https://www.epo.org/en/node/how-proceed-specific

How to proceed in specific scenarios when converting from ST.25 to ST.26

1- Which mol_type qualifier should be used to annotate cDNA in ST.26?

Example: a cDNA from Homo sapiens is disclosed in a parent application with an ST.25 sequence listing. How can this be converted into ST.26?

As a general rule, when converting an ST.25 sequence listing into ST.26 format, if there is no directly equivalent qualifier or qualifier value in ST.26 for a given annotation, then a more general qualifier or qualifier value should be used together with a "note" qualifier, in which the text from the ST.25 sequence listing is to be added to avoid any change to the scope of the disclosure. This is explained in detail in Annex VII to WIPO Standard ST.26.

Regarding the specific question of cDNAs, since they are created in vitro (by reverse transcription of an mRNA), they are not "naturally occurring" because the cDNA sequences do not exist in nature. They are artificially created sequences. Therefore, it is recommended to annotate them as synthetic constructs using the values "synthetic construct" for the "organism" qualifier and "other DNA" for the "mol_type" qualifier. In addition, a "note" qualifier should be added to define that the cDNA has been obtained from a Homo sapiens sequence to avoid any extension of the scope beyond that of the parent application.

Feature key: source
Qualifiers:  /organism=synthetic construct
                 /mol_type=other DNA
                 /note=Homo sapiens cDNA

A less preferred alternative would be to use the "mol_type" value "unassigned DNA" and the "organism" value "Homo sapiens". In this case, a "note" qualifier must be added to indicate that the molecule is "cDNA" to avoid any extension of the scope beyond that of the parent application.

Feature key: source
Qualifiers:  /organism=Homo sapiens
                 /mol_type=unassigned DNA
                 /note=cDNA

Both alternatives would comply with Article 76(1) EPC. The first one is preferred because cDNAs are artificially created molecules.

2-  In ST.26, how should I annotate miRNA or siRNA molecules?

The first point to consider when choosing between the mol_type "other RNA" (synthetic) or "unassigned RNA" (naturally occurring) for the "source" feature key is whether the molecule is artificially created or naturally occurring.

If the sequence is synthetic, the specific type of molecule (e.g. siRNA) should also be added in a "note" qualifier.

If the sequence is naturally occurring, the feature key "ncRNA" with the mandatory qualifier "ncRNA_class" should also be used. The value for this qualifier must be selected from the predefined list (e.g. miRNA or siRNA). If the short RNA disclosed in the parent application is not in this list, then the value "other" should be selected and added in a "note" qualifier.

Example 1: naturally occurring miRNA

Feature key: source
Qualifiers:  /organism=Homo sapiens
                  /mol_type=transcribed RNA

Feature key: ncRNA
Qualifier:  /ncRNA_class=miRNA

Example 2: synthetic siRNA

Feature key: source
Qualifiers:  /organism=synthetic construct
                 /mol_type=other RNA
                 /note=siRNA

3-  How do I convert an ST.25 sequence listing comprising Xaa or n residues into ST.26 format?

In ST.25, it was mandatory to annotate n or Xaa residues. It should be noted that ST.26 defines a default meaning for non-annotated X or n residues (see Annex I to WIPO Standard ST.26, sections 1 and 2). This means that in ST.26, n or X residues should only be annotated if they are used in a meaning that is different to the default meaning.

The conversion of a sequence listing comprising Xaa residues from ST.25 to ST.26 is explained in detail in scenario 5 of Annex VII to WIPO Standard ST.26. Similar considerations apply for a sequence listing comprising n residues.

When using WIPO Sequence software to convert an ST.25 sequence listing into ST.26 format, annotations from <223> are copied into a note in the ST.26 sequence listing to avoid loss of information. The applicant should copy this information into the appropriate ST.26 qualifier. If this is not done, the sequence listing may be compliant with Article 76(1) EPC (assuming that all the information from the ST.25 sequence listing has been copied into the ST.26 sequence listing) but it will not be compliant with ST.26.

4- When the individual residues of a DNA/RNA hybrid sequence are not (all) clearly defined as DNA or RNA in an ST.25 sequence listing, how do I convert the DNA/RNA hybrid sequence into ST.26 format?

In cases where the description and/or previous sequence listing does not contain the location information of each DNA and RNA segment, a possible representation of this mixed molecule could be as follows:

The wording used in the ST.25 sequence listing, e.g. here "mixed DNA/RNA molecule", should be copied into a "note" qualifier associated with a "misc_feature".

Example: sequence in ST.25 cccccccccccuggggggggggggg
annotated as mixed DNA/RNA molecule, 25 nucleotide-long, the nucleotide at position 12 is a RNA nucleotide "u", the other nucleotides are not further defined.

Sequence in ST.26 SEQUENCE LISTING:
ccccccccccctggggggggggggg

Feature key: source, position 1..25
Qualifiers:  /organism=synthetic construct
                 /mol_type=other DNA

Feature key: misc_feature, position 1..11
Qualifier:  /note=mixed DNA/RNA molecule

Feature key: misc_feature, position 12
Qualifier:  /note= RNA

Feature key: misc_feature, position 13..25
Qualifier:  /note=mixed DNA/RNA molecule

5- How do I convert an ST.25 sequence listing comprising short sequences into ST.26 format?

Short sequences (fewer than four specifically defined amino acids or 10 specifically defined nucleotides) cannot be present in an ST.26 sequence listing and are to be replaced by skipped codes. When using WIPO Sequence software to convert an ST.25 sequence listing into ST.26 format, this replacement is done automatically.

To avoid losing subject-matter, it is critical to thoroughly examine which sequences are skipped, and thus deleted (even if the SEQ ID numbers are kept), and to ensure that those skipped/deleted short sequences are disclosed in the application description and, where necessary, add them to the description.