Ex Parte Sherlock et al

Patent Trials and Appeals Board

Mar 4, 2019

14008480 - (D) (P.T.A.B. Mar. 4, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
14/008,480 12/10/2013
77974 7590 03/06/2019
Stanford University Office of Technology Licensing
Bozicevic, Field & Francis LLP
201 REDWOOD SHORES PARKWAY
SUITE 200
REDWOOD CITY, CA 94065
Gavin J. Sherlock
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
STAN-826 4834
EXAMINER
GOLDBERG, JEANINE ANNE
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
03/06/2019 ELECTRONIC
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.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
docket@bozpat.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte GA VIN J. SHERLOCK, JAMES DUANE BROOKS,
RICHARD M. MYERS, YUY A KOBAYASHI, and
DEVIN M. ABSHER
Appeal2017-011677
Application 14/008,480
Technology Center 1600
Before ULRIKE W. JENKS, RYAN H. FLAX, and DAVID COTTA,
Administrative Patent Judges.
JENKS, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellants 1 appeal from Examiner's
decision to reject claims as anticipated and as being directed to non-statutory
subject matter. We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
1 Appellants identify the real party in interest as The Board of Trustees of
the Leland Stanford Junior University and Hudson Alpha Institute for
Biotechnology. Br. 2. We have considered, and herein refer to, the
Specification of September 27, 2013 ("Spec."); Final Office Action of
August 17, 2016 ("Final Act."); Advisory Action of December 9, 2016;
Appeal Brief of April 17, 2017 ("Br."); and Examiner's Answer of May 26,
2017 ("Ans.").
Appeal 2017-011677
Application 14/008,480
STATEMENT OF THE CASE
Claims 1, 3---6, and 8-16 are on appeal, and can be found in the
Claims Appendix of the Appeal Brief. Claim 1 is representative of the
claims on appeal, and reads as follows:
1. A method detecting the presence of prostate cancer cells
in a sample, the method comprising:
obtaining a sample suspected of comprising prostate
cancer cells from an individual;
testing the sample for the presence of methylated
cytosine in a CpG context in promoters ofEIF5A2, EPHA2,
RAB33A, SYN GR I, and EPSTll in DNA, and
detecting prostate cancer cells by the presence of
increased methylated cytosine in a CpG context in promoters of
EIF5A2, EPHA2, RAB33A, SYN GR I, and EPSTll in DNA.
Appellants request review of following rejections made by Examiner:
I. Claims 1, 3---6, and 8-16 underpre-AIA 35 U.S.C. § 101, as
being directed to non-statutory subject matter.
II. Claims 1, 3---6, and 8-16 under pre-AIA 35 U.S.C. § I02(a) as
being anticipated by Sorensen. 2
III. Claims 1, 3---6, and 8-16 underpre-AIA 35 U.S.C. § I02(b) as
being anticipated by Vanaja. 3
I. Patent Ineligible Subject Matter
Examiner rejected claims 1, 3---6, and 8-16 as being directed to a
judicial exception. Ans. 4. In particular, Examiner finds:
2 Sorensen et al., US 2010/0303795 Al, published Dec. 2, 2010
("Sorensen").
3 Vanaja et al., Abstract #5197: Comprehensive DNA methylation analysis,
69 CANCER RESEARCH 5197 (2009) ("Vanaja").
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Claim 1 is directed to "a method detecting the presence of
prostate cancer cells in a sample" by obtaining a sample and
testing ["]the presence of methylated cytosine in a CpG context
in promoters of EIF5A2, EPHA2, RAB33A, SYNGRI and
EPSTll" in [the] sample and detecting prostate cancer cells by
the presence of increased methylated cytosine in a CpG context
in promoters of EIF5A2, EPHA2, RAB33A, SYNGRI and
EPS TI 1. [This relates to] a correlation that preexists in the human
body is an unpatentable phenomenon. Any association between
increased methylation ofEIF5A2, EPHA2, RAB33A, SYNGRI,
and EPSTll and prostate cancer cells is a law of nature/natural
phenomenon.
Ans. 4--5.
Appellants contend "that the present claims provide specific
limitations other than what is well-understood, routine and conventional in
the field." Br. 6. Citing the JUL-I example from the USPTO May 2016
Guidelines for subject matter eligibility, Appellants contend that there is no
need to move on to Step 2B. Id. Specifically, arguing that when viewing the
claim as a whole the process of detecting JUL- I is not focused on the
product per se. Id. Appellants contend that the "claims very specifically call
out a combination of genes that must be tested for methylation, as well as
cytosine methylation specifically in a CpG context." Id. at 7.
Issue Presented
Does a preponderance of the evidence of record support Examiner's
conclusion that claims 1, 3---6, and 8-16 are directed to patent ineligible
subject matter?
Analysis
Unless otherwise noted, we adopt Examiner's findings and reasoning
as set out in the Final Office Action and Answer and agree that the claims
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are unpatentable under 35 U.S.C. § 101. See Final Act. 3-10; see Ans. 2-8,
12-14.
We analyze this appeal under the framework set forth by the Supreme
Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566
U.S. 66 (2012), and applied by our reviewing court in Ariosa Diagnostics,
Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015). As the Ariosa court
explained:
In Mayo . . . , the Supreme Court set forth a framework for
distinguishing patents that claim laws of nature, natural
phenomena, and abstract ideas from those that claim patent-
eligible applications of those concepts. First, we determine
whether the claims at issue are directed to a patent-ineligible
concept. If the answer is yes, then we next consider the elements
of each claim both individually and "as an ordered combination"
to determine whether additional elements "transform the nature
of the claim" into a patent-eligible application. The Supreme
Court has described the second step of this analysis as a search
for an "inventive concept"-i.e., an element or combination of
elements that is "sufficient to ensure that the patent in practice
amounts to significantly more than a patent upon the [ineligible
concept] itself."
Id. at 1375 (alteration in original) (internal citations omitted).
We begin with the first step of the Mayo test, namely, whether a claim
is "directed to" a patent-ineligible concept. On January 7, 2019, the Director
of the USPTO issued the "2019 Revised Patent Subject Matter Eligibility
Guidance" ("Revised Guidance"), which provides further details regarding
how the Patent Office analyzes patent-eligibility questions under 35 U.S.C.
§ 101. 84 Fed. Reg. 50-57 (Jan. 7, 2019). Under the Revised Guidance, the
first step of the Mayo test (i.e., Step 2A of the Revised Guidance) is "a two-
prong inquiry." Id. at 54. In prong one, we evaluate whether the claim recites
a judicial exception, such as laws of nature, natural phenomena, or abstract
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ideas. Id. If the claim recites a judicial exception, the claim is further
analyzed under prong two, which requires "evaluat[ion ofJ whether the claim
recites additional elements that integrate the exception into a practical
application of that exception." Id. The Revised Guidance explains that, "[i]f
the recited exception is integrated into a practical application of the
exception, then the claim is eligible at Prong Two of ... Step 2A [ of the
Revised Guidance]." Id.
Step 2A - Prong One
In our analysis, we must determine whether Appellants' claims are
directed to a law of nature. We select claim 1 as representative. With respect
to the first prong of Step 2A of the Revised Guidance, we agree with
Examiner that independent claim 1 recites a patent-ineligible law of nature.
Specifically, claim 1 recites the relationship between the presence of
increased methylated cytosine in a CpG context in promoters ofEIF5A2,
EPHA2, RAB33A, SYNGRI, and EPSTll and a correlation with prostate
cancer. Examiner points out that "[a] diagnosis step is an abstract mental
process. It is further noted that the recitation of the determining step is an
action than can be performed mentally." Final Act. 6. "[T]he process to
predict the diagnosis of prostate cancer, amounts to no more than an
'instruction to apply the natural law."' Id. at. 8. Examiner explains that
"[a]ny association between increased methylation of EIF5A2, EPHA2,
RAB33A, SYNGRI, and EPSTll and prostate cancer cells is a law of
nature/natural phenomenon. With regard to the natural correlation, as in
Prometheus, the relationship is itself a natural process that exists apart from
any human action." Ans. 4--5.
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We are not persuaded by Appellants contention that the active step of
"detection" as recited in the claim cannot be a "mental step." Br. 7. We
agree with Examiner's position that the claims are directed to patent-
ineligible subject matter because they are directed to a law of nature and
natural phenomenon, namely, the correlation between the presence of
increased methylated cytosine in a CpG context of the recited promoters and
the presence of prostate cancer cells.
Step 2A - Prong Two
Under the Revised Guidance, we must also determine "whether the
claim recites additional elements that integrate the exception into a practical
application of that exception." 84 Fed. Reg. at 54. Limitations that are
indicative of integration into a practical application include applying the
natural law to effect a particular treatment or prophylaxis for a disease or
medical condition. See, e.g., Vanda Pharms. Inc. v. West-Ward Pharms. Int 'l
Ltd., 887 F.3d 1117, 1134--35 (Fed. Cir. 2018) (holding that claims
including a limitation of genotyping to determine if a patient is a CYP2D6
poor metabolizer and then administering a drug in certain amounts
depending upon whether the patient is or is not a CYP2D6 poor metabolizer
where risk of QTc prolongation is correlated to the amount of drug
administered and status as CYP2D6 metabolizer is an application of the
relationship between the drug, CYP2D6 metabolism, and QTc prolongation).
On the other hand, diagnostic methods that simply measure the
concentration of a drug after administration and determine whether a
particular dosage of a drug will prove ineffective or cause harm is not a
practical application. Mayo, 566 U.S. at 77. That is because the method itself
does not recite a use of the natural relationship, it simply provides for an
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observation based on that relationship. Id.; see also Athena Diagnostics, Inc.
v Mayo Collaborative Services, LLC, No. 2017-2508, 2019 WL 453489, at
*5 (Fed. Cir. Feb. 6, 2019) (noting that while the claims include certain
concrete steps, those steps only apply conventional techniques to detect the
natural law, i.e., "observe its operation").
We conclude, as Examiner did, that the steps of obtaining a sample,
testing the sample for CpG levels, and "detecting prostate cancer cells by the
presence of increased methylated cytosine in a CpG context in [the]
promoters" as required by the claim amount to diagnosing the subject. See
Ans. 5 ("[T]he claim is essentially diagnosing by the presence of prostate
cancer cells."). "The testing step essentially tells users to determine the
methylation through whatever known processes they wish to use." Ans. 7.
The detecting step is thereby not an additional element that integrates the
exception into a practical application, nor is the diagnostic observation. See
Ans. 7 ("The detecting prostate cancer cells tells users of the process to
predict the detection or diagnosis of prostate cancer cells which amounts to
no more than an 'instruction to apply the natural law."'). Similar to the
claims in Athena, claim 1 is directed to measuring increased methylated
cytosine in a CpG context in promoters and associating the increased levels
with a diagnosis, as such the claims only encompass the natural law itself.
See Athena, 2019 WL 453489, at *6 ("Claiming a natural cause of an
ailment and well-known means of observing it is not eligible for patent
because such a claim in effect only encompasses the natural law itself.").
Step 2B - Inventive Concept
Having determined that claim 1 is directed to a patent-ineligible law
of nature without an integration into a practical application, we next consider
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whether claim 1 recites "an element or combination of elements that is
'sufficient to ensure that the patent in practice amounts to significantly more
than a patent upon the [ineligible concept] itself."' Ariosa, 788 F.3d at 1375
( citation omitted). We agree with Examiner that it does not. Ans. 5---6.
Examiner finds that " [ t ]he claims also do not add a specific limitation other
than what is well understood, routine and conventional in the field." Ans. 6
( citing the use the Illumina Human Methylation 27 Bead Chip4). The data
gathering step of the claims does not add "significantly more" to the law of
nature/natural phenomenon on which the claim is based so as to provide
eligibility on its own. Appellants present no persuasive evidence to the
contrary.
For the reasons discussed above we are not persuaded that Examiner
erred in rejection claim 1 as patent ineligible. Claims 3---6 and 8-16 were not
separately argued and fall with claim 1. See 37 C.F.R. § 4I.37(c)(l)(iv).
II. Anticipation by Sorensen
Examiner finds that Sorensen teaches methods of diagnosing prostate
cancer using Infinium Human Methylation 27 Bead Chip (Illumina). See
Final Act. 13; Ans. 9-10 (citing Sorensen ,r,r 55, 96,270, claims), 15-19.
Appellants contend that "[ t ]he present claims are drawn to the
identification of prostate cancer cells by specifically determining increased
methylation in the promoter region of the recited genes." Br. 3. "[O]ne of
skill in the art would not have reason to select the specific set for analysis
.... " Id. at 4.
4 See, e.g., Sorensen ,r,r 114, 116,118,433,435,440,441.
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Upon consideration of the evidence on this record, and Appellants'
contentions, we find that the preponderance of evidence supports
Examiner's finding that the subject matter of Appellants' claims is
unpatentable. Accordingly, we affirm Examiner's rejections for the reasons
set forth in the Answer and Final Action, which we adopt as our own,
including Examiner's responses to Appellants' arguments.
Specifically, we agree with Examiner that the claims, by virtue of
using the transitional phrase "comprising," are not limited to determining the
methylated cytosine in a CpG context of the recited promoters. Accordingly,
the broadest reasonable interpretation of the claims does not exclude
identification of the methylation status in additional genes. See Ans. 18.
Because the claims are not limited to the five recited promoters, we agree
with Examiner that Sorensen's disclosure of using the Infinium Human
Methylation 27 Bead Chip (Illumina) (see, e.g., Sorensen ,r,r 114, 116, 118,
433,435,440,441) meets the claim limitation. We note that Appellants
Specification discloses using same Illumina chip as the one disclosed in
Sorensen. See Spec. ,r 81. Under the principles of inherency, if a prior art
device, in its normal and usual operation, would necessarily perform the
method claimed, then the method claimed will be considered to be
anticipated by the prior art device. In re King, 801 F.2d 1324, 1326-27 (Fed.
Cir. 1986). We agree with Examiner's position that the Illumina chip
contains the recited promotors ( as well as other pro motors not recited in
claim 1), and that Sorensen's process of determining the methylation state of
promotors in patient derived samples would simultaneously include
detecting the methylation state of the recited promoters. See Ans. 15-19.
Accordingly, we agree with Examiner's finding that testing patient samples
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for methylation patterns using the Illumina chip for the purpose of detecting
prostate cancer as disclosed in Sorensen would anticipate the claims. We
affirm the rejection of claims 1 and 14 under 35 U.S.C. § 102 by Sorensen.
Claims 3-6, 8-13, 15, and 16 were not separately argued and fall with
claims 1 and 14.
III. Anticipation by Vanaja
Examiner finds that Vanaja teaches methods of diagnosing prostate
cancer using Infinium Human Methylation 27 Bead Chip (Illumina). See
Final Act. 15-16; Ans. 10-11, 19-22.
Appellants contend that "[ t ]he present claims are drawn to the
identification of prostate cancer cells by specifically determining increased
methylation in the promoter region of the recited genes." Br. 4. Appellants
further argue, "[ o ]ne of skill in the art cannot determine from the teachings
of Vanaja anything more than a general indication that there may be a
change, but is not informed where and what the change is." Id. at 5.
Upon consideration of the evidence on this record, and Appellants'
contentions, we find that the preponderance of evidence supports
Examiner's finding that the subject matter of Appellants' claims is
unpatentable. Accordingly, we affirm Examiner's rejections for the reasons
set forth in the Answer and Final Action, which we adopt as our own,
including Examiner's responses to Appellants' arguments.
As discussed above, we agree with Examiner that the claims, by virtue
of using the transitional phrase "comprising," are not limited to the recited
promoters. Accordingly, the broadest reasonable interpretation of the claims
does not exclude additional genes. See Ans. 21-22. Because the claims are
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not limited to the five recited promoters, we agree with Examiner that
Vanaja's disclosure of using the Infinium Human Methylation 27 Bead Chip
(Illumina) meets the claim limitation. Because the Illumina chip contains the
recited promotors ( as well as others promotors not recited in claim 1 ), we
agree with Examiner that Vanaja's process of determining the methylation
state of promotors in patient derived samples would simultaneously include
detecting the methylation state of the recited promotors. See Ans. 19-22.
Accordingly, we agree with Examiner's finding that testing patient samples
for methylation patterns using the Illumina chip for the purpose of detecting
prostate cancer as disclosed in Vanaja would anticipate the claims. See King,
801 F.2d at 1326-27. We affirm the rejection of claims 1 and 14 under 35
U.S.C. § 102 by Vanaja. Claims 3---6, 8-13, 15, and 16 were not separately
argued and fall with claims 1 and 14.
SUMMARY
We affirm the rejection of claims 1, 3-6, and 8-16 as being patent
ineligible.
We affirm the rejection of claims 1, 3-6, and 8-16 as anticipated by
Sorensen.
We affirm the rejection of claims 1, 3-6, and 8-16 as anticipated by
Vanaja.
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
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