Bulk Sequence Documents

Patent applications for Arabidopsis bulk sequences made by Ceres Inc.

The following is an example of a recent patent application by Ceres towards a large group of Arabidopsis sequences. Whilst there are many-more-than 100 sequences in this application (2523 sequence IDs listed), approximately half of these are for the corresponding protein sequence, and some sequences are from corn, soya bean, wheat, brassica, and others. This patent document also provides an example of a more recent bulk sequence application, than those of Paradigm or Mendel. The focus of this application is towards Arabidopsis polypeptides and the sequences encoding them,…

Patent or Publication No. Title, Independent Claims and Summary Applicant
US 2006/0057724 A1

  • Earliest priority – 30 Jun 2004
  • Filed – 30 Jun 2005
  • Granted – Pending
  • Expected expiry – N/A
Title – Nucleotide sequences and polypeptides encoded thereby useful for modifying plant characteristics and phenotypes

Claim 1:
An isolated nucleic acid molecule comprising:
a) a nucleic acid having a nucleotide sequence which encodes an amino acid sequence exhibiting at least 85% sequence identity to an amino acid sequence in the Sequence Listing or in the ortholog alignments of FIG. 1;
b) a nucleic acid which is a complement of a nucleotide sequence according to paragraph (a);
c) a nucleic acid which is the reverse of the nucleotide sequence according to subparagraph (a), such that the reverse nucleotide sequence has a sequence order which is the reverse of the sequence order of the nucleotide sequence according to subparagraph (a); or
d) a nucleic acid capable of hybridizing to a nucleic acid according to any one of paragraphs (a)-(c), under conditions that permit formation of a nucleic acid duplex at a temperature from about 40° C. and 48° Cbelow the melting temperature of the nucleic acid duplex.
Claim 9:
An isolated polypeptide comprising an amino acid sequence exhibiting at least 85% sequence identity of an amino acid sequence of the Sequence Listing or in the ortholog alignments of FIG. 1.

The claims are generally drawn to:

  • A nucleic acid molecule comprising:
    • a) a nucleic acid encoding a peptide with a minimum of 85% sequence identity to a peptide in the Sequence Listing or in FIG. 1.
    • b) a nucleic acid which is a complement of a sequence according to paragraph (a);
    • c) a nucleic acid which is the reverse of the sequence according to subparagraph (a), such that the reverse nucleotide sequence has a sequence order which is the reverse of the sequence order of the sequence according to subparagraph (a); or
    • d) a nucleic acid capable of hybridizing to the sequences of paragraphs (a)-(c), at a temperature from about 40° C. and 48° C. below the melting temperature of the nucleic acid duplex.

The 85% sequence identity at the peptide level is broad, opening the possibility of finding prior art (although this might require analysis tools that may not be available to examiners). The hybridization language used here also allows the possibility of very broad claim scope. Again opening up the possibility of finding prior ar.  The language used, and the 40° C to 48° C below Tm stipulation make it extremely difficult to do a thorough analysis of prior art. However, tools that allow such analysis might very-well lead to prior art discovery. The patent text defines the hybridization temperatures (-40 to -48° C from Tm) of this claim to be equivalent to “low stringency” conditions!

  • An isolated polypeptide comprising an amino acid sequence exhibiting at least 85% sequence identity of an amino acid sequence of the Sequence Listing or in FIG. 1.

One interpretation of this is that claims over the orthologs listed in FIG 1 are also being made, and sequences 85% identical to them.  This again broadens the scope of the claim – and may be enough to read on prior art.  Discovery of such prior art would require a thorough analysis of not only sequences that are 85% identical to the SEQ ID No., but also of the orthologs in the alignment in Fig1. Are examiners able to do this effectively, given the time and resources available to them?

Original Applicant:

CERES, INC.,  Thousand Oaks, CA (US)

For information regarding this application and possible licensing, we would suggest contacting:

Dr Peter Mascia
Ceres, Inc.
Director of Product Development
1535 Rancho Conejo Blvd.
Thousand Oaks, CA 91320
Phone: (805) 376-6500
Fax: (805) 498-1002
pmascia@ceres-inc.com

Remarks   The scope of claimed sequences for this Ceres application relies on “hybridization language”, as does the Paradigm Genetics applications discussed previously.  Such claims scope are difficult to quantify. In this case Ceres has provided a temperature range (compared to Tm) for their hybridisation conditions.  Unfortunately, by comparing this range to the literature (and their own) definition of stringency, their definition constitutes “low stringency” conditions.  Thus their claims to Arabidopsis sequences almost certainly will cover the same or similar sequences from many dicots.

Other patent documents of interest

US 2006/15970 A1 Nucleotide sequences and polypeptides encoded thereby useful for modifying plant characteristics ~65 Arabidopsis sequences