language of the main body of the international application as filed and in a different language required for the purposes of the international search or international publication under Rule 12.3 or 12.4. In this case, it is not required to submit the translation of the main body of the international application at the same time as the sequence listing; the translation of the main body may be provided at a later date and the translation as a whole will be considered as received on the date on which the final part of the translation is received.
Translations of the Sequence Listing
17. Where a translation of the language-dependent free text in the sequence listing of the international application or of an earlier application is required as part of a translation under Rule 12.3, 12.4, 12bis.2(a)(ii), 20.6(a)(iii), 45bis.1(c)(i), 49.5 or 55.2(a), that translation shall be provided in the form of a new sequence listing containing all of the language-dependent free text in the required language, either in addition to or replacing languages in the sequence listing fromwhich the text is being translated. The remainder of the sequence listing shall remain unchanged, save for:
(a) the appropriate attributes of ST26SequenceListing describing the content, notably including the productionDate and, where relevant, nonEnglishFreeTextLanguageCode;
(b) preferably, including the application identification details (IP Office code, international application number and international filing date) if these have been accorded and notified to the applicant, as well as, where applicable, updating any of the other elements of the general information part that havebeen modified since the international application was filed, or translating them into the language of the translated language-dependent free text. The receiving Office or International Authority shall not require correction or updating of any elements in the general information part solely because there are differences from the corresponding details in the remainder of the international application or the element details have changed between the international filing date and the date on which the translation is submitted, nor require translation of such elements
18. The originalFreeTextLanguageCode attribute shall continue to indicate the original language, irrespective of whether that language version is included in the translated sequence listing.
Languages of Sequence Listings Not Forming Part of the International Application
19. Where a sequence listing is furnished under Rule 13ter.1 or 13ter.2 for the purposes of the international search or the international preliminary examination, the language-dependent free text shall be provided in one of the languages accepted by the International Searching Authority or the International Preliminary Examining Authority, normally the same language as that used for the main part of the description. The sequence listing may also include the language-dependent free text in a second language, normally either the language of filing or English.
FILING AN INTERNATIONAL APPLICATION CONTAINING A SEQUENCE LISTING OR FURNISHING A SEQUENCE LISTING AFTER FILING
20. The requirement that a sequence listing be presented as an XML file under WIPO Standard ST.26 means that it can only be filed or furnished in electronic form. An application containing sequences as described in paragraph 6 without such a sequence listing is defective and may be difficult to correct at a later stage. It is strongly recommended that the sequence listing be prepared using WIPO SEQUENCE or equivalent software, which validates the form and aspects of the content of the sequence listing.
21. Where an international application containing a sequence listing is filed in electronic form, whether transmitted by electronic or physical means, the sequence listing should preferably form part of a package filed in accordance with Annex F, with the sequence listing indexed in accordance with the standards set out in that Annex.
22. Notwithstanding paragraph 21, any receiving Office may accept an electronic file appearing to contain a sequence listing submitted separately from the main package on the date of filing and should accept such a separate electronic file in any case where it is not practical for the applicant to include the sequence listing as part of the main package, for example, because the file size is too large to be handled by the software used for preparing or receiving the remainder of the international application. If the receiving Office is not able to process such an application, the application shall be considered to have been received by that Office on behalf of the International Bureau as receiving Office in accordance with Rule 19.4(a)(ii-bis).
SEQUENCE LISTING FILED ON SEPARATE PHYSICAL MEDIA
23. Any physical medium containing a sequence listing filed separately from a package as referred to in paragraph 21 or where the remainder of the international application is filed on paper, shall be clearly labeled "Sequence Listing" or its equivalent in the language of publication, to which the Office to which the sequence listing is submitted shall add the international application number. Where the sequence listing is submitted after the international filing date, the Office shall also indicate the nature of the sequence listing in accordance with the appropriate one of Sections 309 to 310ter, 325, 511, 513, 607 or 610. Preferably, the physical medium used for the transmittal of the sequence listing shall be of a type accepted by both the receiving Office and the International Searching Authority chosen to carry out the international search.
24. Where the file size of a sequence listing is too large to be included on a single physical medium, it shall be split such that the files can be rejoined to form one single contiguous file without any missing or repeating contents in accordance with the procedures set out in paragraphs 2(c) and (c‑bis) of Appendix IV to Annex F of these Administrative Instructions. In addition to the labeling referred to in paragraph 23, the physical media shall each be numbered, for example "DISK 1/3", "DISK 2/3", "DISK 3/3".
SEQUENCE LISTING IN ELECTRONIC FORM WITH THE REMAINDER OF THE INTERNATIONAL APPLICATION FILED ON PAPER
25. Applicants are strongly discouraged from filing international applications with the main body on paper and the sequence listing separately in electronic form. Nevertheless, in accordance with Section 703 paragraphs (d) and (e), any receiving Office may accept an international application filed in that way and should do so if it is apparent that it would not have been practical for the applicant to file the application with the receiving Office in any other way. If the receiving Office is not able to process such an application, the application shall be considered to have been received by that Office on behalf of the International Bureau as receiving Office in accordance with Rule 19.4(a)(ii-bis).
RECEIVING AND PROCESSING AN INTERNATIONAL APPLICATION CONTAINING A SEQUENCE LISTING
CHECKING BY THE RECEIVING OFFICE
Electronic File Appearing to Be a Sequence Listing
26. The receiving Office shall treat any electronic file appearing to be a sequence listing in WIPO Standard ST.26 XML format as a sequence listing forming part of the international application if it is received on or before the date on which the receiving Office determines that the papers purporting to be an international application fulfill all of the requirements under Article 11(1), whether or not that listing is referred to in the main part of the description or in the request, even if it is not correctly marked as such, except for the case where a second sequence listing is provided as part of a translation for international search under Rule 12.3 or international publication under Rule 12.4. This is independent of the question whether or not the electronic file purporting or appearing to be a sequence listing is in fact compliant with WIPO Standard ST.26 (which is not required to be checked by the receiving Office but only by the International Searching Authority). Where the receiving Office finds that a separate electronic file disclosing sequences appears to be in a format other than in WIPO Standard ST.26 XML format, it shall seek clarification from the applicant on whether the content of the file is intended to form part of the description and invite the applicant to furnish the content in the format accepted for the main part of the description if necessary. For this purpose, the receiving Office may require a statement from the applicant that the content of the document resubmitted in the accepted format is identical to that of the electronic file originally submitted. Alternatively, the receiving Office may convert the file to that format on agreement from the applicant.
Checking for Compliance with WIPO Standard ST.26 and for Other Defects
27. The receiving Office shall not be required to perform automated validations to check whether a sequence listing is compliant with WIPO Standard ST.26 or otherwise to check whether its contents are compliant with the requirements of the Rules and these Administrative Instructions. However, where the Office becomes aware of a defect, for example, because its online filing processes or other Office procedures check the sequence listing file using the validation tool provided for the purpose by the International Bureau, the Office may notify the applicant accordingly.
28. Where the receiving Office identifies a discrepancy between any of the information in the general information part of the sequence listing and the corresponding information in the request or application body, the receiving Office may draw the fact to the applicant's attention. The applicant may correct the discrepancy within the time limit provided for in Rule 26.2 but shall not be required to do so. The international application shall be processed on the basis of the indications made in the request.
Calculation of International Filing Fee
29. In accordance with Section 707(a-bis), where the international application as filed contains
an electronic file appearing to be a sequence listing in WIPO Standard ST.26 XML format, the
calculation of the international filing fee shall, in the calculation of the number of sheets, not take
into account any material contained in such an electronic file. However, where the electronic file
is in any other format, or it is obviously not a sequence listing, for example, the main part of the
description, claims or drawings mislabeled as a sequence listing, such a file should be taken into account in the calculation of the number of sheets.
Processing of a Sequence Listing Submitted After the International Filing Date
30. Where a sequence listing is received after the international filing date under any of Rules 12.3 (translation for the purposes of international search), 12.4 (translation for the purposes of international publication) or 26.4 (correction of a defect), the receiving Office shall forward a copy of the sequence listing to the International Searching Authority and to the International Bureau together with any replacement sheets also submitted for the relevant purpose, in accordance with Section 305bis or 325, as applicable under Section 335(a).
31. Where a sequence listing is received after the international filing date under Rule 13ter (sequence listing for the purposes of international search, not forming part of the international application), the receiving Office shall forward it to the International Searching Authority.
CHECKING BY THE INTERNATIONAL SEARCHING AUTHORITY OR THE INTERNATIONAL PRELIMINARY EXAMINING AUTHORITY
32. The International Searching Authority or the International Preliminary Examining Authority shall check that any sequence listing received as part of the search copy, or of a copy of the international application provided for the purposes of international preliminary examination, is compliant with the requirements of WIPO Standard ST.26 and that the language-dependent free text meets the language requirements of the Authority. Where the sequence listing contains defects, or where the international application contains sequences that should have been included in a sequence listing but were not, the Authority may invite the applicant to submit a sequence listing under Rule 13ter.1 for the purposes of international search or Rule 13ter.2 for the purposes of international preliminary examination.
CORRECTION, RECTIFICATION AND AMENDMENT OF A SEQUENCE LISTING
33. Any correction under Rule 26, rectification under Rule 91 or amendment under Article 34(2)(b) of the description submitted in relation to a sequence listing forming part of the international applicationas filed and any sequence listing included in the international application by way of an amendment under Article 34(2)(b) of the description in relation to sequences contained in the international application as filed shall be made by submitting a complete new sequence listing compliant with WIPO Standard ST.26 including the relevant correction, rectification or amendment. The nature of the correction, rectification or amendment shall be clearly explained in an accompanying letter.
34. In compliance with WIPO Standard ST.26, any sequence listing referred to in paragraph 33 shall, where possible, maintain the original numbering of the sequences in the application as filed, representing any "intentionally skipped sequence" as prescribed by WIPO Standard ST.26, where necessary. Otherwise, the sequences shall be numbered in compliance with that Standard in the order in which they appear in the international application.
35. Where the sequence listing referred to in paragraph 33 as proposed to be corrected, rectified or amended is presented on physical media, the media shall be labeled "Sequence Listing -Correction", "Sequence Listing - Rectification" or "Sequence Listing - Amendment", as the case may be, or the equivalents in the language of publication, together with the international application number.
36. Where the new sequence listing is received by the receiving Office, that Office shall not be required to check the content of the sequence listing. The Office may simply check that it has received an electronic file that appears to be a sequence listing, together with an accompanying letter and then forward these items to the International Searching Authority and International Bureau, together with any accompanying corrected, rectified or amended sheets of the main body of the international application.
INCORPORATION BY REFERENCE; MISSING AND ERRONEOUSLY FILED PARTS
37. A sequence listing missing from the international application as filed may be included into the international application under Rule 20.5, or a sequence listing erroneously filed may be removed and replaced under Rule 20.5bis. Where relevant, the appropriate sequence listing may be confirmed as incorporated by reference under Rule 20.6.
38. In accordance with Section 335, the procedures for such arrangements are equivalent to those for other parts of the description. Where the sequence listing is not incorporated by reference and the international filing date is corrected, there is no need to compare the newly provided sequence listing to that from the earlier filed application and the receiving Office need only tag the sequence listing in the appropriate manner and proceed as in Sections 310 and 310bis. Where the sequence listing is incorporated by reference, the procedure in Section 309 applies, in which case the receiving Office shall make the appropriate marking in the filename or metadata of the XML file containing the respective sequence listing. The receiving Office is recommended to seek guidance from the International Bureau if assistance is required in the comparison of sequence listings provided for confirmation of incorporation by reference with the sequence listing from an earlier application.
SEQUENCE LISTING NOT FORMING PART OF THE INTERNATIONAL APPLICATION
39. Any sequence listing furnished under Rule 13ter.1, 13ter.2 and 45bis.5(c) to an International Authority for the purposes of international search or preliminary examination shall not form part of the international application, pursuant to Rule 13ter.1(e) (where applicable, by virtue of Rules 13ter.2 and 45bis.5(c)). Any such sequence listing submitted shall be accompanied by a statement to the effect that the sequence listing does not go beyond the disclosure in the international application as filed.
40. Paragraphs 4 to 20 and 24 of this Annex shall apply mutatis mutandis to any such sequence listing. Such a sequence listing shall contain all sequences disclosed in the international application as filed that meet the criteria referred to in paragraph 6. In compliance with WIPO Standard ST.26, such a sequence listing shall, where possible, maintain the original numbering of the sequences in the application as filed, representing any "intentionally skipped sequence" as prescribed by WIPO Standard ST.26, where necessary. Otherwise, the sequences shall be numbered in compliance with that Standard in the order in which they appear in the international application.
41. Where such a sequence listing is furnished on physical media, the media shall be labeled "Sequence Listing Not Forming Part of the International Application", or its equivalent in the language of publication or of international preliminary examination, together with the international application number
TRANSMISSION OF SEQUENCE LISTINGS BETWEEN OFFICES
42. Where a sequence listing is to be transmitted between any of the receiving Office, the International Bureau, the International Searching Authority, the International Preliminary Examining Authority and a designated or elected Office, it shall be sent with the file contents unchanged from the version received from the applicant. Where the sequence listing is transmitted online, the international application number and type of sequence listing (as filed, corrected, for purpose of international search, etc.) shall be encoded in the filename, referencing XML or equivalent metadata appropriate to the means of online transmission.
43. Where a sequence listing was received on a physical medium, the sequence listing may be transmitted online, in which case, the international application number and type of sequence listing should be encoded in the filename or associated metadata in the same way as if the sequence listing had been received online. If the sequence listing is transmitted on a physical medium, the medium should be physically labelled as indicated in the relevant paragraphs above, without changing any of the content on the medium.
PROCEDURE BEFORE DESIGNATED AND ELECTED OFFICES
44. Rules 13ter.3 and 76.5 require that no designated or elected Office shall require the applicant to furnish to it a sequence listing other than a sequence listing complying with the standard provided for in the Administrative Instructions. Where no sequence listing complying with the standard and containing the language-dependent free text in the language required for national processing is available to the designated or elected Office, that Office may require the applicant to furnish a translation under Rule 49.5 in the form of a new sequence listing according to paragraphs 17 and 18, within a time limit which shall be reasonable in the circumstances.
45. The designated or elected Office shall not require a new sequence listing as part of a translation under Rule 49.5 solely because a sequence listing already provided as part of the international application contains language-dependent free text in a second language in addition to that required for national processing or because the sequence listing does not contain national application identifiers in the general information part of the sequence listing.