For biotechnology and life-sciences patent applicants, sequence listings are an important part of preparing a European patent application. The 2025 Guidelines for Examination in the European Patent Office reaffirm and clarify the European Patent Office’s approach to nucleotide and amino-acid sequences, particularly the use of WIPO Standard ST.26.

The requirements are significant because an incomplete, incorrectly formatted, or late sequence listing can affect searching and examination, while changes to a sequence listing after filing can also raise added-matter concerns.

This article summarizes the principal points applicants should understand when preparing European patent applications in 2025.

1. ST.26 Is the Applicable Standard

Under the 2025 EPO Guidelines, nucleotide and amino-acid sequences falling within the relevant requirements of EPC Rule 30(1) must be represented in a sequence listing complying with WIPO Standard ST.26. 

ST.26 is an XML-based international standard designed to harmonize the preparation and exchange of sequence listings between patent offices.

For European applications, the transition from the older ST.25 standard is particularly important. Applications filed on or after 1 July 2022 use ST.26, while applications filed before that date generally remain subject to ST.25 for the relevant sequence-listing requirements

The filing date therefore matters when determining which standard applies.

2. Which Sequences Need to Be Listed?

The 2025 Guidelines explain that sequences meeting the applicable ST.26 criteria must be included in the sequence listing.

In particular, a sequence must be included when it is disclosed by enumeration of its residues and contains at least:

• 10 specifically defined nucleotides, or
• 4 specifically defined amino acids.

Under ST.26, residues represented by “n” for nucleotides or “X” for amino acids are not considered specifically defined for this purpose

This means applicants should not assume that only complete biological sequences need to be listed.

The EPO states that each qualifying nucleotide or amino-acid sequence disclosed in the application documents—including the drawings—needs to be included, even where the sequence represents only a fragment of another disclosed sequence. 

3. Sequence Identification Numbers Must Be Consistent

Another important requirement concerns SEQ ID Nos.

The sequence identification numbers used in the description must correspond to those used in the ST.26 sequence listing. The same SEQ ID No. must consistently refer to the same sequence. 

This makes careful cross-checking essential before filing.

For example, if the description identifies a particular DNA sequence as SEQ ID NO: 1, the sequence represented by SEQ ID NO: 1 in the XML listing must be the same sequence. An inconsistency can create unnecessary prosecution complications and potentially make the relationship between the disclosure and the sequence listing unclear.

4. XML Filing Is Mandatory

The sequence listing must be provided electronically in XML format compliant with ST.26. The 2025 Guidelines expressly state that sequence listings should not be filed on paper or in PDF format

The EPO identifies several electronic filing routes, including the relevant EPO online filing systems and the Contingency Upload Service

Applicants should therefore treat generation and validation of the ST.26 XML file as a technical filing step, rather than simply converting an existing PDF or text document into XML.

5. The Filing Date Has Important Consequences

The sequence listing filed with the application on its filing date has a particular status.

The EPO’s 2025 decision states that where nucleotide or amino-acid sequences are disclosed in a European patent application, the description must contain an XML sequence listing complying with ST.26. A sequence listing filed on the filing date is published with the application documents and later with the patent specification as part of the description

This makes it especially important to ensure that the initial sequence listing is complete and accurate.

A filing strategy should therefore include a final sequence audit before submission rather than relying on corrections after filing

6. Late-Filed or Corrected Sequence Listings

The EPO’s approach to sequence listings filed after the application date deserves particular attention.

Where a sequence listing is filed or corrected after the filing date, the applicant must submit a statement that the sequence listing does not contain matter extending beyond the content of the application as filed. 

This requirement is closely connected with the prohibition on adding subject matter under Article 123(2) EPC.

A sequence listing should therefore not be treated as a document that can freely be expanded after filing. If a later version introduces a sequence that was not originally disclosed, the amendment may raise substantive added-matter problems.

7. Corrections Require a Complete New Listing

The 2025 Guidelines also explain that when a sequence listing that forms part of the description is corrected or amended, a complete new sequence listing must be filed. 

This is an important practical point.

Applicants should maintain a controlled master version of the sequence data and ensure that any corrected XML file is generated consistently rather than attempting to submit isolated changes to individual entries.

8. Only the Compliant Listing Is Used for Searching

It is possible in certain circumstances for more than one sequence listing to be filed. However, the EPO states that where multiple listings are filed on the filing date, only the sequence listing complying with ST.26 will be used as the basis for the search. This reinforces the practical importance of filing a technically correct ST.26 listing.

A supplementary PDF or alternative sequence representation should not be viewed as a substitute for the required XML listing.

9. Implications for PCT Applications Entering Europe

The rules are also important for Euro-PCT applications.

For international applications filed on or after 1 July 2022, ST.26 applies. The EPO Guidelines state that an electronic ST.26-compliant sequence listing should be available to the EPO as designated or elected Office by expiry of the 31-month period

If the required sequence listing is unavailable, applicants may be invited to provide one under the applicable PCT procedure. Depending on the circumstances, this can involve a late-furnishing fee and a non-extendable period.

For international applications filed before 1 July 2022, ST.25 remains relevant even if the European phase begins after 1 July 2022. 

This filing-date distinction is therefore essential when handling older PCT portfolios.

10. 2025 Filing Developments

The EPO also introduced practical changes concerning electronic filing.

A November 2025 EPO notice explains that, following the decommissioning of the desktop-based Online Filing system at the end of 2025, ST.26 sequence listings could, from 1 January 2026, be filed online through Online Filing 2.0, the EPO Contingency Upload Service and, where applicable, ePCT or MyEPO. 

The EPO also retained electronic data carriers as an option for sequence listings exceeding the applicable upload limits. The notice identifies a current maximum upload size of 50 MB for the relevant electronic filing tools and identifies accepted data-carrier options for oversized XML listings. 

For applicants handling very large biological sequence datasets, these practical filing requirements should be considered well before the filing deadline.

11. Avoiding Problems During Preparation

A robust sequence-listing workflow should include several quality-control checks.

Check the application disclosure

Review the description, claims and drawings to identify every nucleotide and amino-acid sequence that potentially falls within ST.26.

Check the length thresholds

Confirm whether each enumerated sequence meets the applicable ST.26 threshold.

Check SEQ ID numbers

Verify that every SEQ ID referenced in the specification corresponds exactly to the appropriate entry in the XML listing.

Validate the XML

Use appropriate ST.26-compliant validation software before filing.

Check for unintended changes

Particular care should be taken when converting legacy ST.25 data into ST.26. The EPO notes that ST.26 contains recommendations intended to reduce the risk of added or deleted subject matter arising during conversion

Preserve the filing version

The exact sequence listing submitted on the filing date should be retained as part of the application’s internal prosecution record.

12. Practical Impact for Patent Applicants

For biotechnology applicants, sequence-listing compliance should be treated as part of substantive patent preparation, not merely administrative formatting.

The sequence listing can affect:

• The completeness of the application’s disclosure
• The ability of the EPO to perform an effective search
• Consistency between the specification and sequence data
• Added-matter analysis
• PCT-to-European-phase processing
• Subsequent corrections and amendments

A technical error in a sequence listing may therefore have consequences beyond filing formalities.

Conclusion

The EPO’s 2025 Guidelines reinforce a clear framework for sequence listings in European patent applications: qualifying nucleotide and amino-acid sequences must be represented using WIPO Standard ST.26, the listing must be provided in XML, sequence identifiers must remain consistent and late-filed or corrected listings must be accompanied by the appropriate no-added-matter statement. 

For applicants, the key lesson is straightforward: sequence-listing preparation should begin early and be integrated into the overall patent drafting and filing workflow.

A careful pre-filing review of the disclosure, sequence data, SEQ ID numbers, XML structure and applicable filing standard can substantially reduce the risk of avoidable procedural and substantive complications.

The EPO’s official 2025 Guidelines for Examination provide the authoritative reference for the applicable practice