Ex Parte Podlich et al

Board of Patent Appeals and Interferences

Apr 21, 2010

10874813 (B.P.A.I. Apr. 21, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte DEAN PODLICH, MARK COOPER, and CHRIS WINKLER
____________

Appeal 2009-011265
Application 10/874,813
Technology Center 1600
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Decided: April 21, 2010
____________

Before LORA M. GREEN, RICHARD M. LEBOVITZ, and
STEPHEN WALSH, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on appeal from the Patent Examiner’s rejections of
claims 1-26, 28-30, and 32-36. The Board’s jurisdiction for this appeal is
under 35 U.S.C. § 6(b). We affirm-in-part.

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Application 10/874,813

STATEMENT OF THE CASE
The claims are drawn to methods of mapping phenotypic traits in
plants to markers. Claims 1-26, 28-30, and 32-36 are pending and stand
rejected by the Examiner as follows:
1. Claims 1-26, 28-30, and 32-36 under 35 U.S.C. § 103(a) as
obvious in view of Sebastian et al. (U.S. 5,437,697, issued Aug. 1, 1995)
(Ans. 7).
2. Claims 1-22, 24, and 32-36 under 35 U.S.C § 101 because the
claimed invention is directed to non-statutory subject matter (Ans. 3).
3. Claims 23, 25, 26, and 28-30 under 35 U.S.C § 101 and § 112, first
paragraph, because the claimed invention lacks patentable utility (Ans. 5 &
7).
Claims 1 and 23 are representative and read as follows
1. A method for ensuring the validity of a correspondence between at
least one marker and at least one phenotype, the method comprising:
providing a recursively determined estimate of correlation between at least
one marker and at least one phenotype across a plurality of plant
populations, which plant populations collectively comprise progeny of a
plurality of biparental crosses.

23. The method of claim 1, wherein the recursively determined estimate
of correlation is provided by:
a) providing a first estimate of QTL allele effects demonstrating a
correlation between an allele of the at least one marker and the at least one
phenotype in a plurality of plants;
b) selecting at least one plant, which at least one plant is optionally
selected from the plurality of plants of step a), with the allele of the at least
one QTL marker;
c) crossing the selected plant to generate a population of progeny;
d) estimating a correlation between an allele of the same or different at
least one marker and the at least one phenotype in the population of progeny
of step c), thereby generating a second estimate of QTL allele effects;
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e) updating the first estimate of QTL allele effects to generate a first
updated estimate of QTL allele effects; thereby ensuring the correspondence
between the at least one marker and the phenotype.
f) selecting at least one member of the population of progeny a desired
allele of at least one marker validated according to the updated estimate of
QTL allele effects; and,
g) optionally repeating steps c) through f) one or more times to generate
at least one subsequent population of progeny.

1. OBVIOUSNESS
Statement of the issue
The issue in this rejection is whether Sebastian would have suggested
to one of ordinary skill in the art the claimed method of “providing a
recursively determined estimate of correlation between at least one marker
and at least one phenotype.”
Principles of Law
“Rejections on obviousness grounds cannot be sustained by mere
conclusory statements; instead, there must be some articulated reasoning
with some rational underpinning to support the legal conclusion of
obviousness.” In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006), cited with
approval in KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417-18 (2007).

Findings
1. Sebastian identifies genetic markers associated with a phenotypic
selection criteria, such as a “yield potential,” by observing differences in
allele frequency between elite lines and their ancestors (Sebastian, col. 36, ll.
35-42).
2. Once identified, these markers are used by Sebastian to select superior
lines by identifying progeny that comprise the QTL loci (id.).
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3. Thus, Sebastian completed QTL analysis once when comparing genetic
markers from elite and ancestral lines.

Analysis
Claim 1 is drawn to a method of “providing a recursively determined
estimate of correlation between at least one marker and at least one
phenotype across a plurality of plant populations.” The term “marker”
would be understood from the Specification to mean a DNA sequence
present in an individual in a plant population (Spec. 21:13-19). As
explained in the Specification, a marker is “linked” with a “phenotype” (an
observable trait of the plant) when plants which have the phenotype have the
marker, and when plants lack the phenotype, they lack the marker (id. at
19:29-30; 21:20-25).
The Specification defines the phrase “’recursively determined’” to
mean that the “estimate of correlation or estimate of QTL allele effects, is
produced by repeatedly evaluating the statistical relationship between the
marker or haplotype and the phenotype of interest.” (Spec. 19: 20-23.)
“Thus, . . . an estimate of QTL allele effects is recursively determined when
the correlation between the marker or haplotype and the phenotype is
determined in a population of progeny selected from the breeding population
at successive intervals (generations) during the breeding process.” (Id. at 19:
24-28.) In other words, the estimate of a QTL is repeated more than once on
progeny from the successive “plurality of biparental crosses” of claim 1.
QTL or “’quantitative trait locus’” refers to a genetic locus in the plant that
affects a phenotype (id. at 21:9-12).
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The Examiner acknowledged that Sebastian did not describe
recursively determining estimates of correlation between a genotype and
phenotype (Ans. 8). However, the Examiner found “[o]ne of ordinary skill
in the art would understand that successive generations of progeny could be
screened because Sebastian et al teach the screening of progeny lines at
various stages of inbreeding (see, for example, column 37, lines 10-16).”
(Id.) The Examiner determined:
One of ordinary skill in the art would have been
motivated to modify the teachings of Sebastian et al because
Sebastian et al teach “[t]he greatest barrier to progress in
selection for quantitative traits, especially for yield, is the lack
of repeatability of phenotypic traits in different environments.
..[because] environmental effects make it difficult to identify
genetically superior individuals . . . [thus,] identifying
individuals with the most favorable genotype is one of the most
difficult and challenging aspects of plant breeding” (see column
1, lines 34-36).
(Id. at 9.)
The Examiner concluded: “Thus, one of ordinary skill in the art
would have been motivated to use the teachings of Sebastian et al to select
plants having favorable genotypes because phenotypic selection of
quantitative traits is difficult but using markers to select for quantitative
traits would provide a better option.” (Id.)
Appellants contend that the Examiner has not provided an adequate
reason for modifying Sebastian’s disclosure to have arrived at the claimed
method. Citing Sebastian’s teaching that its invention involves the “key
feature of the current invention is a population genetic study that employs
genetic markers to measure allele frequency differences between modern-
day elite lines and their earliest known ancestors” (Sebastian, col. 3, ll. 15-
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48), Appellants contend that there would have been no reason to test
progeny from current plant lines for QTL correlations “in the recursive
manner as claimed” (App. Br. 5 & 8).
It is true, as argued by the Examiner, that Sebastian recognized the
shortcomings in selecting for quantitative traits. One of the barriers
identified by Sebastian was “the lack of repeatability of phenotypic traits in
different environments.” (Sebastian, col. 1, ll. 28-36.) To address this
problem, Sebastian described “conducting genetic marker analysis of a set of
current elite lines and the ancestral population from which they were derived
by decades of plant breeding.” (Id. at Abstract.) “Since the traditional plant
breeding effort has consistently utilized yield as a selection criteria,
deviations from expected allele frequency at certain loci have been used to
identify alleles that confer yield potential. Agronomically superior progeny
can, therefore, be selected utilizing genetic markers.” (Id.) Sebastian
teaches that once “markers for QTL’s affecting agronomic performance have
been identified, the plant breeder will manipulate QTL’s the same way he
would manipulate qualitatively inherited traits,” such as “selection of
superior lines from crosses that are segregating at QTL loci” (id. at col. 36,
ll. 35-42).
In other words, Sebastian identifies genetic markers associated with a
phenotypic selection criteria, such as a “yield potential,” by observing
differences in allele frequency between elite lines and their ancestors. Once
identified, these markers are used to select superior lines by identifying
progeny that comprise the QTL loci (id. at col. 36, ll. 35-42). Thus, as
correctly recognized by the Examiner, Sebastian completed the QTL
analysis once when comparing genetic markers from elite and ancestral
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lines. Despite Sebastian’s failure to perform recursive phenotypic
correlations with genetic markers, the Examiner found it obvious because
one of ordinary skill in the art would understand such screening could be
accomplished and because Sebastian teaches screening at various stages of
inbreeding (Ans. 8).
The Examiner’s rationale is not adequate. Simply because a step
could be performed is not a reason to have performed it. In this case, the
Examiner did not point to any factual basis in Sebastian that would have led
persons of ordinary skill in the art to repeat the QTL analysis successively as
claimed. In fact, Sebastian discloses that phenotype correlations with
genetic markers were most reliable, offsetting environmental effects, when
the correlations (QTL) were determined between ancestor and elite lines
(Sebastian, col. 1, ll. 28-36; col. 1, ll. 46-62; col. 3, ll. 15-48). In view of
this teaching, we agree with Appellants that the rejection did not provide a
reason to repeat the recursive correlation step on progeny from successive
biparental crosses as claimed, since Sebastian explicitly teaches establishing
“new elite lines” utilizing the “alleles” (genetic markers associated with
“high yield” and other “selection criteria”) from the analysis of ancestral
lines (id. at col. 3, ll. 15-48).
As further support for the obviousness rejection, the Examiner pointed
to Sebastian’s statement about screening progeny lines at various stages of
inbreeding (Ans. 8). It is evident this passage of Sebastian is referring to
screening for “favorable alleles” that had been identified as conferring a
favorable characteristic on the plant, such as high yield (Sebastian, col. 37,
ll. 10-20.). This passage does not refer to, nor suggest, performing an
estimate of correlation recursively as claimed.
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The obviousness rejection of claims 1-26, 28-30, and 32-36 is
reversed.

2. SECTION 101: NON-STATUTORY SUBJECT MATTER
Claims 1-22, 24, and 32-36 stand rejected under 35 U.S.C § 101
because the claimed invention is directed to non-statutory subject matter
(Ans. 3).
Principles of Law
However, mental processes-or processes of human
thinking-standing alone are not patentable even if they have
practical application. The Supreme Court has stated that
“[p]henomena of nature, though just discovered, mental
processes, and abstract intellectual concepts are not patentable,
as they are the basic tools of scientific and technological work.”
Benson, 409 U.S. at 67 . . . (emphasis added).

In re Comiskey, 554 F.3d 967, 979 (Fed. Cir. 2009).
The Supreme Court, however, has enunciated a definitive
test to determine whether a process claim is tailored narrowly
enough to encompass only a particular application of a
fundamental principle rather than to pre-empt the principle
itself. A claimed process is surely patent-eligible under § 101
if: (1) it is tied to a particular machine or apparatus, or (2) it
transforms a particular article into a different state or thing. . . .
A claimed process involving a fundamental principle that uses a
particular machine or apparatus would not pre-empt uses of the
principle that do not also use the specified machine or apparatus
in the manner claimed. And a claimed process that transforms a
particular article to a specified different state or thing by
applying a fundamental principle would not pre-empt the use of
the principle to transform any other article, to transform the
same article but in a manner not covered by the claim, or to do
anything other than transform the specified article.
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In re Bilski, 545 F.3d 943, 954 (Fed. Cir. 2008).

Analysis
Claim 1 is to a method “for ensuring the validity of a correspondence
between at least one marker and at least one phenotype.” The method
recites only one step: “providing a recursively determined estimate of
correlation between at least one marker and at least one phenotype across a
plurality of plant populations.” The Examiner rejected the claim, and its
dependents, as unpatentable subject matter under section 101.
To be patentable, a process must be “tied to a particular machine or
apparatus” or “transform[ ] a particular article into a different state or thing.”
In re Bilski, 545 F.3d at 954. Neither of those conditions are met by claim 1.
Claim 1 does not involve a machine or apparatus. The claim requires
“providing a recursively determined estimate of correlation . . . across a
plurality of plant populations.” The term “providing” does require that the
correlation estimate be provided by a machine or apparatus, but is broad
enough to cover verbal communication of a correlation estimate to another,
or a mental process in which the correlation estimate is provided to a reader
who reads it from printed matter. The claim also does not involve
transformation of an article. The claim is drawn to an abstract value – an
“estimate of correlation” – and this value is not changed or altered in the
claimed process, but is merely “provide[d].”
Appellants contend that “the claims require that the plant populations
used in the claim ‘collectively comprise progeny of a plurality of biparental
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crosses.’” (Reply Br. 9.) We do not agree with the interpretation that plants
or plant populations are “used” in the method as claimed.
Claim 1 identifies the plant populations for which the correlation is
provided as comprising “progeny of a plurality of biparental crosses.” The
claim is reasonably interpreted as requiring the “estimate of correlation” to
be determined from information concerning a marker and a phenotype that
was obtained from biparental crosses. But the claimed method does not
have a step that operates on a marker or on a plant to, e.g., produce a
measurable input for the determination of the estimate.
Further, there is no language in the claim that requires that the
biparental crosses to be performed as a step in the claimed method.
Appellants did not identify any language in the claim that would require that
interpretation. Although claims are read in light of the Specification, we
may not import limitations from the Specification to define the invention for
Appellants.
The rejection of claim 1 is affirmed. Claims 2-22, 24, and 32-36 fall
with claim 1 because separate reasons for their patentability were not
provided. 37 C.F.R. § 41.37(c)(1)(vii).

3. SECTION 101 & 112: UTILITY
3. Claims 23, 25, 26, and 28-30 stand rejected under 35 U.S.C § 101
because the claimed invention lacks patentable utility (Ans. 5).
Statement of the issue
The Examiner contends that the claims lack patentable utility because
they “do not recite any particular improvement or resultant characteristic
that is imparted to plant populations of progeny of a plurality of biparental
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crosses generated by the instant method.” (Ans. 6.) The Examiner contends
that the claims “encompass a process of basic research drawn to studying
correlations between at least one marker and at least one phenotype” (id.).
Thus, the issue in this case is whether the Examiner erred in the
determination that the asserted utility fails to fulfill the utility requirement of
35 U.S.C. § 101.
Principles of Law
The “utility requirement” originates with the provision of 35 U.S.C.
§ 101 that a patent may be obtained on “any new and useful process,
machine, manufacture, or composition of matter, or any new and useful
improvement thereof.” An inquiry by the Patent Office into whether a
claimed invention satisfies the utility requirement typically has two distinct
prongs. First, the Patent Office must determine whether the patent applicant
has asserted a specific and substantial utility for the claimed invention. In re
Fisher, 421 F.3d 1365, 1371 (Fed. Cir. 2005). Second, the Patent Office
must ascertain whether there is any evidence that one of ordinary skill in the
art would reasonably doubt the invention’s asserted utility. In re Brana,
51 F.3d 1560, 1566 (Fed. Cir. 1995).
Only one credible assertion of specific utility for the claimed
invention is necessary to satisfy 35 U.S.C. § 101 and 35 U.S.C. § 112. See
Raytheon Co. v. Roper Corp., 724 F.2d 951, 958 (Fed. Cir. 1983), cert.
denied, 469 U.S. 835 (1984).
Analysis
Claim 23 is to the method of claim 1 of “ensuring the validity of a
correspondence between at least one marker and at least one phenotype” and
further requiring, inter alia, crossing a selected plant to generate progeny. It
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is evident from Sebastian and Appellants’ Specification that the claimed
methods are useful in plant breeding to select traits which improve crops
plants and other plants of interest (Spec. 7: 14-28). The claimed methods are
accordingly not the kind basic research the Examiner references “to identify
or reasonably confirm a ‘real world’ context of use” (Ans. 6). The Examiner
did not provide evidence that this utility would have been doubted by
persons of ordinary skill in the art.
The utility rejection of claims 23, 25, 26, and 28-30 is reversed.

SUMMARY
The obviousness rejection of claims 1-26, 28-30, and 32-36 is
reversed.
The section 101 rejection of claims 1-22, 24, and 32-36 as drawn to
non-statutory subject matter is affirmed.
The section 101 and 112, first paragraph, rejections of claims 23, 25,
26, and 28-30 as lacking patentable utility is reversed.

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED-IN-PART

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