Trans-genome claims

Bulk Sequence Claims from other Dicots

As mentioned in previous chapters, one of the problems with bulk sequence claims (not just for researchers but also for patent examiners) is the fact that these applications often try to claim homologous sequences in many other organisms.  This is done typically by the use of such claim language as:

(Note that this is a claim from the Dow Chemical Co. application we discussed in Chapter 6, which contains many Nicotiana benthamiana and “Artificial” sequences )

Although this is not the only way of claiming many related sequences.  It also has the added “advantage” (if you are the applicant!) of being difficult to easily quantify, and hence offers the opportunity of obtaining the broadest possible claim scope.  Those “skilled in the art” will realise that many (possibly only distantly related!)  nucleic acid sequences will hybridise together under low stringency conditions. Further, the term “.., wherein expression of said isolated nucleic acid in a plant results in an altered metabolic characteristic.” provides a way of claiming such nucleic acid sequences with utility.

The probability that an applicant will achieve such claims to all 7554 sequences is small.  However, it is likely (and no doubt the applicant expects) that some of these sequences will be claimed in successful future applications. The uncertainty with this claim is two-fold:

  • Which sequences are going to be successfully claimed in future?, and
  • Will the applicant also acheive claims to related sequences?

At this point we see the connection between such broad bulk-sequence claims in other dicoots (Nicotiana benthamiana claim above) and Arabidopsis.  It is very likely that the bulk of the genes/DNA sequences in claim 1 above will hybridise under low stringency conditions with the corresponding Arabidopsis DNA sequences.  Hence bulk sequence claims for other dicots influence Arabidopsis in the same way that the bulk sequence claims of Paradigm Genetics Inc. would read on sequences from Nicotiana benthamiana!

Bulk claims for Arabidopsis thaliana and Nicotiana benthamiana sequences, may not only interfere with each other,
they may effectively claim sequences from important crop plants such as soya, canola, and potato.

Search Strategy

The search strategy we used in this case was different from those used previously, as it made use of the term “seqdata”.  Sequence listings of considerable size (greater than 300 pages, i.e. those likely to represent larger bulk-sequence applications) are now available for separate download from the USPTOs website (PSIPS).  Most recent, but perhaps not all, applications and patents with large sequence listings can thus be identified with the serach term “seqdata”. A term that forms part of the referring URL found at the end of such patent documents.  Hence this term offers a way of limiting searches to recent bulk-sequence documents.  Another option available is to go to the USPTO’s PSIP site and search the listings via publication date.  This latter option is difficult since there are >1000 patent documents to browse, which contain large sequence listings.

One of the patents discussed in this chapter were identified using the following search strategy.

Search details
Date of search 21 07 2006
Database searched Patent Lens, accessible at
Type of search Structured Search
Collections searched US-A, WO-A, US-B, EP-B, AU-B (add link to “Documents in  Collection” which will take you to a web page that describes the extent of the collection.)
Search terms seqdata AND plant
Results 328
Comments From the 328 results identified using these search terms, we chose several that delt with sequences from dicots.  These were used for comparisons with Arabidopsis patent documents and sequences.

You may find other patents or applications of interest based on your particular circumstances.  We encourage you to go to the Patent Lens to adapt this search to your needs or to update this search.  We invite you to provide comments on patents or applications that you see below or that you identify in your own searches which may be of interest to those reading this landscape, by going to the Add Comment link.