Ex Parte Leamon et al

Patent Trials and Appeals Board

Apr 18, 2019

13443629 - (D) (P.T.A.B. Apr. 18, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/443,629 04/10/2012
131771 7590 04/22/2019
Cooley LLP/454 Life Sciences Corporation
1299 Pennsylvania Avenue NW
Suite 700
Washington, DC 20004
FIRST NAMED INVENTOR
John Harris Leamon
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.
454L-015/C01US 5948
EXAMINER
BERTAGNA, ANGELA MARIE
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
04/22/2019 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):
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zIPPatentDocketingMailbox US @cooley.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JOHN HARRIS LEAMON, WILIAM LUN LEE,
JAN FREDRIK SIMONS, BRIAN DESANY, MICHAEL TODD RONAN,
JAMES DRAKE, KENTON LOHMAN, MICHAEL EGHOLM, and
JONATHAN ROTHBERG
Appeal2017-009408
Application 13/443,629 1
Technology Center 1600
Before JEFFREY N. FREDMAN, ELIZABETH A. LA VIER, and
DAVID COTTA, Administrative Patent Judges.
LA VIER, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellants seek review of the
Examiner's rejections of claims 29, 33-37, 39--43, 45--47, 50, 67, and 68.
We have jurisdiction under 35 U.S.C. § 6(b ). An oral hearing occurred on
April 9, 2019.
For the reasons set forth below, we AFFIRM.
1 Appellants identify the real party in interest as 454 Life Sciences
Corporation. Appeal Br. 3.
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Application 13/443,629
BACKGROUND
The Specification describes methods, reagents, and systems for the
parallel detection and analysis of sequence variants in a population of target
polynucleotides. Spec. 1: 10-13. Claim 29, the only independent claim on
appeal, is illustrative:
29. A method for detecting sequence variants having a
frequency of less than 5% in a heterogeneous nucleic acid
population comprising the steps of:
(a) amplifying a target DNA segment common to said
heterogeneous nucleic acid population comprising a locus to be
analyzed obtained from genomic DNA obtained from the
sample without extraction or purification by a first polymerase
chain reaction using a pair of PCR bipartite nucleic acid
primers, wherein each bipartite primer comprises a 5' primer
region complementary to a sequencing primer or complement
thereof and a 3' primer region complementary to a region on
said target DNA segment, and wherein each bipartite primer
defines the locus to be analyzed to produce a first population of
amplicons that are specific to the locus and that each comprise
said DNA segment, wherein the amplifying is performed
without prior knowledge of a nucleic acid sequence
composition of a region of the DNA segment that is flanked by
the pair of bipartite primers;
(b) delivering the first population of amplicons into aqueous
microreactors in a water-in-oil emulsion such that a plurality of
the aqueous microreactors comprises (1) a single amplicon of
the first population of amplicons; (2) a single bead; and (3) an
amplification reaction solution containing reagents necessary to
perform DNA amplification;
( c) clonally amplifying each member of said first population of
amplicons by a second polymerase chain reaction to produce a
plurality of populations of second amplicons wherein each
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Application 13/443,629
population of second amplicons derives from one member of
said first population of amplicons;
( d) immobilizing the said amplicons to a plurality of the beads
in the microreactors such that each bead comprises one
population of said second amplicons;
( e) breaking the emulsion to recover the beads from the
microreactors;
(f) determining in parallel a nucleic acid sequence for the
second amplicons on each bead at a number of individual
sequence reads of greater than 100 to produce a population of
nucleic acid sequences;
(g) determining an incidence of each type of nucleotide at each
position in the population of nucleic acid sequences, wherein
each type of nucleotide represents a sequence variant, thereby
obtaining the nucleotide frequency for each type of nucleotide
at each position of said nucleic acid sequences; and
(h) identifying those sequence variants that occur with a
frequency of less than 5% in said population of nucleic acid
sequences.
Appeal Br. 29-30 (Claim Appendix).
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REJECTIONS MAINTAINED ON APPEAL
1. Claims 29, 33-37, 39, 45--47, 67, and 68 stand rejected under
35 U.S.C. § I03(a) (pre-AIA) as unpatentable over Berka,2
Woudenberg, 3 Fakhrai-Rad, 4 Lavebratt, 5 and Wang. 6 Ans. 3.
2. Claims 40--43 and 50 stand rejected under 35 U.S.C. § I03(a)
(pre-AIA) as unpatentable over Berka, Woudenberg, Fakhrai-Rad,
Lavebratt, Wang, and Sun. 7 Ans. 11.
DISCUSSION
A. Rejection 1
1. Overview
The Examiner's findings with respect to Rejection 1 are set forth on
pages 4--16 of the Non-Final Action, 8 and are further explained at pages 12-
22 of the Answer. The remainder of this subsection summarizes those
findings for purposes of discussion and context.
2 Berka et al., WO 2004/069849 A2, published Aug. 19, 2004.
3 Woudenberg et al., US 2006/0269934 Al, published Nov. 30, 2006.
4 Fakhrai-Rad et al., Pyrosequencingâ„¢: An Accurate Detection Platform for
Single Nucleotide Polymorphisms, 19 HUMAN MUTATION 479--485 (2002).
5 Lavebratt et al., Pyrosequencingâ„¢-Based SNP Allele Frequency
Estimation in DNA Pools, 23 HUMAN MUTATION 92-97 (2004).
6 Wang et al., Homogenous Real-Time Detection of Single-Nucleotide
Polymorphisms by Strand Displacement Amplification on the BD ProbeTec
ET System, 49 CLIN. CHEM. 1599-1607 (2003).
7 Sun et al., Quantification of Allele-Specific G-Protein /J3 Subunit mRNA
Transcripts in Different Human Cells and Tissues by Pyrosequencing, 13
EURO. J. HUMAN GENETICS 361-369 (2005).
8 Non-Final Action dated June 28, 2016.
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With respect to illustrative claim 29, the Examiner relies on Berka as
teaching or suggesting claimed steps (a) through (f) (see Non-Final Action 5
(citing Berka 1:16-19)), including the use of bipartite PCR9/sequencing
primers (see id. at 8 ( citing Berka 12:2-12)). The Examiner acknowledges,
however, that Berka does not teach or suggest performing a first PCR on a
sample obtained from unprocessed genomic DNA using bipartite primers
with 3' regions complementary to a region on the target DNA sequence, and
each bipartite primer defining the locus to be analyzed (see id.).
Accordingly, the Examiner turns to Woudenberg as teaching a method for
clonal amplification and analysis, including a "first amplification to generate
a mixture of 'non-clonal amplicons' or 'multiplex amplicons "' (id. at 8
(quoting Woudenberg ,r 37)), and the use of bipartite primers with universal
tails to "perform the first amplification" (id. citing Woudenberg ,r 41, Fig.
1)). The Examiner also relies upon Woudenberg's teaching to "use
amplicons tagged with universal tails to perform subsequent clonal
amplification and analysis" after the first amplification (id). For the
requirement in step (a) of claim 29 that the genomic DNA must be "obtained
from the sample without extraction or purification," the Examiner cites
Wang, as teaching detection of SNPs 10 from human samples in real time,
including from unprocessed blood. Id. at 14 ( emphasis omitted) ( citing
Wang 1600).
For steps (g) and (h) of claim 29, the Examiner relies on Fakhrai-Rad
as teaching sequence determination of SNPs and allelic frequency
9 PCR: polymerase chain reaction.
10 SNP: single nucleotide polymorphism.
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determination based on analysis of pyrosequencing data, including the
detection of sequence variants with a frequency of less than 5%. See Non-
Final Action 10-12 (Fakhrai-Rad 482, Fig. 5).
As to the combination of the references, the Examiner finds:
It would have been prima facie obvious to one of ordinary skill
in the art at the time the invention was made to modify the
method of Berka et al. to use the bipartite primers of
Woudenberg et al. to perform an amplification on starting
material to generate amplicons that are tagged universal tails.
Motivation to do so is provided to one of ordinary skill in the
art by explicit teachings Woudenberg et al. and Fakhrai-Rad et
al.
Non-Final Action 10. Specifically, the Examiner points to paragraph 41 of
Woudenberg, which states that when the amplicon tagged with universal
forward and reverse primer sites "is isolated, for example, in a hydrophilic
compartment, the universal forward and reverse can be used as primer sites
for clonal amplification or analysis." Id. (quoting Woudenberg ,r 41).
Furthermore, Fakhrai-Rad uses bipartite primers having a "5' region that is
complementary to a sequencing primer immobilized on a solid support and a
3' region complementary to a region on the DNA segment" (id. at 11 (citing
Fakhrai-Rad 480, Fig. 2)) in a method sensitive enough to detect sequence
variants with a population frequency of less than 5% (id. at 10 ( citing
Fakhrai-Rad 482)), with the goal of improving the search for new
susceptibility genes for genetic disorders (id. (referring to Fakhrai-Rad
479)). The Examiner also cites to Lavebratt as corroborating the reasonable
expectation of success in determining SNP allele frequency from
pyrosequencing data. See id. at 13. As to the motivation to incorporate
Wang's teaching of using unprocessed blood as a starting material for SNP
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detection, the Examiner finds Wang's method would be cheaper because it
eliminates the need for purification of the genomic DNA. See id. at 15.
2. Analysis
Appellants argue that none of the references teaches or suggests the
use of two separate rounds of PCR. See, e.g., Appeal Br. 4. This argument
is pertinent to Woudenberg, on which the Examiner relies for this teaching.
See Non-Final Action 8. According to Appellants, Woudenberg teaches the
use of universal forward and reverse primers as primer sites "for clonal
amplification or analysis (but not both)," and that "Woudenberg is silent
about the use of gene-specific primers with universal tails for both
attachment and sequencing." Appeal Br. 8 (citing Woudenberg ,r,r 41, 56,
80, 100, 11 Fig. 2). This either-but-not-both interpretation of Woudenberg is
not persuasive. Paragraph 41 of Woudenberg, for example, discloses that
"[i]n addition to sequences suitable for priming multiplex amplification of
polynucleotides, one or more multiplex amplification primers can be
designed to introduce sequences into multiplex amplicons that can be used to
facilitate isolation, clonal amplification, and analysis" ( emphasis added).
Paragraph 41 of Woudenberg goes on to state that "the universal forward
and reverse can be used as primer sites for clonal amplification or analysis"
( emphasis added), but the context of the paragraph as a whole does not
indicate that this use of "or" is meant to exclude the possibility of
introducing sequences ( and hence, priming sites) useful for both
amplification and analysis, as discussed expressly at the beginning of the
same paragraph. Cf KSR Int'! Co. v. Teleflex Inc., 550 U.S. 398,421 (2007)
11 The last numbered paragraph of Woudenberg is paragraph 77, so the
citation to paragraphs 80 and 100 is unclear.
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("A person of ordinary skill is also a person of ordinary creativity, not an
automaton."). Accordingly, we find that Woudenberg teaches two separate
rounds of PCR, along with the requisite primers. As such, Appellants'
assertions that the other references do not teach or suggest two rounds of
PCR (see Appeal Br. 7 (discussing Berka), 9 (discussing Lavebratt), 10
(discussing Wang)) are not persuasive. See In re Keller, 642 F.2d 413, 426
(CCP A 1981) ("But one cannot show non-obviousness by attacking
references individually where, as here, the rejections are based on
combinations of references."). 12
Appellants' related argument that there would have been no
motivation to combine the references (save impermissible hindsight), nor a
reasonable expectation of success in doing so, because "none of these
references teaches or suggests a method of detecting low frequency
sequence variants using bipartite primers in two separate rounds of PCR"
(Appeal Br. 12) likewise is not persuasive. Furthermore, Appellants'
assertions that combining the references would have been "impractical" (id.
at 7) or "would not work very efficiently" (id. at 9) are not persuasive
insofar as these are attorney arguments, unsupported by evidence. See
Knorr v. Pearson, 671 F.2d 1368, 1373 (CCPA 1982) ("[A]rguments of
counsel cannot take the place of evidence lacking in the record.").
12 Several of Appellants' other arguments are similarly not persuasive
because they amount to attacking the references individually rather than in
combination (see Appeal Br. 9 ("Fakhrai-Rad utilizes a pair of gene-specific
primers to perform PCR ... [ and] fails to teach or suggest clonal
amplification of single molecules in emulsion."), 10 ( describing Wang as
using adapter primers, not bipartite primers, and as failing, inter alia, to
describe a method for detecting low-frequency sequence variants)).
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Appellants also attempt to rebut the Examiner's prima facie case of
obviousness by asserting that their invention amounts to a critical change
from the prior art, a "qualitatively different" result produced through
performing two rounds of PCR to achieve the ability to detect sequence
variants with a frequency of less than 5%. Appeal Br. 11. This argument is
not persuasive because, as discussed above, Woudenberg teaches performing
two separate rounds of PCR. As the Examiner explains:
Woudenberg clearly motivates the use of a first PCR before the
clonal amplification step in the method of Berka, and Wang
provides sufficient motivation for the use of a crude DNA
sample. As a result, the prior art suggests a method having all
of the required elements and steps, and the advantages listed
above simply result from these steps. The fact that Appellant
has recognized another advantage which would flow naturally
from following the suggestion of the prior art cannot be the
basis for patentability when the differences would otherwise be
obvious.
Ans. 20 (citingExparte Obiaya, 227 USPQ 58, 60 (BPAI 1985)).
Accordingly, for these reasons and those already of record, we are not
persuaded of any reversible error in the Examiner's rejection of claim 29.
As to each of the other claims subject to Rejection 1, i.e., claims 33-
37, 39, 45--47, 67, and 68, Appellants address them under separate headings
(see Appeal Br. 14--18) but offer no distinct arguments from those presented
with respect to claim 29. Accordingly, for the reasons above, we are not
persuaded of any reversible error by the Examiner in rejecting claims 33-37,
39, 45--47, 67, or 68.
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B. Rejection 2
The claims subject to Rejection 2 depend directly or indirectly from
claim 29, and further recite limitations relating to tissue( s) from which the
heterogeneous nucleic acid population is derived. See Appeal Br. 31-33
(Claims Appendix).
Appellants' only distinct argument regarding Rejection 2 is that the
additional reference, Sun, "is concerned with a different problem from that
recited in claim 40 (namely, the quantification of allele-specific G-protein
B3 subunit mRNA transcripts using pyrosequencing)" and thus "nothing in
the teaching of Sun would motivate the skilled artisan to modify the
teachings" of Sun and/or combine it with the other references. Appeal Br.
20. We are not persuaded. The Examiner relies on Sun for the limited
purpose of teaching using various human cells and tissues for SNP and
allele-specific transcript analysis by pyrosequencing. See Non-Final Action
17 (discussing Sun Abstract, 363). Appellants offer no explanation as to
why Sun's teaching of this technique is limited to the specific application to
studying G-protein B3 subunit mRNA transcripts, and we discern none.
Accordingly, for these reasons and those already discussed with
respect to claim 29 (Rejection 1 ), we are not persuaded of any reversible
error by the Examiner in rejecting claim 40.
As to each of the other claims subject to Rejection 2, i.e., claims 41-
43 and 50, Appellants address them under separate headings (see Appeal Br.
21-27) but offer no distinct arguments from those presented with respect to
claim 40 or claim 29. Accordingly, for the reasons above, we are not
persuaded of any reversible error by the Examiner in rejecting claims 41--43
or 50.
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CONCLUSION
We affirm Rejections 1 and 2. No time period for taking any
subsequent action in connection with this appeal may be extended under 37
C.F.R. § 1.136(a)(l )(iv).
AFFIRMED
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