D.4 Sequence listings
Notice from the European Patent Office dated 18 October 2013 concerning the filing of sequence listings
This notice complements the decision of the President on the filing of sequence listings1 (hereinafter referred to as the "decision of the President") and describes the procedure under the EPC and PCT for the filing of sequence listings. It has been updated in order to take into account recent changes in said procedure triggered, inter alia, by decisions of the EPO's boards of appeal.
I. European patent grant procedure
1. Filing of sequence listings
1.1 If nucleotide or amino acid sequences are disclosed in a European patent application, the description must contain a sequence listing complying with WIPO Standard ST.25 (Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in Patent Applications – hereinafter referred to as the "Standard") (Rule 30(1) EPC in conjunction with Article 1 of the decision of the President).
1.2 You can consult and download the current version of the Standard on the WIPO website under "Patents" - "WIPO Standards". The Standard describes in detail both the formal requirements for the filing of Standard-compliant sequence listings and how the sequences contained therein are to be presented.
1.3 The EPO recommends the use of BiSSAP software, which can be downloaded free of charge from the EPO website, to generate Standard-compliant sequence listings. Using the latest version of this software enables applicants to meet the formal requirements of the Standard. Applicants are still free to use other software such as PatentIn.
1.4 Under Article 1(1) of the decision of the President, sequence listings must be submitted in electronic form, i.e. in text format (TXT). Further information about the document format is set out in the Standard. The sequence listing should no longer be filed on paper or, in the case of electronic filing of the application, in PDF format (see Article 1(1) and (2) of the decision of the President). If the applicant also files the sequence listing of his own accord on paper or in PDF format, he must submit a statement that the sequence listings in electronic form and on paper or in PDF format are identical. In this case, the paper or PDF form will be disregarded in the further procedure.
1.5 A Standard-compliant sequence listing in TXT format must be filed for all sequence information that conforms to the length thresholds defined in the Standard (see No. 2(ii)), irrespective of whether this sequence information is claimed or not. As an exception, sequences which belong to the prior art and can be found in publicly accessible sequence databases do not need to be included in the sequence listing if they have been identified by their database accession number and either the version number or the database release number in the application as originally filed. This applies even if reference is made to these sequences in one or more claims or if the sequences are essential features of the invention or necessary for the prior-art search (see J 8/11 of 30 January 2013). If the European patent application discloses nucleotide or amino acid sequences that are fragments or variants of a prior-art sequence, a sequence listing complying with WIPO Standard ST.25 has to be filed for these sequence fragments or variants.
1.6 A sequence listing filed together with the application documents is part of the description. In calculating the additional fee under Rule 38(2) EPC and Article 2, 1a RFees, the pages of the sequence listing are disregarded as long as the listing complies with the Standard and is filed as a separate part of the description. If the sequence information in the sequence listing is reproduced in the description or in other parts of the application, contrary to the recommendation in the Standard, the pages concerned will be taken into account in the calculation of the additional fee (see the notice from the EPO dated 26 January 2009 concerning the 2009 fee structure, OJ EPO 2009, 118, point 3.2; see also the Guidelines for Examination in the EPO ("Guidelines"), A-III, 13.2).
1.7 The above relates equally to European divisional applications. As an independent European patent application, a divisional application must also satisfy the requirements of Rule 30 EPC in conjunction with the decision of the President (see G 1/05, OJ EPO 2008, 271, point 3.1 of the Reasons). Without prejudice to the requirements of Article 76(1), second sentence, EPC, if a sequence listing is to form part of the description of the divisional application, it must be submitted together with the other documents making up the divisional application, unless reference is made to a previously filed application containing a sequence listing as part of the application (Rule 40(1)(c) EPC). However, an applicant who has filed a Standard-compliant sequence listing in TXT format under Rule 30 EPC with regard to the earlier application (parent application) is exempted from having to submit said sequence listing for search purposes only (i.e. not as part of the description) in respect of the divisional application. The Office will add a copy of the Standard-compliant sequence listing in TXT format filed in conjunction with the earlier application for search purposes only (i.e. not as part of the application) to the dossier on the divisional application.
2. Subsequently filed sequence listings/correction of errors – late furnishing fee – loss of rights
2.1 Where the applicant has not filed a Standard-compliant sequence listing in TXT format at the date of filing the European patent application, the Receiving Section will inform the applicant of the deficiencies in question and invite him to file a Standard-compliant sequence listing in TXT format and pay the late furnishing fee within a non-extendable period of two months (Rule 30(1) and (3) EPC in conjunction with Article 2(1) of the decision of the President).
2.2 Where the applicant fails to file a Standard-compliant sequence listing in TXT format and pay the late furnishing fee in due time, the application will be refused under Rule 30(3) EPC. This also applies if a sequence listing is subsequently filed in TXT format but still contains deficiencies with respect to the Standard. Such deficiencies will not prompt the EPO to issue another invitation under Rule 30(3) EPC, triggering a new period of two months, unless the previous invitation did not draw the applicant's attention to such remaining deficiencies (see J 7/11 of 24 January 2012, point 10 of the Reasons).
2.4 A subsequently filed sequence listing may contain only the sequence information – in standardised form – contained in the original application documents. It may contain neither more nor fewer sequences than the number of sequences disclosed in the original description, and the numbering of the sequences must remain unchanged. The applicant must ensure that this is the case and submit a statement to that effect under Article 2(2) of the decision of the President. It is recommended that the statement is worded as set out in the footnote2.
2.5 A sequence listing filed after the date of filing is not part of the description and therefore cannot be used to determine the originally disclosed content of the application (Rule 30(2) EPC). It can only be used for the purposes of the search, and is not published with the application documents or patent specification.
2.6 Without prejudice to Rule 30 EPC, a sequence listing forming part of the description may be corrected or amended in accordance with Rule 139 and/or Article 123(2) EPC. In this case a complete new sequence listing in TXT format containing the corrections or amendments is to be filed.
II. Procedure before the EPO as international authority under the PCT
1. If the international application discloses one or more nucleotide and/or amino acid sequences and if a Standard-compliant sequence listing in TXT format is not available to the EPO as International Searching Authority (ISA), Authority specified for supplementary search (SISA) or International Preliminary Examining Authority (IPEA), the EPO will invite the applicant to furnish to it such a sequence listing under Rule 13ter.1(a) PCT within a non-extendable period of one month from the date of the invitation (Article 4 of the decision of the President).
2. The furnishing of a sequence listing in response to an invitation by the EPO as ISA, SISA or IPEA under Rule 13ter.1(a) PCT is subject to the payment of the late furnishing fee fixed by the President (see Rule 13ter.1(c) PCT and Article 4 of the decision of the President). The late furnishing fee may be refunded only where the amount was paid by mistake, without cause, or in excess of the amount due (Agreement between the EPO and the IB of WIPO, Annex C, Part II, paragraph (1)3).
3. Any Standard-compliant sequence listing in TXT format furnished by the applicant under Rule 13ter PCT for the purposes of the search only must be accompanied by a statement to the effect that the sequence listing does not include matter which goes beyond the disclosure in the international application as filed and/or that the Standard-compliant sequence listing in TXT format furnished under Rule 13ter PCT is identical to the sequence listing in the international application (Annex C, paragraphs 4(v) and (vi)). Any sequence listing furnished under Rule 13ter PCT is not part of the international application.
4. If the applicant fails to furnish the required Standard-compliant sequence listing in TXT format and pay the late furnishing fee due within the period under Article 4 of the decision of the President, the EPO as ISA will issue no further invitation to furnish the sequence listing, and will search the international application only to the extent that a meaningful search can be carried out without the sequence listing (Rule 13ter.1(d) PCT). In this case, the international search report will either indicate that certain claims were found unsearchable or will be replaced by the declaration under Article 17(2)(a) PCT. However, if the Standard-compliant sequence listing in TXT format is received and the late furnishing fee paid after the applicable period yet before the start of the international search, the Standard-compliant sequence listing will be considered as having been received within that period.
5. A sequence listing in TXT format that contains (minor) deficiencies with respect to the Standard is deemed to comply with this Standard where these deficiencies may be corrected ex officio or under Rule 26 PCT or otherwise rectified under Rule 91.1(b)(ii) to (iv) PCT, as the case may be. In the latter two cases a complete new sequence listing in TXT format containing the corrections or rectifications is to be filed.
6. If, contrary to the statement referred to in paragraph 3 above, the EPO as ISA finds that the sequence listing in TXT format furnished under Rule 13ter PCT is not identical to the sequence listing in the international application under Rule 5.2(a) PCT, it will indicate that finding in the international search report and either proceed with the international search if the (minor) deficiency can be corrected or rectified under paragraph 5 above, or otherwise proceed under paragraph 4 above, as if the sequence listing in TXT format had not been furnished under Rule 13ter PCT.
7. If a sequence listing in TXT format is found to be deficient within the meaning of Article 3(1) or (2) of the decision of the President, the applicant will be invited to submit a replacement listing within the period under Article 4 of the decision of the President or, if such an invitation has already been issued, within the time remaining in the period stipulated in the invitation (see paragraph 4 above).
8. If the international search report has not been drawn up in full or in part (see paragraph 4 above), the EPO as IPEA will perform an international preliminary examination only to the extent that a meaningful examination can be carried out (Rule 66.1(e) PCT). The applicant is informed accordingly and an entry is made in the international preliminary examination report (Rules 66.2(a)(vii) and 70.12(iv) PCT). In such case, no invitation to furnish a sequence listing is issued.
9. If, after receipt of the documents specified in Rule 45bis.4(e)(i) to (iv) PCT, the EPO as SISA finds that a Standard-compliant sequence listing in TXT format is not available to it, it will proceed as above, in particular as under paragraph 1. The EPO as SISA will start the supplementary international search in accordance with Rule 45bis.5(a) PCT only if a Standard-compliant sequence listing in TXT format is available to it, i.e. if it is furnished to the IB of WIPO under Rule 45bis.1(c)(ii) PCT and thereafter transmitted to the EPO under Rule 45bis.4(e)(iii) (Agreement between the EPO and the IB of WIPO, Annex E, paragraph 44).
III. Procedure before the EPO as designated or elected Office (regional phase)
1. If a Standard-compliant sequence listing in TXT format is contained in the international application under Rule 5.2 PCT, furnished to the EPO under Rule 13ter.1(a) PCT or made accessible to the EPO by other means, the applicant does not have to submit the Standard-compliant sequence listing again in TXT format on entry into the regional phase before the EPO as designated or elected Office.
2. Where, however, a Standard-compliant sequence listing in TXT format is not available to the EPO on the expiry of the period under Rule 159(1) EPC, the applicant will be invited to file a Standard-compliant sequence listing in TXT format within two months from the invitation and to pay the late furnishing fee. Rule 30(2) and (3) EPC and Article 1 of the decision of the President are to be applied accordingly (see Rule 163(3) EPC in conjunction with Article 5 of the decision of the President).
3. If any deficiencies are not remedied in due time after such an invitation – this also applies to the payment of the late furnishing fee – the application will be refused (Rule 30(3) EPC). The applicant may request further processing of the application under Article 121 EPC.
IV. Publication of sequence listings
1. A sequence listing filed at the date of filing of the European or international patent application will be published with the application documents (Rule 68(1) EPC; Article 153(4) EPC) and the patent specification (Rule 73 EPC) as part of the description (Article 6 of the decision of the President).
2. A sequence listing filed after the date of filing of the European patent application will not be published with the application documents or the patent specification because it is not part of the description (Rule 30(2) EPC).
3. For the purposes of publication (as far as a Standard-compliant sequence listing present on the date of filing is concerned) and file inspection, the Standard-compliant sequence listing filed by the applicant in TXT format is converted by the EPO. The EPO cannot guarantee that the converted version is without error and reflects exactly the original file. On written request to email@example.com, the EPO will supply a copy of the original file submitted by the applicant.
V. Entry into force, and superseded previous EPO notices
From the date of its entry into force on 1 January 2014, the present notice supersedes the notice from the European Patent Office dated 28 April 2011 concerning the filing of sequence listings (OJ EPO 2011, 376).