Ex Parte 6,964,850 et al

Board of Patent Appeals and Interferences

May 19, 2011

95001032 (B.P.A.I. May. 19, 2011)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
95/001,032 03/17/2008 6,964,850 506612800900 3059
52059 7590 05/20/2011
LIFE TECHNOLOGIES CORPORATION
C/O INTELLEVATE
P.O. BOX 52050
MINNEAPOLIS, MN 55402
EXAMINER
PONNALURI, PADMASHRI
ART UNIT PAPER NUMBER
3991
MAIL DATE DELIVERY MODE
05/20/2011 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

XDx, INC.
Requester and Respondent

v.

Patent of SOURCE PRECISION MEDICINE, INC.
Patent Owner and Appellant
____________

Appeal 2011-005235
Reexamination Control 95/001,032
Patent 6,964,850 B2
Technology Center 3900
____________

Before ROMULO H. DELMENDO, SALLY G. LANE, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION

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This is a decision on appeal in an inter partes reexamination of U.S.
Patent No. 6,964,850 B2. The Patent Owner appeals the Examiner’s
decision to reject claims as obvious under 35 U.S.C. § 103. The Board’s
jurisdiction for this appeal is under 35 U.S.C. §§ 6(b), 134, and 315. We
affirm.

STATEMENT OF THE CASE
The patent in dispute in this appeal is U.S. Patent No. 6,964,850 B2,
issued November 15, 2005 (hereinafter, “the ‘850 patent”).
A request for inter partes reexamination of the ‘850 patent was filed
on February 15, 2008 by a Third-Party Requester under 35 U.S.C. §§ 311-
318 and 37 C.F.R. §§ 1.902-1.997 (Request for Inter Partes Reexamination).
The claims of the ‘850 patent involve methods of providing an index
that is indicative of inflammation. The index is a numerical value which is
derived from RNA measurements of various RNAs in a sample taken from a
subject. There is one rejection in this appeal which is as follows:
Claims 1, 2, and 27 stand rejected under 35 U.S.C. § 103(a) as
obvious in view of Bull,1 Dugré,2 Bustin,3 and the Baker Declaration4 (Right

1 U.S. Patent No. 5,506,145, issued Apr. 9, 1996. ,
,2 Francine J. Dugré et al., Cytokine and Cytotoxic Molecule Gene
Expression Determined in Peripheral Blood Mononuclear Cells in the
Diagnosis of Acute Renal Rejection, 70 TRANSPLANTATION 7, 1074-1080
(2000).
3 S.A. Bustin, Absolute Quantification of mRNA Using Real-time Reverse
Transcription Polymerase Chain Reaction Assays, 25 J. MOLECULAR
ENDOCRINOLOGY 169-193 (2000).
4 Declaration of Dr. Joffre Baker in Support of Request for Inter Partes
Reexamintion, executed Jan. 4, 2008..
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of Appeal Notice (“RAN”) 4, dated February 26, 2010, incorporated by
reference into the Examiner’s Answer, dated September 2, 2010).

FINDINGS OF FACT5 (“FF”)
Bull Patent
1. Bull teaches “a method for determining the presence or absence of
an inflammatory condition in an individual by quantifying both the
fibrinogen content and hematocrit in a sample of the individual’s blood, and
calculating a composition Inflammation Index . . . derived from the two
aforesaid variables.” (Col. 1, ll. 8-14.)
2. Bull discloses a general equation I = a(f) + b(h) + c for determining
an individual’s inflammation index using fibrinogen level f, hematocrit or
hemoglobin h, and empirically derived constants a, b, and c (col. 3, ll. 17-
22).
3. Bull teaches that the Inflammation Index is indicative of systemic
inflammation in the donor of the blood sample (col. 4, ll. 7-10).

Dugré
4. Dugré used RT-PCR (reverse transcriptase-polymerase chain
reaction) to measure cytokine and cytotoxic mRNA expression in kidney
transplant patients (p. 1074).
5. Dugré normalized the mRNA levels by beta-actin mRNA (p.
1076).

5 The findings of fact in this Decision are not limited to those enumerated in
this section but may also be found in our Discussion below.
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6. Dugré found “that acute rejection episodes in renal transplant
recipients were associated with an increase in mRNA expression of
cytokines” in blood cells (p. 1074, col. 1). Increased expression, or up
regulation was measured for a given patient by comparing values at early
post transplantation and at rejection episodes to produce differential
expression values (p. 1076).
7. Dugré wrote that “Figure 1 shows that expression of IL-4, IL-5,
and IL-6 mRNA measured in patients’ PBMC was significantly higher . . . at
the time of acute rejection diagnosis compared with the signal levels
determined in the first few days posttransplantation (early post-TX).” (P.
1077, col. 1.)
8. Dugré concluded that the “evaluation of pro-inflammatory
cytokines and cytotoxic molecules prove useful in the clinical identification
of acutely rejecting transplant recipients.” (P. 1074, col. 1.)

Bustin
9. Bustin is a review article discussing quantification of mRNA using
real-time RT-PCR (p. 169).
10. Bustin discloses that “[s]pecificity, sensitivity and reproducibility
will be the most important qualitative characteristics for clinical diagnostic
purposes (p. 170, col. 1).
11. Bustin teaches that the Mg2+ and dNTP concentrations require
“strict control” and explains that Mg2+ dNTP mixtures affect the PCR
reaction (p. 172, col. 1).
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12. Bustin discussed non-competitive procedures in which
“quantification can be unreliable, as the efficiencies of both the RT and PCR
steps are likely to vary” and competitive PCR methods in which
amplification is achieved “with the same efficiency” when the same primer
recognition and internal sequences are shared between the internal standard
and primary (p. 172, col. 2).
13. Bustin teaches that “[s]horter amplicons amplify more efficiently
than longer ones and are more tolerant of reaction conditions.” (P. 178, col.
2.)
14. Bustin explained that the “concept of threshold cycle (Ct) is at the
heart of accurate and reproducible quantification using fluorescence-based
RT-PCR” (p. 179, col. 2).
15. Bustin “constructed standard curves for many target amplicons
[regions amplified by PCR primers] and detected differences in both their
amplification efficiencies and their sensitivities.” (P. 180, col. 2.) Bustin
found that the amplification efficiency for eIF4e was similar to that of
GAPDH (id.).
16. Bustin acknowledged that RT-PCR is characterized by variation
and non-reproducibility, but describes parameters which influence it (p. 180-
181).
17. Bustin stated that “real-time RT-PCR assays are significantly less
variable than any conventional RT-PCR procedure,” with a low coefficient
of variation and with “variability . . . between 0 and 5%” (p. 181, cols. 1-2).
18. In describing multiplex RT-PCR – a process in which more than
one target mRNA is detected by PCR in the same reaction using multiple
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primer sets – Bustin stated that “successful multiplexing is never trivial and
requires careful consideration about the suitability of both chemistry and
instrumentation.” (P. 185, col.1.)
19. Bustin reported that the Taqman multiplex PCR system “has been
used successfully to quantitate up to three . . . targets, with no apparent
reduction in sensitivity compared with the individual reactions” (p. 185, col.
2).
20. Bustin concluded:
The final difficulty is associated with limitations caused by
mutual interference of multiple sets of PCR primers, which can
reduce the dynamic range of the sensitivity and make
quantification unreliable.
(Id.)
21.
Furthermore, the efficacy of multiplex detection is significantly
affected by the extension time and the concentrations of dNTPs,
primers and MgCl2.
(Id.)
22.
Vastly different levels of mRNA will cause quantification
problems even for real-time detection . . . .
(Id.)
23.
Therefore, in practice, if the accurate quantification is the main
aim, it is probably best to limit multiplexing to the detection of
two or three transcripts.
(Id.)

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Perkin-Elmer User Bulletin #26
24. Perkin-Elmer describes methods for quantitating sample RNA or
DNA using PCR and multiplex PCR (p. 1).
25.
Before using the . . . method for quantitation, perform a
validation experiment like that in Figure 6 to demonstrate the
efficiencies of target and reference are approximately equal . . .
If the efficiencies of the two systems are not equal, perform
quantitation using the standard curve method. Alternatively,
new primers can be designed and synthesized for the less
efficient system to try to boost efficiency.
(P. 14.)

DISCUSSION
Claim 1, which we have selected as representative of the claimed
subject matter, is drawn to a method “of providing an index that is indicative
of the state of a subject, as to a biological condition characterized by
inflammation.” The method comprises:
• “using amplification for measuring the amount of RNA of
constituents from the sample of the subject” where the measurements of the
constituents form a first dataset;
• “wherein the measures for each constituent are performed under
measurement conditions that are substantially repeatable”;
• “the efficiencies of amplification for all constituents are substantially
similar”; and

6 APPLIED BIOSYSTEMS, USER BULLETIN #2: ABI PRISM 7700 SEQUENCE
DETECTION SYS. (1997).
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• “applying values from said first profile to an index function . . .
thereby providing a single-valued measure of the biological condition so as
to produce art index pertinent to the biological condition of the subject.”
The claim thus requires measuring more than one RNA (“RNA . . .
constituents”) level in the same sample and using the measurements to create
a single-value.
The Examiner determined that the claimed method was obvious in
view of the Bull patent and the Dugré and Bustin journal articles. The
Examiner also relied upon a written declaration by Dr. Joffre Baker, a Ph.D.
scientist who is currently Chief Scientific Officer of a company that
conducts genomic research (Declaration of Dr. Joffre Baker, dated January
4, 2008).
The Examiner found that the Bull patent described an “index
function” (“Inflammatory Index”), derived from protein measurements,
which served as a “single-valued measure of a biological condition” related
to inflammation as required by claim 1 (RAN 5-7). The Examiner found
that Bull differed from the claimed invention in measuring blood proteins
rather than RNA constituents as in the claim (Id.). The Examiner found that
the Dugré publication described measuring RNA of genes (“gene
expression”) involved in inflammation by PCR amplification (id. at 7-8).
The Examiner concluded that it would have been obvious to the ordinary
skilled worker to use the method of studying gene expression levels taught
by Dugré in the method of constructing an Inflammatory Index as taught by
Bull, since both Dugré and Bull taught measuring gene expression levels for
the purpose of detecting or predicting inflammation. (Id. at 8.)
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The Examiner acknowledged that neither Bull nor Dugré taught the
limitations of claim 1 “wherein the measures for each constituent are
performed under measurement conditions that are substantially repeatable
and the efficiencies of amplification for all constituents are substantially
similar.” (RAN 8.) However, the Examiner found that these limitations
would have been obvious in view of Bustin’s teaching about quantifying
RNA levels and optimizing reactions to ensure efficient RNA amplification
(id. at 8-9). In reaching this determination, the Examiner cited Dr. Baker’s
written testimony about what Bustin taught (id. at 8).
Appellant contends that the Examiner erred in determining that the
claimed subject matter would have been obvious to the ordinary skilled
worker in view of the cited prior art. Appellant contends:
1. None of the cited prior art references discloses or suggests the
claim limitation “the efficiencies of amplification for all constituents are
substantially similar” (App. Br. 11).
2. The combination of Bull with Dugré is internally inconsistent and
based on hindsight (id. at 19).
3. Evidence of unexpected results in the patent was not appreciated
by the Examiner (id. at 33).

1. The “efficiencies of amplification” limitation
The ‘850 patent does not explicitly define the phrase “the efficiencies
of amplification for all constituents are substantially similar.” However, the
following disclosure in the ‘850 patent provides guidance:
“Amplification” here refers to a degree of sensitivity and
specificity of a quantitative assay technique. Accordingly,
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amplification provides a measurement of concentrations of
constituents that is evaluated under conditions wherein the
efficiency of amplification and therefore the degree of
sensitivity and reproducibility for measuring all constituents is
substantially similar.
(‘850 patent, col. 9, ll. 17-23.)
it is desirable that a second criterion also be satisfied, namely
that quantitative measurement of constituents is performed
under conditions wherein efficiencies of amplification for all
constituents are substantially similar (within one to two percent
and typically one percent or less). When both of these criteria
are satisfied, then measurement of the expression level of one
constituent may be meaningfully compared with measurement
of the expression level of another constituent in a given sample
and from sample to sample.
(Id. at col. 12, ll. 18-27.)
Given a defined efficiency of amplification of target transcripts,
the point (e.g., cycle number) that signal from amplified target
template is detectable may be directly related to the amount of
specific message transcript in the measured sample.
(Id. at col. 14, ll. 26-30.)
Based on the above disclosures, the ordinary skilled worker would
have interpreted the claimed requirement that the amplification efficiencies
are substantially similar to mean that the amplification reaction produces the
same amount of product (e.g., DNA in PCR) for each RNA target (“within
one to two percent” (col. 12, ll. 18-27)). When the efficiencies are
comparable, “expression level of one constituent may be meaningfully
compared with measurement of the expression level of another constituent in
a given sample and from sample to sample.” (‘850 patent, col. 12, ll. 18-27.)
There is sufficient evidence that the objective of achieving
substantially similar amplification efficiencies for RNA constituents in the
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same sample was taught in the prior art. Bustin described procedures in
which amplification of more than one target RNA is achieved with the same
efficiency (FF12) and described using shorter amplicons to amplify targets
more efficiently (FF13). Bustin also taught detecting differences in
“amplification efficiencies” for “many target amplicons” and found
efficiencies similar for at least two different target RNAs (FF15).
In multiplex RT-PCR, where more than one target RNA (i.e., “RNA
constituents”) is measured in the same sample, Bustin reported success and
discussed parameters for increasing efficacy and reliability of PCR detection
(FF18, FF19, & FF21). Perkin-Elmer also described determining
amplification efficiency of a target and reference, and to design new primers
if “the efficiencies of the two systems are not equal” (FF25). Thus, the
evidence shows that the ordinary skilled worker recognized amplification
efficiency as a goal when measuring different RNA constituents from the
same sample.
Appellant contends that the Bull and Dugré publications are “utterly
lacking in any teaching or suggestion” of the efficiency requirement (App.
Br. 11). This argument has little merit since the Examiner acknowledged
this difference, but rather relied on Bustin for this teaching. (RAN 8.)
As for Bustin, Appellant contends that Bustin used normalization
procedures in which an internal control is used to correct variations in PCR
(App. Br. 12). Appellant also argues:
Other than in connection with Fig. 6, where Bustin shows
differing efficiencies of amplification for different genes,
Bustin never addresses this circumstance in relation to
measuring the amount of RNA amplification for each
constituent in a panel of constituents. Bustin references
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amplification efficiency only in the context of measuring
transcription of a single target or a single PCR reaction.
(Id.)
Appellant contends that, in Bustin’s discussion about competitive and
non-competitive amplification (FF12), Bustin was only concerned with
measuring a single target, not RNA constituents (i.e., more than one target)
in a sample, as claimed (App. Br. 13). Appellant contends that Bustin added
a “control” to the sample which is “artificial and, therefore” is not an
expressed product of a gene.” (Id.)
This argument is not persuasive. The Examiner cited Bull and Dugré
for suggesting the claimed limitation of “using amplification for measuring
the amount of RNA of constituents from the sample of the subject.” (Claim
1, emphasis added.) Thus, even if it is accurate that Bustin did not suggest
measuring RNA constituents from a single sample as claimed, this
difference does not refute the rejection.
Nonetheless, Appellant acknowledged that Bustin “talks about
measurement of multiple constituents.” (App. Br. 15.) Appellant attempts
to negate this disclosure by pointing out that Bustin shows dissimilar
efficiencies of amplification. (Id.) Appellant insists that Bustin actually
teaches away from achieving similar amplification efficiency because Bustin
characterizes multiplexing as “never trivial” and identifies difficulty in
achieving it (id.; FF18, FF20, & FF22).
There are two issues here. The first issue is whether the ordinary
skilled worker would have had reason to optimize the PCR reaction to
achieve amplification efficiency. The second issue is whether optimization
was enabled by the prior art at the time of the invention.
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As to the first issue, we have already identified the findings of fact
that support the Examiner’s position that amplification efficacy was an
objective of the prior art (FF12, FF13, FF15, FF21, & FF25). As to the
second issue of enablement, as discussed by the Examiner, there is sufficient
evidence that the skilled worker knew how to optimize the amplification
efficiency by adjusting magnesium concentrations, dNTP, primers, and
amplicon target size (FF11, FF13, FF21, & FF25). Dr. Baker’s written
expert testimony supports this position (Baker Decl., ¶ 24). Moreover, while
Bustin acknowledges “difficulty” in multiplexing methods for measuring
RNA constituents, the authors reported success (FF19) and suggested
limiting measurement to two to three targets (“transcripts”) in a single
reaction to achieve accuracy (FF23). Thus, while Bustin stated multiplexing
was “never trivial,” Bustin went on to temper that statement by explaining
that the conditions required “careful consideration” and then identified
result-effective parameters (FF18, FF20, and FF21). Thus, it is apparent that
Bustin believed it was within the ordinary level of skill in the art to
accomplish accurate and efficient measurement of RNA constituents in the
same sample.
Appellant contends that the written declaration by co-inventor Danute
Bankaitis-Davis (Declaration of Danute Bankaitis-Davis, dated July 16,
2008) establishes that “Bustin fails to teach the requirement herein of
substantially similar efficiencies for all RNA constituents” (App. Br. 15).
Dr. Bankaitis-Davis wrote in the declaration:
Bustin notes matter-of-factly that differences in amplification
efficiencies for different amplicons is a consequence of
performing RT-PCR, and then proceeds to discuss
normalization on pages 181-184 for how to correct for this after
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the amplification measurement is already performed. Nowhere
in Bustin is there any recognition that this is a problem that
should be fixed if one wishes to obtain measurements with
predictive value in molecular diagnostics. In addition, nowhere
in Bustin is there any suggestion or teaching of how one might
overcome such differences so that amplification efficiencies can
be obtained that are substantially similar for all constituents.
(Bankaitis-Davis, ¶ 12.)
Beginning on page 181 of the publication, Bustin discusses
normalization techniques for PCR. Dr. Bankaitis-Davis appears to take the
position that normalizing values in a sample is an alternative to, or mutually
exclusive from, adjusting amplification efficiencies in sample. However,
Bankaitis-Davis did not provide an adequate explanation for this conclusion.
To the contrary, in view of Bustin’s mention of amplification efficiency
more than once, as well as the disclosure of it in Perkin-Elmer, it is evident,
even if normalization was an alternative solution, that adjusting
amplification efficiency was still recognized as a viable approach.
Consistent with this factual evidence, Dr. Baker testified in a second written
declaration that persons of ordinary skill in the art would have recognized
amplification efficiency as a problem and would have known how to go
about correcting it (Second Declaration of Dr. Joffre Baker, ¶¶ 24-34, dated
August 18, 2008), a conclusion supported by the findings of fact in this
record (FF11, FF13, FF15, FF18, FF21, FF23, & FF25).
Appellant argues that Bustin teaches away from any hope that the
amplification efficiencies described in the patent could be achieved (App.
Br. 18). To support this position, Appellant cites various disclosures in
Bustin which are said to establish that existing methods are unsatisfactory
and do not achieve similar amplification efficiencies (id.).
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We acknowledge that Bustin, indeed, points to difficulties in
quantitating RNA. However, at the same time, Bustin expressly identifies
parameters that can be adjusted to achieve better quantitation and
amplification efficiency. We are unpersuaded that Bustin only describes
quantifying and efficiency for one target, when there is explicit disclosure
about multiplexing multiple RNA constituents successfully (FF19).
The question, as we already stated, is one of enablement.
The applicant has the burden of coming forward with evidence
in rebuttal, when the prior art includes a method that appears,
on its face, to be capable of producing the claimed composition.
This burden may be met by presenting sufficient reason or
authority or evidence, on the facts of the case, to show that the
prior art method would not produce or would not be expected to
produce the claimed subject matter.
In re Kumar, 418 F.3d 1361, 1368 (Fed. Cir. 2005).
In this case, Bustin reported that multiplexing PCR “has been used
successfully to quantitate up to three . . . targets” and identifies factors to
adjust PCR efficacy (FF19 & FF21). Similarly, Perkin-Elmer describes
factors to boost amplification efficiency and accuracy (FF24 & FF25).
Appellant did not provide adequate evidence that such factors would not
have enabled the ordinary skilled worker to achieve substantially similar
amplification efficiencies. Contrary to Appellant’s statements, Bustin
expressly found amplification efficiency of two targets to be similar (FF15),
cutting against Appellant’s position that there was no hope of achieving
substantially similar amplification efficiencies as claimed.
Moreover, as noted by the Requester, it appears that the ‘850 patent
used methods in the prior art to achieve amplification efficiency, militating
against a conclusion of non-enablement (Respondent Br. 8). For example:
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For measuring the amount of a particular RNA in a sample, we
have used methods known to one of ordinary skill in the art to
extract and quantify transcribed RNA from a sample with
respect to a constituent of a Gene Expression Panel. (See
detailed protocols below. Also see PCT application publication
number WO 98/24935 herein incorporated by reference for
RNA analysis protocols).
(‘850 patent, col. 14, ll. 3-10.)

2. The combination of Bull with Dugré is internally inconsistent and based
on hindsight (App. Br. 19).

a) Appellant contends that Bull’s protein disclosure cannot be
combined with references dealing with measuring RNA constituents.
Appellant argues that Bull’s test was intended to be “quick and easy,” and
that applying it to RNA measurements would have made it “inoperable for
its intended purpose.” (App. Br. 20-21.) Appellant asserts that Dugré uses
measurements at different times from two different samples, not RNA
measurements from a single sample as required by the claim. Appellant also
contends that mRNA levels are poorly correlated with proteins levels,
teaching away from combining Bull’s protein method with Dugré RNA
method (id.).
The Examiner’s reason for combining Bull and Dugré was that both
prior art references dealt with measuring gene expression for the purpose of
diagnosing an inflammatory condition (RAN 8). Bull looked at protein and
Dugré looked at RNA. Appellant questions the characterization of Bull as
describing “gene expression.” (Source Precision Rebuttal Br. 13.)
However, to the extent that a protein is a product of a gene, the Examiner
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correctly found that a protein is expressed by a gene and therefore
representative of “gene expression.”
Bull produced an “Inflammatory Index” using two protein variables
(FF1 & FF2). Bull did not suggest adapting its Inflammatory Index to RNA.
However, an obviousness “analysis need not seek out precise teachings
directed to the specific subject matter of the challenged claim, for a court
can take account of the inferences and creative steps that a person of
ordinary skill in the art would employ.” KSR Int’l Co. v. Teleflex, Inc., 550
U.S. 398, 418 (2007).
[T]he teaching, motivation, or suggestion may be implicit from
the prior art as a whole, rather than expressly stated in the
references. . . . The test for an implicit showing is what the
combined teachings, knowledge of one of ordinary skill in the
art, and the nature of the problem to be solved as a whole would
have suggested to those of ordinary skill in the art.
In re Kahn, 441 F.3d 977, 987-988 (Fed. Cir. 2006).
Having found an “Inflammation Index” comprising two protein
variables useful for determining an inflammatory condition, persons of
ordinary skill in the art would have reasonably been motivated to apply the
Bull teachings to RNA levels because the latter was another recognized
measure of gene expression. Moreover, RNA levels had indeed been used
by Dugré to look at inflammation associated with transplantation (FF4-FF8).
There is no requirement for an explicit suggestion to have been made, as
long as there is rationale for combining the teachings of the prior art, as there
was here.
The argument that adapting Bull’s protein index to RNA would have
run contrary to Bull’s teaching about an easy and quick test puts improper
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emphasis on Bull. The question in an obviousness analysis is what the prior
art as a whole would have suggested to the skilled worker. Kahn, 441 F.3d
at 987-988. Even were it true that Bull’s protein has certain advantages that
would not be achieved with an RNA test, Dugré provides evidence that RNA
expression levels were recognized in the prior art as valid markers for
predictive diagnosis,7 giving the ordinary skilled worker reason to use it.
According to Dr. Sidney Hecht, a Ph.D. scientist “well acquainted
with RNA expression and regulation,” “there is a good reason to believe
from first principles that the use of proteins as the basis for creating indexes
suitable to monitor specific biological conditions will not correlate well in
many cases with the results obtained monitoring RNA levels for those
proteins.” (Declaration of Sidney M. Hecht, July 17, 2008, ¶¶ 10 & 18.)
Dr. Hecht explained this lack of correlation as due to the presence of
riboswitches and other RNA types (id.).
In this specific case, as noted by Dr. Baker in his written declaration,
cytokine protein levels had been known to be associated with inflammation
(Baker Decl., ¶ 21). This provided Dugré with a reason to study the
corresponding RNA expression levels (p. 1074). Moreover, Dugré wrote:
Recently, gene expression of cytolytic molecules as well as the
cytokine transcripts [RNA], determined in peripheral blood

7 The ‘850 patent acknowledged that the “prior art has utilized gene
expression data to determine the presence or absence of particular markers
as diagnostic of a particular condition.” (Col. 1, ll. 21-24.) Gene expression
is defined in the ‘850 patent as RNA or protein, and thus the relative
interchangeability of the two biomolecules appears to have been recognized
by Appellant.

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lymphocytes of patients, have been found correlated with their
intragraft mRNA during allograft rejection.
(P. 1074, col. 2.) [FF27.] Thus, both proteins and RNA were recognized in
the context of inflammation (e.g., transplant rejection) as useful variables to
measure.
The claims require measuring RNA constituents from one sample and
using that information to derive an inflammatory index. Appellant
repeatedly argues that Dugré utilized two samples in its analysis, while Bull
used only one. For this reason, Appellant contends that it would not have
been obvious to have combined the two prior art references for diagnostic
purposes.
It is true Dugré measured RNA constituent levels from different genes
in two different samples (after transplantation and during acute rejection) for
the same subject. While Dugré compared the RNA levels in the two
different samples to produce a “differential expression” value (p. 1076, col.
2; FF6), it cannot be ignored that Dugré first measured “the amount of RNA
of constituents from the sample of a subject,” the same step recited in claim
1. This data was reported by Dugré in Figure 1 and discussed (FF7). In
sum, Dugré considered the levels of RNA constituents from one sample
relevant to his analysis.
b) Appellant contends Dugré’s method “raises a question to the
person of ordinary skill in the art whether the gene expression value of a
sample from a patient at any given time, taken by itself, is even useful.”
(App. Br. 24.) To support this position, Appellant directs attention to
Dugré’s Figure 1. Figure 1 shows expression levels of the different genes
shortly after kidney transplantation (from a first sample) and then at the time
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of acute rejection (from a second sample). Focusing on the expression levels
of IL-4, Appellant asserts that at least one of the baseline values (following
kidney transplantation, but before acute rejection diagnosis) was higher than
all but one of the RNA levels at the time of acute rejection – and thus is not
a reliable baseline.8 Appellant also states that some of the RNA levels at the
time of acute rejection were about the same as the baseline level. Because of
this variability, Appellant contends that the skilled worker would not have
expected any single value to be useful for predicting a disease or condition.
We do not dispute Appellant’s observation that Figure 1 of Dugré
shows that baselines levels (early post-transplantation) for RNAs said to be
up-regulated during an acute transplantation rejection were not uniformly
lower than the RNA levels measured at the time of acute rejection. For
example, for IL-4, at least one baseline value measured shortly after
transplantation was higher than several values measured at acute rejection
(App. Br. 23-25). Additionally, several of the acute rejection levels
appeared to be about the same as the baseline levels (id.). Based on this
data, Appellant argues:
Dugré's data do not permit inference about an individual's
biological condition based solely on gene expression
measurements determined from a single sample from the
subject. Consequently, to a person of ordinary skill in the art,
Dugré teaches that gene expression measurements from a
sample taken on a single occasion are not informative of
biological condition because they have too great a range of
variation. Dugré further teaches that such measurements need to

8 Appellant’s position is that baseline RNA levels should be lower than all
the acute rejection levels in genes characterized by Dugré as being up-
regulated.
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be put in context by a comparison with another set of
measurements from another sample taken, on a different
occasion, from the same subject, so that a comparison can be
made to identify a change in gene expression in the subject
caused by different conditions on the two occasions.
(Id. at 25-26.)
Despite the “variation” in data noted by Appellant, there are values in
Dugré’s reported experiments in which the individual RNA levels during
acute rejection were higher than baseline levels. Appellant did not deny this
fact. Thus, in at least several cases, the ordinary skilled worker would have
recognized that individual RNA levels for a particular gene were indicative
of the inflammatory state. This conclusion is additionally reflected in
Dugré’s statement that “Expression of IL-4, IL-5, and IL-6 mRNA was
significantly higher at the time of acute rejection than during the first few
days post-TX [transplantation].” (Dugré at p. 1078; see also FF7.) There
was therefore a general trend in the data in which individual RNA levels
during the acute rejection phase were higher for IL-4, IL-5, and IL-6 than at
baseline. Based on Dugré’s own conclusion coupled with the general trend
in the data, the ordinary skilled worker would have reasonably expected that
single values for IL-4, IL-5, and IL-6 RNA would be pertinent to the
inflammatory condition of the subject patient.
According to Dr. Hecht, “[f]alse positive and negative rates of the
order described in [Dugré] argue against the utility of the method as
described.” (Hecht Decl. ¶ 19.)
We have given consideration to Dr. Hecht’s opinion, but do not find it
persuasive. Specifically, statements by Dugré lead the other way. Dugré
wrote in the Discussion section (p. 1079) [FF28]:
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The up-regulation of . . . IL-4 [etc.] . . . might be a potential
indicator of a rejection event . . . In the perspective of
confirming their usefulness as a prognostic tool in clinical
rejection, we are applying this protocol to new transplant
patients.
Thus, while Dugré characterized its results as a “potential indicator of
a rejection event,” Dugré still considered the results reliable enough to apply
to a new clinical trial. The standard applied by Appellant appears to be too
stringent, requiring absolute proof that the prior art method worked 100% of
the time to have been considered by the ordinary skilled worker as useful.
To the contrary, Dugré’s own statement indicates that even preliminary
results were sufficient in this case to give the ordinary skilled worker a
reasonable basis to believe that the method was a useful diagnostic tool,
including the individual RNA levels measured during acute transplant
rejection.

3. Unexpected Results
In making an obviousness determination, the Supreme Court instructs
us “to look at any secondary considerations that would prove instructive.”
KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398, 415 (2007). Appellant states
that the ‘850 patent Specification shows evidence of “unexpected results,” a
secondary consideration which Appellant contends was unappreciated by the
Examiner (App. Br. 33). According to Appellant, the unexpected results,
among other things, show that an inflammatory index requires only a single
sample using RNA measurements, and that the index provides a reliable
measure of the extent of disease, and enables monitoring, tracking and
quantitative assessment of therapies used to treat the disease (id. at 41-42).
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Appellant also contends that the RNA expression levels obtained by its
method are tightly regulated and normally distributed (id.).
While secondary considerations must always be considered in making
an obviousness determination, they are not dispositive, but must be weighed
against other indices of obviousness.
The existence of such evidence, however, does not control the
obviousness determination. See Newell, 864 F.2d at 768 (“First,
as indicated, obviousness is not a factual inference; second,
although these factors must be considered, they do not control
the obviousness conclusion.”) (citations omitted); Ryko, 950
F.2d at 719 (the weight of secondary considerations may be of
insufficient weight to override a determination of obviousness
based on primary considerations). Therefore, we must consider
all of the evidence under the Graham factors before reaching
our decision.
Richardson-Vicks, Inc. v. The Upjohn Co., 122 F.3d 1476, 1483 (Fed. Cir.
1997).
Because Appellant contends that the results obtained by the claimed
method are “unexpected,” we first look at the relevant legal principles to be
considered when establishing unexpected results. According to In re Soni,
54 F.3d 746, 750-51 (Fed. Cir. 1995), prima facie obviousness can be
rebutted with
a showing of “unexpected results,” i.e., to show that the
claimed invention exhibits some superior property or advantage
that a person of ordinary skill in the relevant art would have
found surprising or unexpected. The basic principle behind this
rule is straightforward - that which would have been surprising
to a person of ordinary skill in a particular art would not have
been obvious.
. . . .
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[W]hen an applicant demonstrates substantially improved
results, as Soni did here, and states that the results were
unexpected, this should suffice to establish unexpected results
in the absence of evidence to the contrary.
In this case, there is limited testimony by persons of ordinary skill in
the art that the claimed method produced unexpected results. At column 11,
lines 61-63 of the ‘850 patent, it is stated:
We have found that valuable and unexpected results may be
achieved when the quantitative measurement of constituents is
performed under repeatable conditions.
However, the need for reproducibility was recognized by Bustin
(Abstract; FF10, FF14, & FF17). Bustin stated that optimization and
consistency were critical for obtaining reproducible results, and described
real-time RT-PCR Taqman assays as having a low coefficient of variation
(p. 181; FF10, FF16, & FF17). Thus, as found by the Examiner, Bustin
described a reproducible method for measuring RNA levels (RAN 8), the
same result which Appellant now characterizes as “unexpected.” Therefore,
the property characterized as “unexpected” would have been possessed by
the prior art and consequently is not a persuasive basis to establish non-
obviousness. As stated in In re Baxter Travenol Labs., 952 F.2d 388, 392
(Fed. Cir. 1991):
Baxter argues that the unexpected hemolysis-suppression
quality of DEHP rebuts any prima facie showing of
obviousness. However, when unexpected results are used as
with the closest prior art. . . . Since the prior art bags
plasticized with DEHP were inherently suppressing hemolysis,
albeit unknown at the time of the Becker document, this
hemolysis-suppressing function is not a basis for rebutting a
prima facie finding of obviousness.
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Appellant’s “unexpected results” boil down to the demonstration that
a method of providing an inflammatory index, based on RNA constituents in
a single sample from a subject, predicts inflammation in a specific disease
with a high degree of confidence. The issue is whether there was a
reasonable expectation that the claimed method, using RNA, could be
arrived at successfully based on the prior art.
The evidence put forward by the Examiner shows:
• Bull’s teaching of an Inflammatory Index based on two protein
variables;
• Dugré’s teachings that RNA levels had been used as a marker for
inflammatory disease, albeit not as a composition index as shown in the Bull
patent publication; and
• The prior art (Dugré and Bustin) enabled producing reproducible
quantification of mRNAs with similar amplification efficiencies. Bustin,
contrary to Appellant’s arguments, describes reproducibility and
amplification efficiency as desired outcomes in PCR (FF10, FF13, FF17),
identified process parameters (FF11, FF13, FF21), and acknowledged that
multiplexing had been used “successfully to quantitate up to three . . .
targets, with no apparent reduction in sensitivity as compared with the
individual reactions” (FF19).
In view of such disclosures, the Examiner had a credible basis to shift
the burden to Appellant to show evidence of a lack of expectation of
success.
We find Appellant’s evidence unavailing. As already discussed,
Dugré showed a general trend in its single-point data toward high RNA
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levels during acute rejection, providing evidence that success would be
expected. Success does not have to be guaranteed as long as the skilled
worker would have perceived a reasonable likelihood of success. Alza Corp.
v. Mylan Labs., Inc., 464 F.3d 1286, 1295 (Fed. Cir. 2006).
Secondly, both Bustin and Perkin-Elmer, as mentioned above,
provided evidence that parameters were known in the prior art about how to
achieve reproducibility and amplification efficiency. Appellant has not
established through objective evidence that such parameters would not work.
We have considered the testimony of Dr. Bankaitis-Davis and others on this
issue, but do not find that it outweighs the factual evidence in the Bustin and
Perkin-Elmer publications.
For example, Dr. Bankaitis-Davis stated that “Bustin never discusses
or suggests measurements conditions wherein the efficiencies for all
constituents are substantially similar, except to teach away from this claim
limitation” (Bankaitis-Davis Decl. ¶ 9). However, Bustin, in fact, refers to
targets having similar amplification efficiency (FF15), a statement that Dr.
Bankaitis-Davis did not address in the declaration. Dr. Bankaitis-Davis also
said that “even today the industry still does not understand that amplification
efficiencies for all constituents should be substantially similar.” (Bankaitis-
Davis Decl. ¶ 14). However, this conclusion appears inconsistent with
statements in Bustin about efficiencies, and Perkin-Elmer’s instruction
(FF24):
If the efficiencies of the two systems are not equal, perform
quantitation using the standard curve method. Alternatively,
new primers can be designed and synthesized for the less
efficient system to try to boost efficiency.
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The Bankaitis-Davis Declaration reported that amplification
efficiencies were not consistent across ABI reagent lots (¶ 19). This
evidence does not establish a lack of a reasonable likelihood of success.
First, Dr. Bankaitis-Davis did not indicate that the ABI lots and experiments
were prior art. Second, and independently, both Bustin and Perkin-Elmer
recognized that amplification efficiency might be different for different
samples, and indicated that optimization had to be done if such differences
were found.

SUMMARY
We affirm the Examiner’s rejection of claims 1, 2, and 27 under 35
U.S.C. § 103(a) as obvious in view of Bull, Dugré, Bustin, and the Baker
Declaration.

TIME PERIOD FOR RESPONSE
Requests for extensions of time in this inter partes reexamination
proceeding are governed by 37 C.F.R. § 1.956. See 37 C.F.R. § 41.79.

AFFIRMED

bim

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