How should sequence variants be represented in a Sequence Listing XML?

This page is an FAQ based on guidance from the Manual of Patent Examining Procedure. It is provided as guidance, with links to the ground truth sources. This is information only: it is not legal advice.

Representation of sequence variants in a Sequence Listing XML is important for accurately describing genetic variations. According to MPEP 2413.01(g):

• Each primary sequence and its variants must be included in the sequence listing with their own sequence identifiers.
• Variants disclosed as a single sequence with enumerated alternative residues should be represented by a single sequence using the most restrictive ambiguity symbol.
• Variants disclosed only by reference to deletions, insertions, or substitutions in a primary sequence may be included in the sequence listing.

For variant annotation:

“Annotation of a sequence for a specific variant must include a feature key and qualifier, as indicated in the table above, and the feature location. The value for the ‘replace’ qualifier must be only a single alternative nucleotide or nucleotide sequence using only the symbols in set forth Table 1: List of Nucleotides Symbols, or empty.”

Proper representation of variants ensures that all relevant genetic information is accurately captured in the patent application.