Appeal No. 2006-1569 Page 5
Application No. 10/159,997
3. Anticipation
The examiner rejected claim 1 under 35 U.S.C. § 102(a) as anticipated by
Honkura.1 The examiner reasoned that
Honkura et al. discloses a computer method for identifying alternative
mRNA splice isoforms of known genes via the Gene Resource Locator
(GRL) to assemble gene maps (Abstract, etc.). Honkura et al. aligns full-
length enriched cDNA sequences with authentic 5’-terminal start points for
identification [of] promoter regions (page 222, column 2, last paragraph).
. . . The method of Honkura et al. involves the alignment of ESTs from
various sources, such as UniGene and full-length cDNA databases
(mRNA sequences).
Examiner’s Answer, pages 8-9.
Appellants argue that Honkura’s method does not meet all the limitations of the
instant claims: “Honkura includes no step comparable to our first step: identifying target
gene sequences by mapping mRNA sequences of an mRNA sequence data set to
genomic sequence. In contrast, Honkura directly aligns ESTs of Unigene [database]
with genomic sequence. . . . The inputs to Honkura’s analysis pipeline are EST
sequences and genomic sequence. . . . The initial inputs to our protocol are the well-
characterized RefSeq genes [i.e., mRNAs] whose coding regions are known and
genomic sequence. In a later step, ESTs are aligned to the RefSeq loci to reveal
patterns of alternate splicing.” Appeal Brief, page 9.
The standard for anticipation is one of strict identity. See Verdegaal Bros., Inc. v.
Union Oil Co., 814 F.2d 628, 631, 2 USPQ2d 1051, 1053 (Fed. Cir. 1987) (“A claim is
1 Honkura et al., “The Gene Resource Locator: gene locus maps for transcriptome analysis,” Nucleic
Acids Research, Vol. 30, pp. 221-225 (2002)
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