Bio-Rad Laboratories, Inc.

Patent Trials and Appeals Board

May 14, 2021

IPR2021-00132 (P.T.A.B. May. 14, 2021)

Trials@uspto.gov Paper: 11
571-272-7822 Date: May 14, 2021

UNITED STATES PATENT AND TRADEMARK OFFICE

BEFORE THE PATENT TRIAL AND APPEAL BOARD

10X GENOMICS, INC.,
Petitioner,
v.
BIO-RAD LABORATORIES, INC.,
Patent Owner.

IPR2021-00132
Patent 10,190,115 B2

Before SHERIDAN K. SNEDDEN, ZHENYU YANG, and
CHRISTOPHER G. PAULRAJ, Administrative Patent Judges.
SNEDDEN, Administrative Patent Judge.
DECISION
Denying Institution of Inter Partes Review
35 U.S.C. § 314, 37 C.F.R. § 42.4

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Patent 10,190,115 B2

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I. INTRODUCTION
A. Background and Summary
10X Genomics, Inc. (“Petitioner”) filed a Petition requesting an inter
partes review of claims 1–26 of U.S. Patent No. 10,190,115 B2 (“the ’115
patent,” Ex. 1001). Paper 2 (“Pet.”). Bio-Rad Laboratories, Inc. (“Patent
Owner”) filed a Preliminary Response to the Petition. Paper 7 (“Prelim.
Resp.”).
To institute an inter partes review, we must determine that the
information presented in the Petition shows “a reasonable likelihood that the
petitioner would prevail with respect to at least 1 of the claims challenged in
the petition.” 35 U.S.C. § 314(a). The Supreme Court has held that a
decision to institute under 35 U.S.C. § 314 may not institute on less than all
claims challenged in the petition. SAS Inst., Inc. v. Iancu, 138 S. Ct. 1348,
1359–60 (2018). After considering the evidence and arguments presented in
the Petition, we determine that Petitioner has not demonstrated a reasonable
likelihood of success in proving that at least 1 claim of the ’115 patent is
unpatentable.
B. Real Parties in Interest
Petitioner 10X Genomics, Inc. and Patent Owner Bio-Rad
Laboratories, Inc. each asserts it alone is the real party in interest. Pet. 57;
Paper 5, 1.
C. Related Matters
Petitioner has filed a second petition for inter partes review in
IPR2021-00133 for U.S. Patent No. 10,190,115. The parties indicate the
’115 patent is asserted against Petitioner in Bio-Rad Laboratories, Inc., et al
v. 10X Genomics, Inc., 3:20-cv-03207-VC (N.D. Cal.). Pet. 57; Paper 5, 1.
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D. The ’115 Patent (Ex. 1001)
The ’115 patent discloses “methods, compositions, and kits for assays,
many of which involve amplification reactions such as digital PCR or
droplet digital PCR.” Ex. 1001, Abstract. The assays may be used for
applications such as sequencing. Id.
The ’115 patent discloses that “[s]eparate library preparations can be
prepared for each sample, and each sample can have its own unique barcode.
Id. at 3:67–4:2. When the prepared libraries are pooled and sequenced,
“[e]ach sequence read of the resulting dataset can be traced back to an
original sample via the barcode in the sequence read.” Id. at 4:2–6. Pooling
samples reduces the cost of sequencing per sample while retaining the ability
to determine from which sample a sequence read is derived. Id. at 3:64–67.
More specifically, the ’115 patent discloses separating
polynucleotides in a sample into a plurality of partitions, e.g., droplets, and
supplying adaptors with oligonucleotide barcode sequences (or tags) to each
of a plurality of partitions comprising polynucleotides. Id. at 4:7–9, 10:26–
43. The adaptor with a barcode can then be attached to a polynucleotide by
ligation. Id. at 7:38–39. When polynucleotides with barcode adaptors are
sequenced, “the barcodes can be used determine if two or more sequence
reads were generated from one or more polynucleotides in the same
partition.” Id. at 4:11–14.
The ’115 patent discloses “[b]arcode adaptors can be bundled within a
partition, e.g., an aqueous phase of an emulsion, e.g., a droplet.” Id. at 4:15–
16. Barcode tagging is accomplished by merging partitions filled with
adaptors and partitions containing sample polynucleotide. Id. at 4:15–16.
Figure 1A, reproduced below, shows a method “of merging droplets
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comprising a sample with droplets comprising adaptors with barcodes.” Id.
at 3:40–42.

Figure 1A shows an adaptor-filled partition/droplet that is merged with a
sample-polynucleotide-containing partition/droplet, resulting in an adaptor
attached to a polynucleotide. Id. at 4:19–27. As illustrated in FIG 1A,
partitions containing sample polynucleotide may be greater than (e.g., 1.5-
fold or 100,000-fold) the average volume of adaptor-filled partitions. Id. at
4:27–32.
In some cases, sample-polynucleotide-containing partitions contain
adaptor-filled partitions. Id. at 4:39–41. For example, adaptor-filled
partitions “can be emulsified with a polynucleotide sample so that sample-
polynucleotide-containing partitions (e.g., droplets) end up containing
adaptor-filled partitions.” Id. at 4:41–45. The ’115 patent discloses “[t]he
adaptor-filled droplets can be burst (e.g., through [a stimulus such as a]
temperature adjustment) to release reaction components (e.g., PCR or
ligation components) that can be used for library preparation.” Id. at 4:45–
48.
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E. Illustrative Claim
Independent claims 1 and 14, reproduced below, are illustrative of the
claimed subject matter of the ’115 patent.
1. A composition comprising a plurality of second partitions
containing first partitions, wherein:
a. said first partitions are degradable upon the application
of a stimulus to said first partitions such that contents of a first
partition is mixed with contents of a second partition; and
b. said first partitions are contained within the second
partitions;
c. said first partitions contain an oligonucleotide barcode;
and
d. the first partitions have on average a first average
volume and the second partitions have on average a second
average volume, wherein the second average volume is at least
twice as large as the first average volume.

14. A device comprising a plurality of second partitions,
wherein:
a. at least one second partition of the plurality of second
partitions contains a first partition comprising an oligonucleotide
barcode, and the first partition has a first volume and the at least
one second partition has a second volume, wherein the second
volume is at least twice as large as the first volume; and
b. said first partition is degradable upon the application of
a stimulus to said first partition such that contents of a first
partition is mixed with contents of a second partition.
Ex. 1001, 49:2–50:41.
Claims 2–13 depend from independent claim 1. Id. Claims 15–26
depend from independent claim 14. Id.
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F. Evidence
Petitioner relies upon information that includes the following.
Ex. 1005, Hindson et al., US 2014/0155295 A1, published June
5, 2014 (“Hindson”).
Ex. 1006, Anderson et al., US RE41,780 E, issued Sept. 28, 2010
(“Anderson”).
Petitioner also relies upon the Declaration of Dr. John Quakenbush
(Ex. 1004) to support its contentions.
G. Asserted Ground of Unpatentability
Petitioner asserts that claims 1–26 would have been unpatentable on
the following grounds:
Ground Claim(s)
Challenged 35 U.S.C. § Reference(s)/Basis
1 1–26 102 Hindson (with Anderson incorporated-by-reference)

II. ANALYSIS
A. Claim Construction
We interpret a claim “using the same claim construction standard that
would be used to construe the claim in a civil action under 35 U.S.C.
282(b).” 37 C.F.R. § 42.100(b) (2019). Under this standard, we construe
the claim “in accordance with the ordinary and customary meaning of such
claim as understood by one of ordinary skill in the art and the prosecution
history pertaining to the patent.” Id.
Petitioner proposes construction for several claimed terms, including
“first partition” and “droplet.” Pet. 28–30. Patent Owner does not address
claim construction in its Preliminary Response. Having considered the
parties’ positions and evidence of record, we determine that no express
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construction of any claim term is necessary to determine whether to institute
inter partes review. Nidec Motor Corp. v. Zhongshan Broad Ocean Motor
Co., 868 F.3d 1013, 1017 (Fed. Cir. 2017) (“[W]e need only construe terms
‘that are in controversy, and only to the extent necessary to resolve the
controversy.’” (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200
F.3d 795, 803 (Fed. Cir. 1999))). To the extent further discussion of the
meaning of any claim term is necessary to our decision, we provide that
discussion below in our analysis of the asserted grounds of unpatentability.
B. Summary of Cited Prior Art
1. Summary of Hindson (Ex. 1005)
Petitioner’s anticipation challenges rely on Hindson, which
incorporates-by-reference Anderson. Pet. 31, 37; Ex. 1005 ¶ 32.
Hindson relates to microwell capsule array devices capable of
performing one or more sample preparation operations. Ex. 1005, Abstract.
Hindson discloses that the device is an assembly of partitions (e.g., droplets)
that are loaded with microcapsules. Id. at ¶ 26.
Hindson discloses a composition for the device including a first
microcapsule, a gel bead, which comprises an oligonucleotide barcode. Id.
at ¶ 5. The microcapsule is degradable upon the application of a stimulus
(i.e., a biological, chemical, thermal, electrical, magnetic, or photo stimulus,
and combinations thereof). Id. at ¶ 6. Hindson discloses a second
microcapsule, which may comprise the first microcapsule. Id. at ¶ 7.
Figure 1B, reproduced below, shows a microcapsule. Id. at ¶ 36.
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Figure 1A shows a plurality of smaller microcapsules, or
compartments 140, that are contained within the larger microcapsule. Id. at
¶ 37. Compartments 140 have polymerized shells, and each compartment
can hold a different reagent. Id.
The release of reagents, such as oligonucleotide barcodes, can be
controlled. Id. at ¶¶ 38, 56. For example, a reagent designed to be released
upon a heat trigger may be contained within compartments having heat
activatable polymerized shells, while reagents to be released upon a different
trigger may be present in compartments with different types of polymerized
shells. Id. at ¶ 37.
Hindson further discloses that the second microcapsule, which
comprises the first microcapsule, may be a droplet. Id. at ¶ 7. Hindson
refers to and incorporates-by-reference Anderson, which describes droplets
and methods for droplet generation. Id. at ¶ 32.
2. Summary of Anderson (Ex. 1006)
Hindson incorporates Anderson by reference, and, in the following
excerpt, specifically relies upon Anderson for its disclosure of droplets:
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Droplets and methods for droplet generation, for example, are
described in U.S. Pat. No. RE41,780, which is incorporated
herein by reference in its entirety for all purposes.
Ex. 1005 ¶ 32.
Anderson discloses a “system for nucleic acid amplification of a
sample compris[ing] partitioning the sample into partitioned sections and
performing PCR on the partitioned sections of the sample.” Ex. 1006,
Abstract. Anderson describes partitioning into droplets. Id. at 3:24, 5:8.
Regarding droplet volume, Anderson discloses, for example, droplets of
“picoliter type volumes,” “microdroplets (each with a volume of 5x10⁻9
liters),” and “[a] pL microdroplet.” Id. at 5:4–6, 7:40–44, 8:22–23.
C. Anticipation of Claims 1–26 by Hindson, with Anderson
Incorporated-By-Reference
Petitioner contends claims 1–26 of the ’115 patent are anticipated by
Hindson. Pet. 31–56. Hindson was filed August 13, 2013 with an earliest
effective filing date of August 14, 2012 and published as Publication No.
2014/0155295 on June 5, 2014. Ex. 1005. The ’115 patent, however, claims
the benefit of priority to Patent Application No. 13/456,121 (“the ’121
application”), filed April 25, 2012. Ex. 1001. Petitioner contends that
Hindson is prior art to the ’115 patent because the claims lack written
description support and thus the ’115 patent is not entitled to the benefit of
priority to the ’121 application. Pet. 19–20. In particular, Petitioner
contends that Patent Owner’s infringement contentions filed in the related
parallel litigation assert that the first partition is a dissolvable gel bead (id. at
18–19), however, “[t]here is no disclosure in the 115 Patent that partitions—
or first partitions in particular—are beads or that beads are degradable upon
the application of a stimulus” (id. at 2). Thus, according to Petitioner,
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“under the constructions applied in Bio-Rad’s infringement assertions in
district court, the claims of the 115 Patent would only be entitled to a
priority date of September 22, 2014,” the filing date of the ’115 patent. Pet.
6.
In its Preliminary Response, Patent Owner contends, “[b]ecause this
specification of the ’115 patent is the same specification as the specification
of [the ’121 application] to which the ’115 patent claims priority, and
because the ’121 filing precedes the filing of Hindson, the ’115 patent claims
cannot be anticipated by Hindson.” Prelim. Resp. 7.
We have considered the parties’ arguments, summarized above, but
determine that Patent Owner has the better position. In particular, we are not
persuaded by Petitioner’s contentions that the claims fail the written
description requirement for the claimed “partitions” because the term “gel
beads” are not adequately described. Pet. 19–20. The claims do not recite
the term “gel beads”. Ex. 1001, 49:2–50:41. Rather, the claims of the ’115
patent are directed to compositions (claim 1–13) and devices (clam 14–26)
having a plurality of second partitions containing first partitions, wherein the
second partitions may be droplets (claims 4–6 and 18–20). Id. To the extent
that Petitioner contends that the ’115 patent does not provide adequate
written description support for those elements of the challenged claims, we
disagree. For example, claim 1 recites a composition “comprising a plurality
of second partitions containing first partitions” where “first partitions are
contained within the second partitions.” Support for those elements is
found, for example, in the following portions of the ’115 patent:
In general, described herein are methods, compositions, and kits
for library preparation for sequencing polynucleotides. The
methods, compositions, and kits can be used to separate a
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sample of polynucleotides into a plurality of partitions, and
each of the plurality of partitions can be provided with a unique
set of adaptors comprising a barcode.
Ex. 1001 at 3:50–55 (emphasis added);
“In some cases, sample-polynucleotide-containing partitions are
formed so that they contain adaptor-filled partitions. For
example, adaptor-filled partitions (e.g., droplets) can be
emulsified with a polynucleotide sample so that sample-
polynucleotide-containing partitions (e.g., droplets) end up
containing adaptor-filled partitions.”
Id. at 4:39–45 (emphasis added); and
“In some cases, the first partitions are first droplets and the
second partitions are second droplets; and prior to the merging,
the at least one second droplet comprises the at least one first
droplet.”
Id. at 2:1–4.
As another example, claim 1 recites, “first partitions are degradable
upon the application of a stimulus to said first partitions such that contents of
a first partition is mixed with contents of a second partition.” Support for
that element is found, for example, in the following portions of the ‘115
patent:
In some cases, sample-polynucleotide-containing partitions are
formed so that they contain adaptor-filled partitions. For
example, adaptor-filled partitions (e.g., droplets) can be
emulsified with a polynucleotide sample so that sample-
polynucleotide-containing partitions (e.g., droplets) end up
containing adaptor-filled partitions. The adaptor-filled droplets
can be burst (e.g., through a temperature adjustment) to release
reaction components (e.g., PCR or ligation components) that can
be used for library preparation.
Id. at 4:39–48 (emphasis added);
In some cases, an inner droplet (or partition) can be fused with
an outer droplet (or partition) by heating/cooling to change
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temperature, applying pressure, altering composition (e.g., via a
chemical additive), applying acoustic energy (e.g., via
sonication), exposure to light (e.g., to stimulate a photochemical
reaction), applying an electric field, or any combination thereof.
Id. at 6:44–50; and
This disclosure provides methods that can be used in sequencing
and other applications. In some instances, this disclosure
provides a method comprising: a. subdividing a plurality of
adaptors into a plurality of first partitions . . . wherein the
adaptors comprise unique barcodes; b. subdividing a sample
comprising multiple polynucleotides into a plurality of second
partitions . . . c. merging at least one of the first partitions with
at least one of the second partitions to form a merged partition;
and d. tagging one of the multiple polynucleotides, or fragment
thereof, with at least one of the adaptors.
Id. at 1:31–44.
Accordingly, in view of the above, we are not persuaded by
Petitioner’s arguments that the claims of the ’115 patent lack written
description support and, thus, are not entitled to claim the benefit of priority
to the ’121 application. Consequently, we determine that Hindson does not
qualify as prior art to the ’115 patent and therefore cannot anticipate the
claims of the ’115 patent.
III. CONCLUSION
Petitioner has failed to establish a reasonable likelihood of prevailing
in demonstrating that claims 1–26 are unpatentable over prior art set forth in
the asserted ground.
IV. ORDER
In consideration of the foregoing, it is hereby:
ORDERED that the Petition is denied and no trial is instituted.

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For PETITIONER:
Samantha A. Jameson
Daniel M. Radke
Tensegrity Law Group LLP
samantha.jameson@tensegritylawgroup.com
daniel.radke@tensegritylawgroup.com

For PATENT OWNER:

Derek C. Walter
Garland T. Stephens
Justin L. Constant
Weil, Gotshal & Manges LLP
derek.walter@weil.com
garland.stephens@weil.com
justin.constant@weil.com