Ex Parte Watson et al

Patent Trial and Appeal Board

Feb 20, 2018

13930852 (P.T.A.B. Feb. 20, 2018)

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.
13/930,852 06/28/2013 James Douglas WATSON 191186.401 8107
500 7590 02/22/2018
SFFD TNTFT T FFTT TAT PROPFRTY T AW GROT TP T T P
EXAMINER
701 FIFTH AVE BUNKER, AMY M
SUITE 5400
SEATTLE, WA 98104 ART UNIT PAPER NUMBER
1639
NOTIFICATION DATE DELIVERY MODE
02/22/2018 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):
US PTOe Action @ S eedIP .com
pairlinkdktg @ seedip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JAMES DOUGLAS WATSON, CLARE ELTON,
and DAVID REX MUS GRAVE1
Appeal 2016-000791
Application 13/930,852
Technology Center 1600
Before DEMETRA J. MILLS, ERIC B. GRIMES, and ULRIKE W. JENKS,
Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35U.S.C. § 134 involving claims to methods
of detecting the presence or monitoring progression of a disorder, which
have been rejected for lack of adequate written description, being directed to
patent-ineligible subject matter, anticipation, and obviousness. We have
jurisdiction under 35 U.S.C. § 6(b).
We affirm.
STATEMENT OF THE CASE
The Specification states that “[t]he present disclosure relates to
methods and compositions for diagnosing and defining the staging or
1 Appellants identify the Real Party in Interest as Caldera Health Ltd. (Br. 3.)
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Application 13/930,852
progress of disorders such as prostate cancer.” (Spec. 1:10—11.) “Unlike
many cancer types, specific patterns of gene expression have not been
consistently identified in prostate cancer progression. . . . However, a few
genes have emerged . . . which have been shown experimentally to have
probable roles in prostate carcinogenesis.” {Id. at 5:8—28.)
The Specification states that “[t]he methods disclosed herein allow the
determination of the frequency of multiple RNA biomarkers simultaneously
using a process known as multiplexing.” {Id. at 8:35—36.) “More
specifically, the disclosed methods employ oligonucleotides specific for
RNA biomarkers known to be associated with the presence and/or
progression of a disorder, such as prostate cancer.” {Id. at 9:12—14.)
Massive parallel sequencing made possible by next
generation sequencing (NGS) technologies is another way to
approach the enumeration of RNA transcripts in a tissue sample
and RNA-seq is a method that utilizes this. It is currently the
most powerful analytical tool used for transcriptome analyses,
including gene expression level difference between different
physiological conditions, or changes that occur during
development or over the course of disease progression.
(Id. at 7:15-20.)
Claims 1, 3—20, 23, and 24 are on appeal. Claims 1 and 12 are the
independent claims and read as follows:
Claim 1: A method for detecting the presence of a disorder in a
subject, comprising:
(a) determining the relative frequency of expression of a
plurality of ribonucleic acid (RNA) biomarkers simultaneously
in a biological sample obtained from the subject, wherein the
relative frequency of expression is determined using next
generation sequencing of an amplicon deoxyribonucleic acid
(DNA) library prepared using a plurality of oligonucleotide
primers specific for the plurality of RNA biomarkers; and
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(b) comparing the relative frequency of expression of the
plurality of RNA biomarkers in the biological sample with a
predetermined threshold value, wherein increased or decreased
relative frequency of expression of the plurality of RNA
biomarkers in the biological sample relative to the predetermined
threshold value indicates the presence of the disorder in the
subject.
Claim 12: A method for monitoring progression of a disorder in
a subject, comprising:
(a) determining the relative frequency of expression of a
plurality of RNA biomarkers simultaneously in a biological
sample obtained from the subject at a first time point, and
determining the relative frequency of expression of the plurality
of RNA biomarkers simultaneously in a biological sample
obtained from the subject at a second, subsequent, time point,
wherein the relative frequency of expression is determined using
next generation sequencing of an amplicon DNA library
prepared using a plurality of oligonucleotide primers specific for
the plurality of RNA biomarkers; and
(b) comparing the relative frequency of expression of the
plurality of RNA biomarkers in the biological sample with a
predetermined threshold value, wherein an increase or decrease
in the relative frequency of expression of the plurality of RNA
biomarkers in the biological sample at the second time point
compared to the relative frequency of expression of the plurality
of RNA biomarkers at the first time point indicates the
progression of the disorder in the subject.
The claims stand rejected as follows:
Claims 1, 3—20, 23, and 24 under 35 U.S.C. § 101 as being directed to
patent-ineligible subject matter (Ans. 6);
Claims 1, 3—20, 23, and 24 under 35 U.S.C. § 112, first paragraph, for
lack of adequate written description in the Specification (Ans. 3);
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Claims 1, 3, 11—13, 20, 23, and 24 under 35 U.S.C. § 102(a) as
anticipated by Joyce,2 as evidenced by Applied Biosystems,3 Illumina,4 and
Illumina Sequencing5 (Ans. 9); and
Claims 1, 3—20, 23, and 24 under 35 U.S.C. § 103(a) as obvious based
on Hood,6 Twine,7 and Prensner,8 as evidenced by Illumina, Illumina
Sequencing, Chasin,9 and Joyce (Ans. 11).
I
The Examiner has rejected all of the claims on appeal under 35 U.S.C.
§ 101, on the basis that “the claimed invention is directed to a judicial
exception (i.e., a law of nature, a natural phenomenon, or an abstract idea)
without significantly more.” (Ans. 6.) Specifically,
the claims are directed to a natural phenomenon and an abstract
idea, which are the natural presence of naturally occurring RNA
in a subject that may be differentially expressed in a subject with
a disorder and the mathematical analysis and/or correlation of the
2 Cailin E. Joyce et al., Deep sequencing of small RNAs from human skin
reveals major alterations in the psoriasis miRNAome, 20 Hum. Mol. Gen.
4025^10 (2011).
3Product Bulletin, TaqMan® MicroRNA Assays, Quantitate microRNAs with
the specificity and sensitivity of TaqMan® assay chemistry, Applied
Biosystems \-A (2006).
4 Data Sheet: Illumina® Sequencing, TruSeq™ RNA and DNA Sample
Preparation Kits v2, Illumina® 1—4 (2011).
5 Illumina®, Multiplexed Sequencing with the Illumina Genome Analyzer
System, Illumina® Sequencing \-A (2008).
6 Hood et al., WO 2008/021290 A2; publ. Feb. 21, 2008.
7 Twine et al., US 7,611,839 B2; iss. Nov. 3, 2009.
8 John R. Prensner et al., Transcriptome sequencing across a prostate cancer
cohort identifies PCAT-1, an unannotated lincRNA implicated in disease
progression, 29 NAT. biotechnol. 742-50 (2011).
9 Chasin et al., US 2013/0217585 Al; publ. Aug. 22, 2013.
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relative frequency of expression of biological markers with a
disorder.
(Id. at 7.)
“Appellant acknowledges that independent claims 1 and 12 recite the
judicial exception of RNA biomarkers that are differentially expressed in the
presence of a disorder.” (Br. 16.)
The Examiner finds that “claim(s) 1 and 12 do not recite something
significantly different than a judicial exception” because “the detection and
quantification of RNA biomarkers, the use of oligonucleotide primers
specific for a plurality of RNA biomarkers and comparing the frequency of
expression of a subject with that of a reference value[] are well-known,
purely conventional or routine in the art.” (Ans. 7—8.) The Examiner cites
Marguerat,10 Ren,11 and Prensner as evidence that “the determination of the
relative frequency of expression of RNA biomarkers using next generation
sequencing (NGS) and oligonucleotide primer pairs specific for a biomarker
is well-known, conventional and routine.” (Id. at 8.)
Appellants argue “both claims 1 and 12 recite additional elements that
ensure that the claims amount to significantly more than the judicial
exception.” (Br. 16.) Appellants submit that,
[i]n response to the Examiner’s assertion that the claimed
methods are well-known, routine and conventional in the art as
evidenced by the US 2008/0274458 to Latham et al. and WO
2010/120803A2 to Kazakov et al.,. .. neither of these references
10 Samuel Marguerat & Jiirg Bahler, RNA-seq: from technology to biology,
67 Cell. Mol. Life Sci. 569-79 (2010).
11 Shancheng Ren et al., RNA-seq analysis of prostate cancer in the Chinese
population identifies recurrent gene fusions, cancer-associated long
noncoding RNAs and aberrant alternative splicings, 22 Cell Res. 806—21
(2012).
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teaches or suggests the use of NGS to determine the relative
frequency of expression of a plurality of RNA biomarkers in a
biological sample and thereby either detect the presence of a
disorder (as recited in claim 1) or monitor the progression of a
disorder (as recited in claim 12).
(Id.)
We conclude that the rejection under § 101 is supported by a
preponderance of the evidence of record. Marguerat states that “[n]ext-
generation sequencing technologies are now being exploited not only to
analyse static genomes, but also dynamic transcriptomes in an approach
termed RNA-seq.” (Marguerat 569, Abstract.) Marguerat reviews
“[a]pplying RNA-seq to probe the breadth and depth of genome
transcription” and “[ajpplying RNA-seq to interrogate post-transcriptional
gene regulation.” (Id. at 571, 573.)
Ren describes a study of transcriptome profiles in prostate cancers and
normal counterparts in the Chinese population using RNA-seq. (Ren 806,
abstract.) Ren states that the study showed diversity among prostate cancers
with respect to gene fusions, long noncoding RNAs, alternative splicing and
somatic mutations. (Id.) Prensner describes an RNA-Seq analysis of long
intergenic noncoding RNAs (lincRNAs) in prostate cancer tissue samples and
cell lines. (Prensner 742, left col.) Prensner
characterized one ncRNA, PCAT-1, as a prostate-specific
regulator of cell proliferation and show[ed] that it is a target of
the Polycomb Repressive Complex 2 (PRC2). We further found
that patterns of PCAT-1 and PRC2 expression stratified patient
tissues into molecular subtypes distinguished by expression
signatures of PCAT-1—repressed target genes.
(Id. at 742, abstract.)
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The Examiner concludes that these disclosures demonstrate that “the
determination of the relative frequency of expression of RNA biomarkers
using next generation sequencing (NGS) and oligonucleotide primer pairs
specific for a biomarker is well-known, conventional and routine.” (Ans. 8.)
Appellants dispute that conclusion, but only on the basis that Latham (US
2008/0274458 Al) and Kazakov (WO 2010/120803 A2), do not “teach[] or
suggest[] the use of NGS to determine the relative frequency of expression
of a plurality of RNA biomarkers in a biological sample and thereby either
detect the presence of a disorder (as recited in claim 1) or monitor the
progression of a disorder (as recited in claim 12).” (Br. 16.)
The Examiner, however, does not rely on Latham or Kazakov to
provide evidence in support of the rejection; the Examiner relies on
Marguerat, Ren, and Prensner. Granted, the Examiner relied on Latham and
Kazakov for the same purpose in the Final Office Action (mailed March 6,
2015), but Appellants did not petition to have the rejection in the Answer
designated a new ground of rejection, nor did Appellants file a Reply Brief
responding to the Examiner’s citation of Marguerat, Ren, and Prensner.
Thus, Appellants have not disputed, on this record, that Marguerat, Ren, and
Prensner support the proposition for which the Examiner has cited them.
We therefore conclude that the rejection is supported by a preponderance of
the evidence in the record.
Appellants also argue that “claims 1 and 12 do not prevent anyone
from using RNA biomarkers in other methods (such as RT-PCR) to
diagnose the presence and/or monitor the progression of a disorder and
therefore do not tie-up any law of nature or pre-empt others from using a law
of nature.” (Br. 16—17.)
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This argument is unpersuasive. “While preemption may signal patent
ineligible subject matter, the absence of complete preemption does not
demonstrate patent eligibility. . . . Where a patent’s claims are deemed only
to disclose patent ineligible subject matter under the Mayo framework, as
they are in this case, preemption concerns are fully addressed and made
moot.” Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F3d 1371, 1379
(Fed. Cir. 2015).
For the reasons discussed above, we affirm the rejection of claims 1
and 12 under 35 U.S.C. § 101. Claims 3—11, 13—20, 23, and 24 have not
been argued separately and therefore fall with claims 1 and 12. 37 C.F.R.
§ 41.37(c)(l)(iv).
II
The Examiner has rejected all of the claims on appeal on the basis that
they lack adequate written description in the Specification. The Examiner
finds that
the instant claims broadly embrace all RNA biomarkers for any
disorder detected using any oligonucleotide primer specific for
the plurality of RNA biomarkers in any subject. While the
specification provides guidance for the use of a specific set of
probes for next generation sequencing for diagnosing the
presence of, and/or monitoring the progression of, prostate
cancer,... it does not provide guidance for the use of any and/or
all oligonucleotide probes specific for any/all biomarkers for
detecting the presence of any other disease, disorder or other
cancer type in any subject.
(Ans. 5.)
The Examiner also finds that the Specification’s
disclosure is not deemed to be descriptive of the wide-range of
genetic variation for determining RNA biomarkers among
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different races or different species, particularly, in conjunction
with all possible disorders and all possible oligonucleotide
primers, as one of skill in the art cannot envision all the modified
forms based on the teachings in the specification.
This limited information is not deemed sufficient to
reasonably convey to one skilled in the art that Applicant is in
possession of the claimed genus of RNA biomarkers and
oligonucleotide primers specific a plurality of RNA biomarker[s]
to detect all disorders in all subject/species at the time the
invention was made.
(Id. at 6.)
We agree with the Examiner that the Specification does not
demonstrate that Appellants were in possession of the methods of claims 1
and 12 at the time the instant application was filed. “[T]he test for
sufficiency [of written description] is whether the disclosure of the
application relied upon reasonably conveys to those skilled in the art that the
inventor had possession of the claimed subject matter as of the filing date.”
AriadPharms., Inc. v. EliLilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010)
(en banc).
[A] sufficient description of a genus . . . requires the disclosure
of either a representative number of species falling within the
scope of the genus or structural features common to the members
of the genus so that one of skill in the art can “visualize or
recognize” the members of the genus.
Id. at 1350.
Here, claims 1 and 12 recite a genus of RNA biomarkers; specifically,
RNA biomarkers that indicate the presence (claim 1) or progression (claim
12) of a disorder when their expression is increased or decreased relative to a
threshold value. Claims 1 and 12 are generic to any such biomarkers that are
diagnostic for any disorder. Thus, an adequate written description of the
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genus requires description of either a set of species that are representative of
the genus, or structural features that are common to the genus.
The Specification identifies no structural characteristics of RNA
biomarkers that are diagnostic of a disorder when over- or underexpressed.
The Specification does disclose a number of species of RNA biomarkers that
are either overexpressed (Table 1) or underexpressed (Table 2) in subjects
with prostate cancer. (Spec. 23:24—27.) However, the Specification
discloses no such RNA biomarkers for any disorder other than prostate
cancer. We therefore conclude that the Specification does not provide a
written description of the methods of claims 1 and 12 that demonstrates that
Appellants were in possession of the claimed genus. See AbbVie
Deutschland GmbH & Co. v. Janssen Biotech, Inc., 759 F.3d 1285, 1299—
1300 (Fed. Cir. 2014):
One factor in considering the question is how large a genus is
involved and what species of the genus are described in the
patent. . . . [Ajnalogizing the genus to a plot of land, if the
disclosed species only abide in a comer of the genus, one has not
described the genus sufficiently to show that the inventor
invented, or had possession of, the genus. He only described a
portion of it.
Appellants argue that
claims 1 and 12 ... are drawn to specific methods employing
NGS in which RNA biomarkers that have been previously
identified as being specific for a particular disorder are employed
in the diagnosis of, and/or monitoring the progression of, that
disorder in much the same way that pre-determined biomarkers
can be employed in other methodologies.
(Br. 11-12.)
This argument is unpersuasive, because claims 1 and 12 are not
limited to using any particular RNA biomarkers, such as those that had been
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previously identified as diagnostic of the presence or progression of a
particular disorder as of the filing date of the instant application. Rather, as
the Examiner has pointed out (Ans. 5), they read on using any RNA
biomarkers that are over- or underexpressed in any disorder in order to
detect the presence or progression of the disorder.
Appellants argue that the methods of claims 1 and 12 “are described at
page 20, line 34 — page 23, line 19, of the present specification.” (Br. 12.)
Appellants also argue that the Specification describes “over 120 RNA
biomarkers showing either elevated or reduced expression levels in prostate
cancer compared to normal, or healthy, tissues, together with primers for
these RNA biomarkers.” (Id.)
These arguments are also unpersuasive. Regarding the specific
biomarkers that are disclosed in the Specification, as discussed above, they
are all limited to those that are diagnostic of prostate cancer; no biomarkers
that are diagnostic for any other disorder are described. The specific
biomarkers therefore do not show possession of the genus of RNA
biomarkers that is recited in claims 1 and 12.
In addition, the Specification describes (at pages 20-23), four
methods for determining “[t]he relative frequency of expression of specific
RNA biomarkers.” (Spec. 20:35.) This portion of the Specification,
however, does not provide a description of the genus of RNA biomarkers, or
any species within that genus, that is recited in claims 1 and 12.
With regard to claims 4, 6, 8, 14, and 17, Appellants argue that these
claims are limited to prostate cancer and to oligonucleotide primer pairs that
are specifically described in the Specification as being over- or
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underexpressed in prostate cancer tissue. (Br. 12—13.) Appellants make a
similar argument with respect to claims 10 and 19. {Id. at 13.)
We agree with Appellants that claims 4, 6, 8, 10, 14, 17, and 19 find
adequate written descriptive support in the Specification. These claims are
limited to methods of detecting the presence or progression of prostate
cancer using specific, structurally defined primers (claims 4, 6, 8, 14, and
17) or genes (claims 10 and 19) that are disclosed in the Specification as
being either overexpressed or underexpressed in prostate cancer tissue.
For the reasons discussed above, we affirm the rejection of claims 1
and 12 under 35U.S.C. § 112, first paragraph, for lack of adequate written
description. Claims 3, 5, 7, 9, 11, 13, 15, 16, 18, 20, 23, and 24 have not
been argued separately and therefore fall with claims 1 and 12. 37 C.F.R.
§ 41.37(c)(l)(iv). We reverse the rejection under 35 U.S.C. § 112, first
paragraph, for lack of adequate written description with respect to claims 4,
6, 8, 10, 14, 17, and 19.
Ill
The Examiner has rejected claims 1,3,11—13, 20, 23, and 24 as
anticipated by Joyce, as evidenced by Applied Biosystems, Illumina, and
Illumina Sequencing. The Examiner finds that Joyce teaches analyzing
miRNA (microRNA) expression profiles in psoriasis “where small RNA
reads representing known and putative novel miRNAs were generated and
analyzed by next generation sequencing (Abstract, lines 1-5). Joyce et al.
teach that relative frequency of expression was calculated.” (Ans. 9.)
The Examiner also finds that Joyce teaches that “qRT-PCR of mature
miRNAs was performed with TaqMan miRNA assays according to
manufacturer’s instructions, which includes target-specific stem loop
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primers as evidenced by Applied Biosystems (corresponding to primers
specific for RNA biomarkers).” (Id. at 10.)
Appellants argue that Joyce “describe[s] the use of NGS to sequence
the entire miRNAome from normal and psoriatic skin.” (Br. 22.)
Appellants argue that Joyce does not “teach or suggest methods for the
diagnosis of, and/or for monitoring the progression of, a disorder wherein
NGS is performed on amplicon DNA libraries prepared using a plurality of
oligonucleotide primers specific for a set of predetermined biomarkers, as
recited in independent claims 1 and 12.” (Id. at 22—23.).
We agree with Appellants that Joyce does not disclose a method
meeting all of the limitations of claims 1 and 12, which both require
determining relative frequency of expression “using next generation
sequencing of an amplicon deoxyribonucleic acid (DNA) library prepared
using a plurality of oligonucleotide primers specific for [a] plurality of RNA
biomarkers.”
Joyce “describe [s] a comprehensive analysis of the normal and
psoriatic skin miRNAome with next-generation sequencing.” (Joyce 4025,
abstract.) Joyce “generated 6.7 x 108 small RNA reads representing 717
known and 284 putative novel microRNAs (miRNAs).” (Id.) Joyce
“identified 80 known and 18 novel miRNAs that were differentially
expressed.” (Id. at 4026, left col.)
More specifically, Joyce “extracted total RNA using a method that
preserved small RNAs and constructed small RNA libraries. . . . [Joyce]
independently sequenced each of the 67 libraries on the Illumina GAIIx
platform, generating 1.1 billion raw and 670 million qualified reads.” (Id. at
4026, right col.) Illumina, which the Examiner has cited as an evidentiary
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reference, describes its RNA sample preparation method as follows:
“Starting with total RNA, the messenger RNA is first purified using polyA
selection . . ., then chemically fragmented and converted into single-
stranded cDNA using random hexamer priming.” (Illumina 2.)
We agree with Appellants that Joyce does not describe “using next
generation sequencing of an amplicon deoxyribonucleic acid (DNA) library
prepared using a plurality of oligonucleotide primers specific for the
plurality of RNA biomarkers,” as required by claims 1 and 12. Rather,
Joyce describes using next generation sequencing to generate hundreds of
millions of reads from the total RNA of psoriatic and healthy tissue. Joyce’s
method does not use oligonucleotide primers specific for particular RNA
biomarkers; it uses random hexamer primers that, collectively, would
amplify the entire RNA transcriptome.
The Examiner points to Joyce’s disclosure that “qRT-PCR of mature
miRNAs was performed with TaqMan miRNA assays . . . , which includes
target-specific stem loop primers as evidenced by Applied Biosystems
(corresponding to primers specific for RNA biomarkers).” (Ans. 10.)
Reverse transcription/quantitative PCR (qRT-PCR or RT-qPCR), however,
is a different technique than next-generation sequencing. See Spec. 7:5—17
(“A common technology used for measuring RNA abundance is RT-qPCR
where reverse transcription (RT) is followed by real-time quantitative PCR
(qPCR). . . . Massive parallel sequencing made possible by next generation
sequencing (NGS) technologies is another way to approach the enumeration
of RNA transcripts in a tissue sample and RNA-seq is a method that utilizes
this.” (emphasis added)).
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“[Ajnticipation requires that the four comers of a single, prior art
document describe every element of the claimed invention, either expressly
or inherently, such that a person of ordinary skill in the art could practice the
invention without undue experimentation.” Advanced Display Sys., Inc. v.
Kent State Univ., 212 F.3d 1272, 1282 (Fed. Cir. 2000). Because Joyce does
not describe every element of claims 1 and 12, either expressly or inherently,
we reverse the rejection of those claims, and dependent claims 3, 11, 13, 20,
23, and 24, as anticipated by Joyce.
IV
The Examiner has rejected all of the claims on appeal as obvious
based on Hood, Twine, and Prensner, as evidenced by Illumina, Illumina
Sequencing, Chasin, and Joyce. The Examiner finds that Hood teaches,
among other things, “that substantially all transcripts from a cDNA library
are identified using sequencing by synthesis (SBS), massively parallel
sequencing (MPSS) or similar technology, such as that developed by Solexa
(now part of Illumina, as noted in Hood et al.) (corresponding to next
generation sequencing of an amplicon cDNA library).” (Ans. 12.)
Appellants argue that that Hood
teaches the use of MPSS and SBS to identify and/or to measure
the actual frequency of expression of all RNA sequences within
a specific tissue sample. This is essentially the same as the
known use of next-generation sequencing to examine expression
of every transcript within an entire genome as referenced on page
7, lines 15-25, of the current specification.
(Br. 27—28.) Appellants argue that, in contrast to the claimed method,
“Hood does not teach or suggest... the relative frequency of expression of a
plurality of RNA biomarkers ... by preparing NGS ready targeted cDNA
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amplicon libraries using a plurality of oligonucleotide primers specific for
the plurality of RNA biomarkers.” (Id. at 28.)
We agree with Appellants that Hood does not teach the disputed
limitation. The Examiner points to Hood’s disclosure that:
A short signature sequence of about 16-20 base pairs (Brenner,
P. et al., supra) is generated simultaneously from each of the
hundreds of thousands of beads (or more) in the flow cell, each
having attached thereto copies of a unique transcript from the
sample. This technique is termed massively parallel signature
sequencing (MPSS).
The resulting sequences (e.g., MPSS signature sequences), are
generally about 17-20 bases in length.
(Hood 165:30 to 166:7.)
The beginning of the paragraph that ends with a discussion of MPSS
reads as follows: “All or substantially all of the unique transcripts of RNA
or from a cDNA library, e.g., representing virtually or substantially all genes
functioning in the organ of interest, can be identified and quantified using
any of a variety of techniques known in the art.” (Id. at 165:6—9.) Thus, the
context of Hood’s discussion of MPSS is for use in identifying and
quantifying RNA transcripts representing virtually or substantially all of the
genes functioning in an organ of interest. We therefore agree with
Appellants that Hood does not teach or suggest the limitation of claims 1 and
12 requiring “using next generation sequencing of an amplicon
deoxyribonucleic acid (DNA) library prepared using a plurality of
oligonucleotide primers specific for [a] plurality of RNA biomarkers.”
The Examiner has not pointed to any disclosure in the other cited
references that makes up for this deficiency in Hood. See Ans. 13—15. We
therefore reverse the rejection of claims 1 and 12, and dependent claims 3—
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11, 13—20, 23, and 24, under 35 U.S.C. § 103(a) based on Hood, Twine, and
Prensner, as evidenced by Illumina, Illumina Sequencing, Chasin, and Joyce.
SUMMARY
We affirm the rejection of claims 1, 3—20, 23, and 24 under 35 U.S.C.
§101.
We affirm the rejection of claims 1, 3, 5, 7, 9, 11—13, 15, 16, 18, 20,
23, and 24 under 35 U.S.C. § 112, first paragraph, for lack of adequate
written description.
We reverse the rejection of claims 4, 6, 8, 10, 14, 17, and 19 under 35
U.S.C. § 112, first paragraph, for lack of adequate written description.
We reverse the rejection of claims 1,3,11—13, 20, 23, and 24 under
35 U.S.C. § 102(a) as anticipated by Joyce, as evidenced by Applied
Biosystems, Illumina, and Illumina Sequencing.
We reverse the rejection of claims 1, 3—20, 23, and 24 under 35
U.S.C. § 103(a) based on Hood, Twine, and Prensner, as evidenced by
Illumina, Illumina Sequencing, Chasin, and Joyce.
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
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