Ex Parte Collis et al

Patent Trial and Appeal Board

Feb 13, 2017

12165069 (P.T.A.B. Feb. 13, 2017)

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.
12/165,069 06/30/2008 Matthew Colli s BECTON 3.0-074 1364
63863 7590 02/15/2017
David W. Highet, VP & Chief IP Counsel
Becton, Dickinson and Company
(Lerner David Littenberg)
1 Becton Drive , MC 110
Franklin Lakes, NJ 07417-1880
EXAMINER
DAUNER, JOSEPH G
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
02/15/2017 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
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PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MATTHEW COLLIS and MICHAEL LIZZI
Appeal 2016-002418
Application 12/165,069
Technology Center 1600
Before JEFFREY N. FREDMAN, RYAN H. FLAX, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35U.S.C. § 134 involving a method for
extracting DNA. The Examiner rejected the claims as obvious. We have
jurisdiction under 35 U.S.C. § 6(b). We affirm.
Statement of the Case
Background
“In diagnostic and biochemical methodologies, access to extracted or
purified cellular components, such as nucleic acids, and access to extracted
or purified forms of proteins is imperative” (Spec. 1). According to
Appellants, “[t]he methods described [in Appellants’ Specification], . .
present improved processes for optimizing extraction of nucleic acids,
1 Appellants identify the Real Party in Interest as the Becton, Dickinson and
Company (see App. Br. 1).
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Application 12/165,069
proteins and other biological molecules from biological samples. These
optimized extraction processes significantly increase the separation and
recovery of nucleic acids, purified protein, and other biological molecules
for further diagnostic and biochemical methodologies” (Spec. 5).
The Claims
Claims 1,3, 10—16, and 18—23 are on appeal. Claim 1 is
representative and reads as follows:
1. A method for extracting DNA components of a
biological sample that is clinical, forensic or environmental,
comprising:
(i) Reversibly binding at least one DNA component of
the biological sample to at least one ferric oxide paramagnetic
particle;
(ii) separating the at least one ferric oxide paramagnetic
particle bound DNA component from unbound components of
the biological sample;
(iii) washing the at least one ferric oxide paramagnetic
particle bound DNA component;
(iv) separating the at least one ferric oxide paramagnetic
particle DNA bound component from the wash;
(v) removing the at least one DNA component from the
at least one ferric oxide paramagnetic particle by eluting the at
least one ferric oxide paramagnetic particle bound DNA
component with a pH elution buffer that is not further
combined with a neutralizing buffer during the removing step
thereby yielding an eluted sample; and
(vi) neutralizing the eluted sample by subsequently
adding a neutralizing buffer to the eluted sample containing the
pH elution buffer and the at least one ferric oxide paramagnetic
particle thereby yielding an optimized buffer.
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The Issues
A. The Examiner rejected claims 1, 11—16, and 18—23 under 35 U.S.C.
§ 103(a) as obvious over Collis ’2182 and Barbara3 (Final Act. 2—7).
B. The Examiner rejected claims 3 and 10 under 35 U.S.C. § 103(a) as
obvious over Collis ’218, Barbara, and Peterson4 (Final Act. 19—20).
A. 35 U.S.C. § 103(a) over Collis ’218 andBarbaro
The Examiner finds:
Collis ’218 discloses binding DNA to iron oxide particles
in a tube. Unbound sample was separated from the DNA/iron
oxide complexes by aspiration. The tubes and DNA/iron oxide
complexes were washed. The DNA/iron oxide complexes were
locked to the side of the tube and the fluid was aspirated. The
DNA was eluted using an elution buffer comprising the base
potassium hydroxide (KOH) to yield an eluted sample which is
transferred to a new tube after locking down the iron oxide.
The eluted sample is neutralized by adding a neutralization
buffer comprising bicine to yield an optimized buffer for use in
an amplification assay. See Examples 4-7.
(Final Act. 3). The Examiner acknowledges that “Collis ’218 does not
specifically disclose the eluted sample is neutralized by adding a
neutralizing buffer to the eluted sample containing the pH elution buffer and
the at least one ferric oxide paramagnetic particle” (Final Act. 3).
The Examiner finds it obvious “to have modified the method
disclosed by Collis ’218 by neutralizing the eluted sample in the presence of
2 Collis et al., US 2004/0157218 Al, published Aug. 12, 2004 (“Collis”).
3 Barbaro et al., DNA profiling by different extraction methods, 1261
International Congress Series 562-64 (2004) (“Barbaro”).
4 Peterson et al., US 5,783,431, issued July 21, 1998 (“Peterson”).
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the iron oxide paramagnetic particles” because the “ordinary artisan would
recognize that performing a DNA extraction process using paramagnetic
particles in a single tube reduces the loss of material based on disclosure of
Barbara” and because “Collis ’218 discloses an embodiment in which
samples are simultaneously eluted and neutralized in the presence of iron
oxide” (Final Act. 4).
The issues with respect to this rejection are:
(i) Does the evidence of record support the Examiner’s conclusion
that Collis ’218 and Barbara render claim 1 prima facie obvious?
(ii) If so, have Appellants presented evidence of secondary
considerations, that when weighed with the evidence of obviousness, is
sufficient to support a conclusion of non-obviousness?
Findings of Fact
1. Collis ’218 teaches: “The present invention addresses the need
for a simple and rapid method to treat biological samples such as plasma and
blood for extraction of nucleic acid therefrom” (Collis ’218 | 8).
2. Example 3 of Collis ’218 teaches a method of extracting RNA
from a simulated plasma sample comprising the steps:
(i) binding the RNA to a paramagnetic particle (see Collis ’218135;
“[Pjlasma was added to 64 tubes, each containing 40-45 mg of iron oxide.
. . . All of the tubes were then spiked with 2,500 copies of HIV in vitro
transcript to simulate a plasma sample containing 5,000 copies/mL HIV
RNA”);
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(ii) separating RNA bound to the paramagnetic particle (see Collis
’218 135; “The iron oxide particles were then magnetically locked to the
sides of the tubes, and the unbound samples were removed by aspiration”);
(iii) washing the paramagnetic particles (see Collis ’218135; “The
particles were washed twice with 1 mL of 90 mM glycine/HCl by aspirating
and dispensing 800 uL for a total of 12 times”);
(iv) separating the paramagnetic particle from the wash (see Collis
’218135; “After each wash, the particles were locked to the sides of the
tubes and the fluid was removed by aspiration from each tube”);
(v) eluting the RNA from the paramagnetic particles (see Collis ’218
135; “The samples were eluted from the particles with the addition of
120 uL of elution buffer composed of 75 mM Bicine, 85 mM KOH and
mixing by aspirating and dispensing 100 uL at a time for a total of 15
times”);
(vi) neutralizing the eluted sample by subsequently adding a
neutralizing buffer to the sample containing the pH elution buffer and the
paramagnetic particle (see Collis ’218135; “The samples were then
neutralized by adding 60 uL of neutralization buffer composed of 400 mM
Bicine to each tube and mixed by aspirating and dispensing 100 uL at a time
for a total of 15 times. The eluted samples were transferred to new tubes as
described in Example 1”).
3. Example 4 of Collis ’218 teaches extraction of DNA from a
simulated plasma sample, differing from the process of Example 3 in two
ways: first, the step of eluting the DNA from the paramagnetic particles
used a different “[e]lution buffer (120 uL) composed of 105 mM KOH and
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14% DMSO”; second, after elution, the “samples were then transferred to
new tubes” that did not contain paramagnetic particles prior to the final step
of addition of the neutralization buffer (see Collis ’218138).
4. Barbara teaches “systems like IQ allow a better surrender and
an excellent reproducibility since the paramagnetic IQ resin used binds a
known quantity of DNA . . . the use of a single tube for DNA extraction
reduces the loss of material” (Barbara 563).
Principles of Law
“The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSRInt’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
Analysis
We adopt the Examiner’s findings of fact and reasoning regarding the
scope and content of the prior art (Final Act. 2—7; FF 1—4) and agree that
claim 1 is rendered obvious by Collis ’218 and Barbara. We address
Appellants’ arguments below.
(i) Prima facie obviousness
Appellants contend
Collis ’218 describes a “four-step method.” First, the sample
was eluted by an elution buffer. Second, the iron particles are
locked to the side of the tube. Third, the sample eluent is
aspirated from the tubes and transported into a different tube(s).
Finally, the neutralization buffer is added to the eluted sample
in the new tube(s).
(App. Br. 7).
We do not find this argument persuasive because Collis ’218
describes two different methods. While Example 4 of Collis ’218 employs
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the method characterized by Appellants as “four-step,” with removal of the
eluted sample to a new tube prior to addition of a neutralization buffer (FF
3), Example 3 of Collis ’218 teaches addition of an elution buffer, followed
by addition of a neutralization buffer, prior to removal of the eluted and
neutralized sample to a new tube (FF 2). As the Examiner points out “Collis
’218 describes methods (Example 3) in which samples were not transferred
to new tubes prior to neutralizing and Collis ’218 was able to detect and
analyze specific nucleic acids extracted from the sample” (Ans. 7).
Thus, Appellants incorrectly characterize the teachings of Collis ’218,
whose Example 3 teaches a process that arguably does not differ from claim
1, and if there is a difference, it lies solely in the presence of bicine in both
the elution buffer and neutralizing buffer (FF 2; cf. App. Br. 7 “what the
Examiner characterizes as the ‘elution buffer’ is actually a mixture of elution
agent (KOH) and neutralization agent (Bicine)”). We recognize that claim 1
recites the use of “a pH elution buffer that is not further combined with a
neutralizing buffer during the removing step,” but Example 3 of Collis ’218
clearly uses the elution buffer containing bicine as an elution buffer, not as a
neutralization buffer (FF 2).
We therefore agree with the Examiner that, in Example 3, the
elution buffer is a separate and distinct buffer from the
neutralization buffer. While both contain Bicine, the levels
differ by about at least 5-fold. Thus, the elution in Example 3 is
not performed in the presence of the neutralization buffer
because the two solutions are distinct and the level of Bicine is
so dramatically different
(Ans. 8).
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However, even if the presence of bicine in the elution buffer of
Example 3 were interpreted as excluded by the recitation in claim 1,
Example 4 of Collis ’218 teaches the use of an elution buffer composed of
KOH and DMSO that does not contain the bicine neutralization component
(FF 3). The ordinary artisan would have found it obvious to substitute the
elution buffer of Example 4 into Example 3 because these are taught as
obvious equivalent elution buffers, used for the same purpose of eluting
nucleic acid from paramagnetic particles, and are subsequently neutralized
by similar bicine neutralization buffers (FF 2—3). See KSR, 550 U.S. at 417
(“If a person of ordinary skill can implement a predictable variation, § 103
likely bars its patentability.”) Moreover, an “[e]xpress suggestion to
substitute one equivalent for another need not be present to render such
substitution obvious.” In re Font, 675 F.2d 291, 301 (CCPA 1982))
Appellants, citing Lizzi Third Suppl. Decl. 5, contend that “Collis
’218 teaches that elution and neutralization should be performed separately
for two reasons: 1) if neutralization is performed in the presence of iron
oxide, some of the sample would rebind to the iron oxide and 2)
neutralization in the presence of the iron oxide is not considered an ideal
condition” (App. Br. 8).
We have considered the Lizzi Third Supplemental Declaration5, but
are not persuaded. Dr. Lizzi contends that “in Collis ’218 [] elution and
neutralization should be performed in separate tubes in order to be sure the
sample is in its purest form and to reduce loss of sample to paramagnetic
5 Third Supplemental Declaration of Dr. Michael Lizzi, dated
March 27, 2014.
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particles” (Lizzi Third Suppl. Decl. 6). However, Dr. Lizzi does not
address Example 3, where elution and neutralization were performed in the
same tube (FF 2), nor does Dr. Fizzi identify any statement in Collis ’218
itself that identifies these issues as problems or concerns.
We also are not persuaded by Dr. Fizzi’s statement that “[w]hile
Barbaro makes a generalized statement that the use of a single tube for DNA
extraction reduces the loss of material, there is no data presented in Barbaro
to support that statement” (Fizzi Third Suppl. Decl. 9). As we balance the
express teaching of the Barbaro reference suggesting the use of a single tube
in assays purifying DNA using magnetic beads (FF 4) against the opinion of
the inventor, we find Barbaro more persuasive. See In re Bulina, 362 F.2d
555, 559 (CCPA 1966) (“[A]n affidavit by an applicant or co-applicant as to
the advantages of his invention is less persuasive than one made by a
disinterested person.”)
Appellants contend “Collis ’218 clearly does not teach the same
method recited in claim 1 and actually teaches away from the present
method to utilize a single tube for elution and neutralization” (App. Br. 8).
We find this argument factually incorrect and unpersuasive. As noted,
Example 3 of Collis ’218 teaches the use of a single tube for elution and
neutralization (FF 2). Moreover, a teaching away requires a reference to
actually criticize, discredit, or otherwise discourage the claimed solution.
See In re Fulton, 391 F.3d 1195, 1201 (Fed. Cir. 2004) (“The prior art’s
mere disclosure of more than one alternative does not constitute a teaching
away from any of these alternatives because such disclosure does not
criticize, discredit, or otherwise discourage the solution claimed”).
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Appellants do not identify, and we do not find, any teaching in Collis ’218
that criticizes, discredits, or otherwise discourages the use of a single tube
for elution and neutralization.
Appellants contend that there is “no suggestion or disclosure in
Barbaro that would cause one of skill in the art to believe that the methods
of Collis ’218 could be modified to be performed in a single tube when
Collis ’218 is so obviously concerned with separating the extracted nucleic
acid from sample impurities” (App. Br. 9).
We are not persuaded. Collis ’218 expressly performs the elution and
neutralization in a single tube (FF 2) and Barbaro provides reason to use a
single tube, because that “reduces the loss of material” (FF 4). These
teachings provide a reason to use a single tube when loss of material is a
concern, and the ordinary artisan would have no reason to doubt that using a
single tube would be successful in light of the fact that Collis ’218 performs
a single tube elution and neutralization in Example 3 (FF 2).
Appellants contend the “only way that Barbaro might be read to
modify Collis ’218 is by hindsight reconstruction” (App. Br. 9). Appellants
also contend that “[dismissing the evidence in the Lizzi Declaration allowed
the Examiner to combine Collis ’218 and Barbaro in a manner using
Applicant’s claim as a template (which is a classic improper hindsight
reconstruction) in support of a conclusion of obviousness” (App. Br. 18).
We are not persuaded. While we are fully aware that hindsight bias
may plague determinations of obviousness, Graham v. John Deere Co., 383
U.S. 1, 36 (1966), we are also mindful that the Supreme Court has clearly
stated that the “combination of familiar elements according to known
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methods is likely to be obvious when it does no more than yield predictable
results.” KSR, 550 U.S. at 416. In the instant case, purification using a
single tube as suggested by Barbaro in a magnetic nucleic acid purification
assay and as performed by Example 3 of Collis ’218 predictably “reduces
the loss of material” (FF 4). This provides both an explicit reason to
combine and an implicit motivation to reduce material loss that are
technology-independent reasons to combine the teachings of Barbaro and
Collis. See DyStar Textilfarben GmbH & Co. Deutschland KG v. C.H.
Patrick Co., 464 F.3d 1356, 1368 (Fed. Cir. 2006) (“[W]e have repeatedly
held that an implicit motivation to combine[, and, thus, supports a finding of
obviousness] exists not only when a suggestion may be gleaned from the
prior art as a whole, but when the ‘improvement’ is technology-independent
and the combination of references results in a product or process that is more
desirable, for example because it is stronger, cheaper, cleaner, faster, lighter,
smaller, more durable, or more efficient.”).
(ii) Secondary considerations
Appellants contend
The claimed two-step process unequivocally (and
unexpectedly) yields better results than the single-step process
for isolating DNA in Collis ’138, which was performed in a
single tube. As explained in the Fizzi Declaration, it was
unexpected that additional nucleic acid capable of being
extracted from the paramagnetic particles was still present after
the one-step process was performed. That led to the
development of the claimed two-step process. Fizzi Third
Suppl. Decl. ]fl3.
(App. Br. 11). Appellants contend that the “Fizzi Declaration explains
Exhibit C, which is a direct comparison between the one-step process and
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two-step process” (App. Br. 12) and that the “two-step process
unequivocally demonstrates a statistically significant difference in standard
deviation between the claimed two-step process compared to the one-step
process” (App. Br. 13).
We do not find the evidence in the Lizzi Third Supplemental
Declaration persuasive of unexpected results for several reasons.
First, as Appellants point out, the comparison is between the one-step
and two-step processes (see Lizzi Third Suppl. Decl. 35). However, the
Declaration does not clearly explicate what specific steps were performed
between the two processes and even the protocols presented do not discuss
the elution and neutralization buffers used, nor clearly explain which process
steps were performed regarding the “one-step,” “two-step,” or “four-step”
processes identified by Appellants (see Lizzi Third Suppl. Decl. Exhibit B,
“6.0 Test or Experiment Description”).
Consequently, there does not appear to be a comparison with the
closest prior art of Example 3 of Collis ’218, which differs from the claim
solely in the elution buffer used and not in the number of steps as in
Example 4. See In re De Blauwe, 736 F.2d 699, 705 (Fed. Cir. 1984)
(“When an article is said to achieve unexpected (i.e. superior) results, those
results must logically be shown as superior compared to the results achieved
with other articles. . . . Moreover, an applicant relying on comparative tests
to rebut a prima facie case of obviousness must compare his claimed
invention to the closest prior art”).
Second, the Lizzi Third Supplemental Declaration experiment entitled
“Viper Elution Buffer Robustness Study” teaches the “elution buffer
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components center points are 125mM Bicine, 71 mM KOH, and 9.8%
DMSO” (see Lizzi Third Suppl. Decl. Exhibit A, “9.0 Conclusions”; cf.
Lizzi Third Suppl. Decl. 22). This elution buffer, according to Appellants’
interpretation discussed above, does not fall within the scope of claim 1.
Even in an experiment entitled “2-Step Elution MSA”, the evidence teaches
a 2X elution solution composed of “251 mM Bicine, 21.8%DMSO, 19%
Glycerol, with 0.1 % Tween 20 and 0.03% Proclin300” (see Lizzi Third
Suppl. Decl. Exhibit C, “3.0 Definitions).
Consequently, the Lizzi Third Supplemental Declaration evidence
appears to rely upon elution compositions that Appellants, at least, contend
are excluded from the scope of claim 1 (see App. Br. 6). Therefore, the
evidence does not clearly establish a nexus between the results presented and
the requirements of claim l6. See In re GPACInc., 57 F.3d 1573, 1580
(Fed. Cir. 1995) (“For objective evidence to be accorded substantial weight,
its proponent must establish a nexus between the evidence and the merits of
the claimed invention”); In re Huai-Hung Kao, 639 F.3d 1057, 1069 (Fed.
Cir. 2011) (“[T]he Board, in considering the evidence of unexpected results,
should determine whether there is a nexus between the unexpected [result]
and aspects of the claimed invention not already present in the prior art.”)
Third, we recognize the evidence in the Specification of a CpK for the
two-step method “that was 1.46 higher” and “a CpK that was 0.94 higher
than that of the one-step elution method” (Spec. 29) as well as the evidence
6 We note that if an elution solution containing bicine falls within the scope
of claim 1, then Example 3 of Collis anticipates claim 1, as well as renders
claim 1 obvious by using a bicine and KOH containing elution buffer (see
FF 2).
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in the Lizzi Third Supplemental Declaration showing “the two-step process
achieved better performance than the one-step process. While PAT and
PAT RFU scores appear to be relatively similar, the difference in standard
deviations between the two processes is significant” (Lizzi Third Suppl.
Decl. 139).
However, we find this evidence insufficient, when weighed against
the strong prima facie case of obviousness. Not only was this evidence not
compared with Example 3 of Collis ’218, but even if there is some showing
of unexpected results, the showing is insufficient to overcome the strong
showing of obviousness in this case. See Pfizer, Inc. v. Apotex, Inc., 480
F.3d 1348, 1372 (Fed. Cir. 2007) (“[W]e hold that even if Pfizer showed that
amlodipine besylate exhibits unexpectedly superior results, this secondary
consideration does not overcome the strong showing of obviousness in this
case. Although secondary considerations must be taken into account, they
do not necessarily control the obviousness conclusion.”).
In this case, given both the specific suggestion by Barbara to perform
the assay in a single tube (FF 4), the assay of Collis ’218 in Example 3 that
differs from claim 1 solely in the composition of the elution buffer (FF 2),
and the teaching by Collis ’218 in Example 4 of a suitable equivalent elution
buffer (FF 3), we find that even if there is some evidence of improved
“reproducibility,” that evidence, which was not compared with the closest
prior art and did not use the reagents required by claim 1, is also insufficient
to overcome the strong showing of obviousness over Collis ’218 and
Barbara.
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Appellants contend that the “Examiner did not give the Lizzi
Declaration proper consideration” (App. Br. 14).
We are not persuaded. The Examiner points out that:
The data presented by Appellant compares the method of the ’138
patent and the claimed invention as clearly stated in the Appeal Brief
and confirmed by Mr. Lizzi in an interview held /5/14/2014 (See
Interview Summary dated 5/29/2014).
It is the Examiner’s position that any unexpected results should
be demonstrated as compared to the Collis ’218 method, which
utilizes distinct elution and neutralization steps, and not the Collis
’138 method, which involves a single combined step of
elution/neutralization.
(Ans. 16). The portions of the Lizzi Third Suppl. Declaration found
unpersuasive by the Examiner dealt with the characterizations of how the
ordinary artisan would construe the Collis ’218 and Barbara references (see
Lizzi Third Suppl. Decl. Tflf 4—12). We also do not find the Lizzi Third
Suppl. Declaration persuasive, for the reasons discussed above, and note,
regarding those portions of the declaration based on the opinion of Dr. Lizzi,
that the “Board is entitled to weigh the declarations and conclude that the
lack of factual corroborations warrants discounting the opinions expressed in
the declarations.” In re Am. Acad. ofSci. Tech Ctr., 367 L.3d 1359, 1368
(Led. Cir. 2004). We have already addressed the portions of the Declaration
based upon experimental evidence above.
Conclusion of Law
(i) The evidence of record supports the Examiner’s conclusion that
Collis ’218 and Barbara render claim 1 prima facie obvious.
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(ii) Appellants have not presented evidence of secondary
considerations, that when weighed with the evidence of obviousness, is
sufficient to support a conclusion of non-obviousness.
B. 35 U.S.C. § 103(a) over Collis ’218, Barbaro, and Peterson
Appellants do not separately argue the limitations of claims 3 and 10,
but simply contend “Peterson does not remedy deficiencies of either Collis
’218 or Collis ’218 informed by Barbaro as an obviating reference” (App.
Br. 20). Because we agree with the Examiner that Collis ’218 and Barbaro
render claim 1 obvious for the reasons given above, we also find that the
further combination with Peterson renders claims 3 and 10 obvious for the
reasons given by the Examiner (see Final Act. 19—20).
SUMMARY
In summary, we affirm the rejection of claim 1 under 35 U.S.C.
§ 103(a) as obvious over Collis ’218 and Barbaro. Claims 11—16 and 18—23
fall with claim 1.
We affirm the rejection of claims 3 and 10 under 35 U.S.C. § 103(a)
as obvious over Collis ’218, Barbaro, and Peterson.
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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