Conrad, Richard et al.

Patent Trials and Appeals Board

Oct 31, 2019

15162373 - (D) (P.T.A.B. Oct. 31, 2019)

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.
15/162,373 05/23/2016 Richard Conrad 6541 US C3 9201
52059 7590 10/31/2019
LIFE TECHNOLOGIES CORPORATION
Attn: IP Department
5823 Newton Drive
Carlsbad, CA 92008
EXAMINER
POHNERT, STEVEN C
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
10/31/2019 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):
PatentDocketing@thermofisher.com
pair_thermofisher@firsttofile.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte RICHARD CONRAD and EMILY ZERINGER
____________

Appeal 2019-003093
Application 15/162,373
Technology Center 1600
____________

Before DONALD E. ADAMS, TIMOTHY G. MAJORS, and
MICHAEL A. VALEK, Administrative Patent Judges.

VALEK, Administrative Patent Judge.

DECISION ON APPEAL
Appellant1 submits this appeal under 35 U.S.C. § 134(a) involving
claims to methods of isolating RNA and determining an amount of full-
length RNA from a fixed tissue sample. We have jurisdiction under
35 U.S.C. § 6(b).
We AFFIRM.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42(a). Appellant identifies Applied Biosystems, LLC as the real
party in interest. Appeal Br. 1. Herein, we refer to the Final Action mailed
August 3, 2018 (“Final Act.”); Appellant’s Appeal Brief filed October 29,
2018 (“Appeal Br.”); Examiner’s Answer mailed January 31, 2019 (“Ans.”);
and Appellant’s Reply Brief filed March 7, 2019 (“Reply Br.”).
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STATEMENT OF THE CASE
The Specification explains that “RNA is often isolated from fixed
tissue however, due to the processes involved in fixing tissue, such as the
use of formaldehyde, the RNA obtained is fragmented.” Spec. 1. According
to the Specification, the present “invention is effective for obtaining RNA by
isolating, extracting, and enriching for RNA, including full-length and
substantially full-length RNA, from a sample using a digestion buffer or
solution that includes a polyanion.” Id. at 3. “It is thus contemplated that
methods . . . of the invention can be employed to obtain a better yield of
RNA from a sample.” Id.
Claims 1, 4–6, 8, 10, 13, 16, 20, 33, 36–39, 42, and 43 are on appeal
and can be found in the Claims Appendix of the Appeal Brief. Claims 1 and
39 are independent and representative of the claims on appeal. They read as
follows:
1. A method for isolating RNA from a fixed tissue
sample comprising:
(a) contacting the fixed tissue sample with a
digestion buffer comprising a polycarboxylate selected
from sodium citrate, 1,4-cyclohexanedicarboxylic acid,
1,3,5-cyclohexanetriccarboxylic acid, isocitric acid,
succinic acid or a combination thereof, and a protease to
produce a lysate wherein the digestion buffer lacks
guanidinium and lacks Mg2+;
(b) adding guanidinium and a sodium salt to the
lysate from (a); and
(c) extracting RNA from the lysate from (b) using
solid-phase extraction.

39. A method for determining an amount of full-length
RNA from a fixed tissues sample comprising:
(a) contacting the fixed tissue sample with a
digestion buffer comprising a polycarboxylate and a
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protease to produce a lysate wherein the digestion buffer
lacks guanidinium and lacks Mg2+;
(b) adding an alcohol solution to the lysate;
(c) applying the lysate to a mineral support;
(d) eluting the full-length RNA from the mineral
support with an elution solution; and
(e) amplifying the eluted RNA.
Appeal Br. 11, 13.
Appellant seeks review of the following rejections:
I. Claims 1, 4, 6, 8, 10, 16, 20, 33, 36–39, 42, and 43 under 35 U.S.C.
§ 103 as unpatentable over Roche2 in view of Light3 and Colpan4;
and
II. Claims 5 and 13 under 35 U.S.C. § 103 as unpatentable over Roche
in view of Light, Colpan, Goelz,5 Masuda,6 and Ebeling.7
Appeal Br. 3–9. Appellant does not argue claims 4, 6, 8, 10, 16, 20, 33, 36–
38, 42, and 43 separately from the independent claims so those claims stand
or fall with claims 1 and 39. 37 C.F.R. § 41.37 (c)(1)(iv).

2 Roche Molecular Biochemicals, High Pure RNA Paraffin Kit Instruction
Manual, Cat. No. 3 270 289 (2001) (“Roche”).
3 WO 01/29265 A1; published April 26, 2001 (“Light”).
4 US 6,383,393 B1; issued May 7, 2002 (“Colpan”).
5 Goelz et al., Purification of DNA from Formaldehyde Fixed and Paraffin
Embedded Human Tissue, Biochemical and Biophysical Research Comm’n,
Vol. 130(1), 118–126 (1985) (“Goelz”).
6 Norikazu Masuda et al., Analysis of Chemical Modification of RNA from
Formalin-Fixed Samples and Optimization of Molecular Biology
Applications for Such Samples, Nucleic Acids Research, Vol. 27(22), 4436–
4443 (1999) (“Masuda”).
7 Wolfgang Ebeling et al., Proteinase K from Tritirachium Album Limber,
Eur. J. Biochem. Vol. 47, 91–97 (1974) (“Ebeling”).
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The issue is: Does the preponderance of evidence of record support
Examiner’s conclusion that the cited prior art renders the claimed methods
obvious?
Findings of Fact
FF1. Roche teaches a procedure for isolating RNA from fixed tissue
sections. Roche 7–9. According to this procedure, the tissue is contacted
with a digestion buffer containing Proteinase K, i.e., a protease, and
incubated overnight. Id. at 8. This digestion buffer does not contain
guanidinium or magnesium. See id. at 3, 6 (describing components in
“Tissue Lysis Buffer” and “Proteinase K working solution”). After
incubation, a binding buffer comprising guanidinium and ethanol is added to
the lysate and the solution is pipetted into a filter tube where it selectively
binds to a solid glass fiber surface therein. Id. After washing, the RNA is
eluted using an elution buffer and further purified. See id. at 8–9. Roche
teaches that the RNA isolated using this procedure is suitable for
amplification by RT-PCR. Id. at 4.
FF2. Light teaches in situ hybridization techniques that include
pretreatment with a digestion buffer comprising proteinase K and 2X SSC at
7.0 pH. Light 15. Light teaches that digestion with this buffer “permit[s]
penetration of the labeled nucleic acid probes” and “reduce[s] non-specific
backgrounds which may be necessary for a given specimen.” Id. at 9.
FF3. Colpan teaches a method for the “purification and separation of
nucleic acid mixtures by chromatography” that involves “absorbing the
nucleic acids to be separated and purified from a solution with a high
concentration of salts (ionic strength) and/or a high concentration of alcohol
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on a substrate.” Colpan, Abstr. Colpan teaches that suitable salts for this
method include both sodium and guanidine salts. Id. at 5:20–32.
FF4. Goelz teaches a method for extracting DNA from fixed tissue
involving contacting the tissue with a digestion buffer, i.e., “TE9 (500 mM
Tris, 20 mM EDTA, 10 mM NaCl, pH 9.0) containing 1% SDS and 500
μg/ml proteinase K” to digest the tissue before isolating the DNA. Goelz
119–20.
FF5. Masuda teaches the extraction of RNA from fixed tissue using a
digestion buffer comprising “200 mM Tris-HCl, 200 mM NaCL, 1.5 mM
MgCl2, 2% SDS, pH 7.5) with 500 μg proteinase K” with a 1 hour incubation
period. Masuda 4437.
Analysis
I. Rejection of Claims 1, 4, 6, 8, 10, 16, 20, 33, 36–39, 42, and 43
Examiner finds that Roche teaches the elements of claims 1 and 39
other than the presence of a polycarboxylate in the digestion buffer. Final
Act. 3–8. Examiner further finds that Light teaches a digestion buffer
comprising a polycarboxylate because “SSC is NaCl and sodium citrate.”8
Id. at 4. Examiner determines it would have been obvious “to substitute the
lysis buffer of Roche with the lysis buffer of Light since a person of ordinary
skill in the art would recognize the lysis buffer of [L]ight is [an] art-accepted
suitable alternative for proteinase K digestion.” Id. Examiner further
determines it would be obvious to add a sodium salt, along with the
guanidinium and alcohol already taught in Roche’s protocol, after digestion

8 Appellant does not dispute Examiner’s finding that “SSC,” as taught in
Light, includes sodium citrate, i.e., one of the polycarboxylate’s recited in
the Markush group of claim 1. See FF2.
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because Colpan teaches that adding those components “increases the
specificity of the absorption after digestion” by “altering specificity of
binding to the support.” Id. at 6.
Appellant argues that Examiner’s rejection should be reversed for two
reasons. First, Appellant argues that Light teaches in situ hybridization and
therefore is “specifically directed to retaining the nucleic acid in its location
in the specimen but allowing the hybridization probe to enter so it can bind
with the target nucleic acid.” Appeal Br. 4. For this reason, Appellant
contends “Light is directed to an entirely different method than Roche, and
therefore, one skilled in the art would not be motivated to” use Light’s
digestion buffer in Roche’s method “as there is no reasonable expectation
that the modification would be successful.” Id. at 3; see also Reply Br. 2–4.
Second, Appellant argues that Colpan teaches “combining the reagents
necessary for digestion (where a lystate is produced) and the chaotropic
agents, such as guanidinium, high salt concentration, etc., which allow for
absorption of the nucleic acids on the solid support” at the same time. Id. at
6. Thus, urges Appellant, Colpan teaches away from “adding guanidinium
and a sodium salt (or an alcohol solution) to the lysate after digestion, as
required in claims 1 and 39.” Id.
We are not persuaded by Appellant’s arguments and agree with
Examiner’s statement of the rejection and responses to Appellant’s
arguments in the Answer and Final Action, which we adopt and incorporate
by reference. We further address Appellant’s arguments below.
We are not persuaded by Appellant’s argument that it would not be
obvious to use Light’s digestion buffer in Roche’s method. Both Light and
Roche teach the use of a digestion buffer containing the same protease, i.e.,
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Proteinase K, for the same purpose, i.e., digesting tissue. FF1; FF2. “When
a patent simply arranges old elements with each performing the same
function it had been known to perform and yields no more than one would
expect from such an arrangement, the combination is obvious.” KSR Int’l
Co. v. Teleflex Inc., 550 U.S. 398, 417 (2007) (internal quotations and
citation omitted). The fact that Light’s method is directed to a different end
(in situ hybridization as opposed to RNA isolation/quantification) does not
suggest that Light’s buffer would be unsuitable for Roche’s method. To the
contrary, Light teaches that its Proteinase K digestion buffer is sufficient to
digest tissue in a deparaffinized tissue specimen similar to that in Roche’s
method. See Light 15 (Ex. 1). Accordingly, we agree with Examiner that a
skilled artisan would reasonably expect that Light’s digestion buffer would
be successfully used to digest tissue in Roche’s method. See, e.g., In re
Mayne, 104 F.3d 1339, 1340 (Fed. Cir. 1997) (“Because the applicants
merely substituted one element known in the art for a known equivalent, this
court affirms [the rejection for obviousness].”).
We are also unpersuaded by Appellant’s argument that Colpan
teaches away from the claimed method. Colpan teaches that digestion may
occur “in a per se known manner” and “[a]fter larger cell constituents . . .
have been removed by centrifugation or filtration” the solution containing
the nucleic acids from the digested sample is “contacted with a mineral
substrate material in order to absorb the nucleic acids . . . on the mineral
substrate.” Colpan 2:39–50. Colpan further describes a “modification” of
this method wherein “digestion of the nucleic acids [is performed] directly
within the buffer system employed for the adsorption.” Id. at 2:51–55. It is
this “modification” that Appellant relies upon for its argument that Colpan
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teaches away from adding guanidinium and sodium salt to the lysate after
digestion. See Appeal Br. 6 (quoting Colpan 2:51–55). But Colpan teaches
that the absorption step can occur either concurrently or “[a]fter” digestion.
Thus, the premise of Appellant’s argument is flawed, because Colpan, in
fact, teaches the addition of guanidinium, sodium salt and alcohol to
improve binding after digestion of the sample.9 FF3. That Colpan
additionally teaches an alternative embodiment where the digestion occurs
concurrently and thus the digestion buffer includes these components does
not “teach away” from the method in claims 1 and 39. See Merck & Co. v.
Biocraft Labs., Inc., 874 F.2d 804, 807 (Fed. Cir. 1989) (“[I]n a section 103
inquiry, ‘the fact that a specific [embodiment] is taught to be preferred is not
controlling, since all disclosures of the prior art, including unpreferred
embodiments, must be considered.’”) (quoting In re Lamberti, 545 F.2d 747,
750 (CCPA 1976)).
For these reasons, we determine that the preponderance of the
evidence supports Examiner’s rejection of claims 1, 4, 6, 8, 10, 16, 20, 33,
36–39, 42, and 43 as obvious over Roche in view of Light and Colpan.
II. Rejection of Claims 5 and 13
Examiner’s rejection of claims 5 and 13 is premised on the same
findings concerning Roche, Light, and Colpan discussed above. Ans. 9. In
addition, Examiner points to components of digestion buffers taught in
Goelz and Masuda and the one hour incubation time taught in Masuda as

9 Appellant’s argument also appears to assume that claims 1 and 39 exclude
the addition of sodium salt and alcohol until after digestion is complete, but
there is no such requirement in claim language. Indeed, claim 5 depends
from claim 1 and recites the presence of “about 200 mM NaCl” in the
digestion buffer itself.
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evidence that the limitations recited in claims 5 and 13 would be obvious.
See id.
Appellant advances that the same arguments against Examiner’s
rejection of claims 5 and 13 as for the other claims. Appeal Br. 9 (arguing
that “none of Goelz, Masuda, or Ebeling, either alone or in combination,
cures the above noted deficiencies of Roche, Light, and Colpan”). As
explained above, we are not persuaded by those arguments. In addition,
with respect to claim 5, Appellant argues that Colpan teaches a higher (1 M)
salt concentration than the claimed concentration of “about 200 mM NaCl.”
Id.; see also Reply Br. 9–10.
We are unpersuaded by Appellant’s additional argument concerning
claim 5. The cited art teaches digestion buffers comprising the various
components recited in claim 5. FF1, FF2, FF4, and FF5. Indeed, Masuda
teaches a Proteinase K digestion buffer containing the same concentration of
NaCl (200 mM) as that in claim 5. As Examiner explains, “where the
general conditions of a claim are disclosed in the prior art, it is not inventive
to discover the optimum or workable ranges by routine experimentation.”
Ans. 9–10 (quoting MPEP § 2144.05(II) (citing In re Aller, 220 F.2d 454,
456 (CCPA 1955)). Here, the record supports that the general conditions,
i.e., digestion buffers comprising the various components recited in claim 5
and the incubation time recited in claim 13, were known in the art.
Appellant has not presented any evidence to the contrary. See, e.g., Merck,
874 F.2d at 806–09 (explaining “[p]atentability may be imparted . . . if the
results achieved at the designated concentrations are ‘unexpectedly good’”)
(quoting In re Antonie, 559 F.2d 618, 620 (CCPA 1977)). Accordingly, we
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determine that Examiner’s rejection of claims 5 and 13 is supported by the
preponderance of the evidence.

DECISION SUMMARY

Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1, 4, 6, 8,
10, 16, 20,
33, 36–39,
42, 43
103 Roche, Light,
Colpan
1, 4, 6, 8,
10, 16, 20,
33, 36–39,
42, 43

5, 13 103 Roche, Light,
Colpan, Goelz,
Masuda, Ebeling
5, 13
Overall
Outcome
1, 4–6, 8,
10, 13, 16,
20, 33,
36–39, 42,
43

No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv).

AFFIRMED