Complete Genomics, Inc. v. Illumina, Inc.
MEMORANDUM ORDER REGARDING CLAIM CONSTRUCTION. Signed by Judge Maryellen Noreika on 2/16/2021. (dlw)
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IN THE UNITED STATES DISTRICT COURT
FOR THE DISTRICT OF DELAWARE
COMPLETE GENOMICS, INC.,
ILLUMINA, INC. and ILLUMINA
COMPLETE GENOMICS, INC., BGI
AMERICAS CORP. and MGI AMERICAS
C.A. No. 19-970 (MN)
At Wilmington this 16th day of February 2021:
IT IS HEREBY ORDERED that the claim terms of U.S. Patent Nos. 9,222,132 (“the ’132
Patent”), 10,662,473 (“the ’473 Patent”), 9,217,178 (“the ’178 Patent”), 9,303,290 (“the ’290
Patent”) and 9,970,055 (“the ’055 Patent”) 1 with agreed-upon constructions are construed as
follows (see D.I. 115 at 14; D.I. 105 at 4-5; see also D.I. 171 & 200):
“sequencing-by-extension” means “sequencing by synthesis” (’132 Patent,
claim 1; ’473 Patent, claim 1)
The ’132 and ’473 Patents are asserted by Complete Genomics, Inc., whereas the ’178,
’290 and ’055 Patents are asserted by Illumina, Inc. and Illumina Cambridge Ltd.
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“detection position” means “a position in a target sequence for which
sequence information is desired” (’132 Patent, claims 1 & 5)
“ascorbic acid” means “an organic compound with the chemical formula
C6H8O6 and one of the following structures
(’178 Patent, claims 1 & 6; ’290 Patent, claims 1, 2 & 7; ’055 Patent,
claims 1 & 2)
“inhibiting light-induced degradation of nucleic acids during a detection
step of a nucleic acid sequencing reaction,” which only appears in the
preamble, is a limitation (’178 Patent, claim 1; ’290 Patent, claim 2) 2
“a salt thereof / the salt of” does not require construction (’178 Patent,
claims 1 & 6; ’290 Patent, claims 1, 2 & 7; ’055 Patent, claims 1 & 2)
“a [first / second] fluorescent label” means “at least one fluorescent element,
isotope, or chemical compound attached to enable the detection of the
compound” 3 (’132 Patent, claims 5-8)
Further, as announced at the continued hearing on January 29, 2021, IT IS HEREBY
ORDERED that the disputed claim terms of the ’132, ’473, ’178, ’290 and ’055 Patents are
construed as follows:
The parties reached agreement on this construction in the time between the original hearing
and the continued hearing. (See D.I. 200; see also D.I. 214 at 57:11-20).
The parties reached agreement on this construction at the hearing. (See D.I. 214 at 52:2453:9; see also D.I. 200).
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“nucleic acid templates” means “nucleic acid molecules derived from target
nucleic acid(s) that may include one or more adaptors” (’132 Patent,
“for each of a plurality of said single-stranded nucleic acid templates,
determining the identity of nucleotides at detection positions in the nucleic
acid template in multiple cycles of a sequencing-by-extension reaction”
means “for each of a plurality of said single-stranded nucleic acid templates,
determining the identity of a nucleotide at a detection position in the nucleic
acid template in each of multiple cycles of a sequencing by extension
reaction” (’132 Patent, claims 1-4)
“a [first / second] fluorescent signal” means “light emitted by a fluorescent
molecule or molecules that is detected within a defined wavelength range”
(’132 Patent, claims 1-4)
“polynucleotide template[s]” means “nucleic acids derived from target
nucleic acid(s) that may include one or more adaptors” (’473 Patent,
claims 1-3 & 5)
“the first/second nucleotide and the first/second type of third nucleotide
have different fluorescent intensities” shall be given its plain and ordinary
meaning (’473 Patent, claim 1)
“amplicons” means “products of one or more polynucleotide amplification
reactions” (’473 Patent, claim 3)
“irradiating” does not require construction (’178 Patent, claim 1; ’290
Patent, claim 2)
The parties briefed the issues (see D.I. 104, 105 & 115) and submitted an appendix
containing intrinsic and extrinsic evidence, including expert declarations (see D.I. 106), and
Illumina Cambridge Ltd. and Illumina, Inc. (together, “Illumina”) also provided a tutorial
describing the relevant technology (see D.I. 107). The Court carefully reviewed all submissions
in connection with the parties’ contentions regarding the disputed claim terms, heard oral argument
(see D.I. 180 & 214) and applied the following legal standards in reaching its decision:
“[T]he ultimate question of the proper construction of the patent [is] a question of law,”
although subsidiary fact-finding is sometimes necessary. Teva Pharms. USA, Inc. v. Sandoz, Inc.,
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135 S. Ct. 831, 837-38 (2015). “[T]he words of a claim are generally given their ordinary and
customary meaning [which is] the meaning that the term would have to a person of ordinary skill
in the art in question at the time of the invention, i.e., as of the effective filing date of the patent
application.” Phillips v. AWH Corp., 415 F.3d 1303, 1312-13 (Fed. Cir. 2005) (en banc) (internal
citations and quotation marks omitted). Although “the claims themselves provide substantial
guidance as to the meaning of particular claim terms,” the context of the surrounding words of the
claim also must be considered. Id. at 1314. “[T]he ordinary meaning of a claim term is its meaning
to the ordinary artisan after reading the entire patent.” Id. at 1321 (internal quotation marks
The patent specification “is always highly relevant to the claim construction analysis . . .
[as] it is the single best guide to the meaning of a disputed term.” Vitronics Corp. v. Conceptronic,
Inc., 90 F.3d 1576, 1582 (Fed. Cir. 1996). It is also possible that “the specification may reveal a
special definition given to a claim term by the patentee that differs from the meaning it would
otherwise possess. In such cases, the inventor’s lexicography governs.” Phillips, 415 F.3d at
1316. “Even when the specification describes only a single embodiment, [however,] the claims of
the patent will not be read restrictively unless the patentee has demonstrated a clear intention to
limit the claim scope using words or expressions of manifest exclusion or restriction.” Hill-Rom
Servs., Inc. v. Stryker Corp., 755 F.3d 1367, 1372 (Fed. Cir. 2014) (internal quotation marks
omitted) (quoting Liebel-Flarsheim Co. v. Medrad, Inc., 358 F.3d 898, 906 (Fed. Cir. 2004)).
In addition to the specification, a court “should also consider the patent’s prosecution
history, if it is in evidence.” Markman v. Westview Instruments, Inc., 52 F.3d 967, 980 (Fed. Cir.
1995) (en banc), aff’d, 517 U.S. 370 (1996). The prosecution history, which is “intrinsic evidence,
. . . consists of the complete record of the proceedings before the PTO [Patent and Trademark
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Office] and includes the prior art cited during the examination of the patent.” Phillips, 415 F.3d
at 1317. “[T]he prosecution history can often inform the meaning of the claim language by
demonstrating how the inventor understood the invention and whether the inventor limited the
invention in the course of prosecution, making the claim scope narrower than it would otherwise
In some cases, courts “will need to look beyond the patent’s intrinsic evidence and to
consult extrinsic evidence in order to understand, for example, the background science or the
meaning of a term in the relevant art during the relevant time period.” Teva, 135 S. Ct. at 841.
Extrinsic evidence “consists of all evidence external to the patent and prosecution history,
including expert and inventor testimony, dictionaries, and learned treatises.” Markman, 52 F.3d
at 980. Expert testimony can be useful “to ensure that the court’s understanding of the technical
aspects of the patent is consistent with that of a person of skill in the art, or to establish that a
particular term in the patent or the prior art has a particular meaning in the pertinent field.”
Phillips, 415 F.3d at 1318. Nonetheless, courts must not lose sight of the fact that “expert reports
and testimony [are] generated at the time of and for the purpose of litigation and thus can suffer
from bias that is not present in intrinsic evidence.” Id. Overall, although extrinsic evidence “may
be useful to the court,” it is “less reliable” than intrinsic evidence, and its consideration “is unlikely
to result in a reliable interpretation of patent claim scope unless considered in the context of the
intrinsic evidence.” Id. at 1318-19. Where the intrinsic record unambiguously describes the scope
of the patented invention, reliance on any extrinsic evidence is improper. See Pitney Bowes, Inc.
v. Hewlett-Packard Co., 182 F.3d 1298, 1308 (Fed. Cir. 1999) (citing Vitronics, 90 F.3d at 1583).
THE COURT’S RULING
The Court’s ruling regarding the disputed claim terms of the ’132, ’473, ’178, ’290 and
’055 Patents was announced from the bench at the conclusion of the hearing as follows:
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. . . At issue are two patents asserted by Complete Genomics against
Illumina with seven disputed terms and three patents asserted by
Illumina against Complete Genomics. There is just one disputed
term in the Illumina patents.
I am prepared to rule on all of the disputes. I will not be
issuing a written opinion, but I will issue an order stating my rulings.
I want to emphasize before I announce my decisions that although I
am not issuing a written opinion, we have followed a full and
thorough process before making the decisions I am about to state. I
have reviewed the patents in dispute and all of the evidence
submitted in the extensive Joint Appendix. There was briefing on
each of the disputed terms, and Illumina submitted a technology
tutorial. We had an argument on December 22nd of last year and
another here today. All of that has been carefully considered.
Now as to my rulings. As an initial matter, I am not going
to read into the record my understanding of claim construction law
generally. I have a legal standard section that I have included in
earlier opinions, including somewhat recently in Best Medical
International v. Varian Medical Systems, Inc., C.A. No. 18-1599. I
incorporate that law and adopt it into my ruling today and will also
set it out in the order that I issue.
I’ll start with the disputed terms of the Complete Genomics
patents and address the first and fifth terms together as they involve
essentially the same dispute.
The first term is “nucleic acid template[s]” in claims 1
through 8 of the ’132 Patent. Complete Genomics proposes the
construction “nucleic acid molecules derived from target nucleic
acid(s) that may include one or more adaptors.” Illumina proposes
the construction “a nucleic acid with one or more interspersed
adaptors” and adds that “[a]n interspersed adaptor is an
oligonucleotide that is inserted at spaced locations within the
interior region of a target nucleic acid.”
The fifth term is “polynucleotide template[s]” in claims 1, 2,
3 and 5 of the ’473 Patent.
Complete Genomics proposes the construction “nucleic
acids derived from target nucleic acid(s) that may include one or
more adaptors.” Illumina proposes “a nucleic acid with one or more
The parties did not raise any disputes as to the person of ordinary skill in the art that are
relevant to the issues raised in connection with claim construction.
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interspersed adaptors” and once again adds its definition of an
For these terms, the main dispute is whether the templates at
issue may include adaptors or must include adaptors, or more
particularly interspersed adaptors, as Illumina argues.
Here, I will construe the first and fifth terms to mean
“nucleic acid molecules derived from target nucleic acid(s) that may
include one or more adaptors” and “nucleic acids derived from
target nucleic acid(s) that may include one or more adaptors,”
These constructions are supported by the intrinsic evidence.
First, allowing the templates to include adaptors but not requiring
them to include adaptors is consistent with the claim language. For
example, claims 2 and 7 of the ’132 Patent are dependent claims that
add the further limitation that the nucleic acid template comprises
adaptors. If I were to construe the first and fifth disputed terms to
require not only adaptors but interspersed adaptors, the dependent
claims would be broader than the independent claims – or the
additional limitation would be meaningless.
Similarly, the specification supports my construction.
Although the specification in places references “the present
invention” in discussing embodiments including adaptors, I do not
think that the “present invention” language is so clear as to override
the claim language and read into the term “template” a requirement
that it include adaptors.
Instead, as I read the “present invention” language, it refers
to embodiments of the present invention. Indeed, not all statements
of “the present invention” include adaptors. For example, the
Abstract states: “The present invention is directed to methods and
compositions for acquiring nucleotide sequence information of
target sequences. In particular, the present invention provides
methods and compositions for improving the efficacy of sequencing
reactions by using fewer labels to distinguish between nucleotides
and by detecting nucleotides at multiple detection positions in a
Similarly, the summary of the invention states that “the
present invention provides methods and compositions for base
calling in sequencing reaction” without reference to adaptors.
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In looking at the patents as a whole and at all the uses of the
“present invention” language, I understand the references to the
“present invention” that Illumina cites to be discussions of
embodiments. That is consistent with how the patentee used the
term “present invention” in most instances.
And my construction is also consistent with statements the
patentee made to clarify that the invention was broader than use of
DNBs [DNA nanoballs] with concatemers and adaptors. For
example, at column 18, lines 51 through 58, the ’132 Patent states
that “[t]he present invention provides methods and compositions for
identifying multiple bases in a target nucleic acid by utilizing sets of
probes that can distinguish between four possible bases at one or
more positions in a target sequence using fewer than four labels in a
set of sequencing probes. The methods of the present invention
allow for multiple base calls per sequencing cycle, thus reducing the
time and cost of sequencing and detection of sequences of target
nucleic acids.” Again, this language does not refer to use of
adaptors. It also goes further, stating at lines 59 through 63:
“Although the following description of sequencing applications of
the present invention is provided in terms of DNBs, it will be
appreciated that these methods can be applied to any nucleic acid
targets and are not necessarily limited to concatemers comprising
target sequence and adaptors.”
My reading of the specification is also consistent with other
discussions of embodiments that suggest that use of adaptors is not
mandatory. For example, at column 9, lines 20 to 22, the ’132 Patent
states: “These fragmented nucleic acids are used to produce target
nucleic acid templates that generally include one or more adaptors.”
The use of the word “generally” in that passage connotes that the
use of adaptors may be the common approach, but it does not convey
that adaptors are required.
And finally, I note that my construction is also consistent
with how Illumina and its expert understood a claim term including
a template in the IPR. Specifically, when addressing the limitation
that recites “providing an array comprising single-stranded nucleic
acid templates disposed at positions on a surface,” Illumina stated:
(See also ’132 Patent at 8:33-39 (“Although the embodiments of the invention described
herein are generally described in terms of circular nucleic acid template constructs, it will
be appreciated that nucleic acid template constructs may also be linear. Furthermore,
nucleic acid template constructs of the invention may be single- or double-stranded, with
the latter being preferred in some embodiments.”)).
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“Limitation 1(a) recites the routine aspect of sequencing by
synthesis using an array of single-stranded templates.”
Of course, that is not dispositive, but it suggests that it is not
so clear and apparent from the specification that templates had to
include adaptors, let alone interspersed adaptors. And it reflects
how a person of skill in the art, Illumina’s expert, would read the
The second term is “for each of a plurality of said singlestranded nucleic acid templates, determining the identity of
nucleotides at detection positions in the nucleic acid template in
multiple cycles of a sequencing-by-extension reaction” in claims 1
through 4 of the ’132 Patent. Complete Genomics proposes the
construction “for each of a plurality of said single-stranded nucleic
acid templates, determining the identity of a nucleotide at a
detection position in the nucleic acid template in each of multiple
cycles of a sequencing-by-extension reaction.” Illumina proposes
“for each of a plurality of said single-stranded nucleic acid
templates, determining the identity of nucleotides at multiple
detection positions in the nucleic acid template in each of multiple
cycles of a sequencing-by-extension reaction.”
The crux of the dispute is whether the claim term requires a
sequencing-by-synthesis (or “SBS”) method in which one
nucleotide is detected per template per SBS cycle or one in which
multiple nucleotides must be detected in a single template in a single
Here, I will construe the term to mean “for each of a plurality
of said single-stranded nucleic acid templates, determining the
identity of a nucleotide at a detection position in the nucleic acid
template in each of multiple cycles of a sequencing by extension
This construction is consistent with the plain meaning as
supported by the prosecution history and the specification.
During prosecution of the application that became the ’132
Patent, the patentee added language to claim 37 that the sequencing
reactions involve “extending individual anchor probes by one
nucleotide per cycle” in one or more SBS cycles and that each of
those SBS cycles involved “determining the identities of nucleotides
(D.I. 106-1, Ex. 7 at 18).
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at the detection positions . . . .” In describing that amendment, the
patentee stated that “[e]xtension by one nucleotide per cycle was
added at the suggestion of the Examiner and is a property of
sequencing by synthesis.” Thus, the language about “determining
the identities” plural of “nucleotides” also plural at “detection
positions” is referring to the addition of one nucleotide per cycle.
And this language, consistent with the specification, makes clear
that the patent included sequencing by extension, which involves
extension by one nucleotide at a time.
The third term is “a [first / second] fluorescent signal” in
claims 1 through 4 of the ’132 Patent. Complete Genomics proposes
the construction “light emitted by a fluorescent molecule or
molecules that is detected within a defined wavelength range.”
Illumina proposes “the wavelength and intensity of the fluorescent
light arising from the first/second label.”
Here, not only do the parties dispute what the term means,
they dispute what the dispute is. Illumina says that the dispute is the
number of labels that are used. Complete Genomics says that the
dispute is two-fold: (1) whether signal means the same thing as label
and (2) does the signal need to be defined with respect to two
components, both the wavelength, the color, and the intensity at
which it is fluorescent.
I will try to address each of the purported disputes. First, I
disagree that a signal and a label are the same. The patentee
described two different words to describe these aspects of the claims
and it is not clear from the intrinsic evidence that the patentee
intended to use them interchangeably. Although a signal may arise
from a label, that does not necessarily mean that the two are the same
Second, I agree with Plaintiff that wavelength or color is
used to define a signal, and that intensity may be used, but it is not
required. For example, at column 32, lines 38 to 56, the ’132 Patent
specification describes detecting the presence of incorporated
nucleotides by taking images which show a binary event, either the
presence or absence of fluorescent light of a particular color which
(D.I. 106-1, Ex. 10 at 346).
(Id. at 348).
(’132 Patent at 9:34-43).
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indicates the presence or absence of the incorporated nucleotide.
These examples do not refer to distinguishing signals based on
intensity, only whether the image taken shows the presence or
absence of a particular fluorophore based on color detection. The
claim language is similar. The detecting step (element 1(b)(ii))
requires: “the presence or absence of fluorescent signals(s)
associated with complementary nucleotides.” It does not refer to
intensity. And, in fact, in the ’132 Patent IPR, Illumina and its
expert similarly interpreted detection of the “signals” in claim 1 as
being met by detecting the presence or absence of fluorescent
emission of particular colors.
And finally, I agree with Complete Genomics that the first
and second signals are defined and detected in a wavelength range.
Fluorescent molecules fluoresce at wavelengths over a range, not at
one single wavelength value. As Illumina’s expert explained in his
IPR Declaration for the ’132 Patent, fluorescent dyes are excited by
the absorption of light in a range. In response, they emit light across
a different wavelength range, and their signal is detected across a
range. That is evidence of how a person of skill in the art would
understand the way fluorescent labels work. And there is nothing in
the specification or claims that limits detecting the fluorescent signal
to a single integer value rather than a range for a given color.
To sum all of that up, I will construe “a [first / second]
fluorescent signal” to mean “light emitted by a fluorescent molecule
or molecules that is detected within a defined wavelength range.”
The fourth term is “a [first / second] fluorescent label” in
claims 5 through 8 of the ’132 Patent. In an effort to compromise,
Complete Genomics now proposes “at least one fluorescent
element, isotope, or chemical compound attached to enable the
detection of the compound.” That construction uses the language
describing a label in the ’132 Patent, but specifies that the label be
fluorescent. Illumina agrees to that construction with the caveat that
it may later need to argue about what that term means. I will address
that if necessary at a later time, but for now will adopt the agreedupon construction.
The sixth term is “the first / second nucleotide and the first /
second type of the third nucleotide have different fluorescent
(’132 Patent at 35:38-56 (“An image is then taken. . . . [T]he first image would show a C1
+ C3 signal. . . . When the next image is taken, only a C3 signal remains . . . .”); see also
id. at 2:46-49, 26:60-67 (other examples using two colors on one of the nucleotides)).
(See, e.g., D.I. 106-2, Ex. 7 at 24-26 & Ex. 8 ¶¶ 76-80).
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intensities” in claim 1 of the ’473 Patent. Complete Genomics
asserts that no construction is necessary, but that if the term is
construed it should mean “the first/second nucleotide molecule
comprising a fluorescent dye emits light of a different intensity than
the first/second type of the third molecule of the third nucleotide
molecule comprising a fluorescent dye.” Illumina proposes the
construction “the collection of molecules within the pool comprising
the first/second nucleotide having a different fluorescent intensity
than the collection of molecules within the pool comprising the
first/second type of the third nucleotide.”
The dispute is whether the claim requires different intensities
of emitted light from the individual nucleotides or from
“collections” of those nucleotides.
I think that this term does not need to be construed and will
give it its plain and ordinary meaning. This is consistent with the
words of claim 1. The word “collection” does not appear anywhere
in the claim. And the claim language uses the singular, referring to
“a  nucleotide” or “the  nucleotide,” and to “a  fluorescent dye”
or “the  fluorescent dye.” It does not necessarily require plural
“nucleotides” or “dyes.”
My construction is also supported by the intrinsic evidence.
The specification discloses ways of using “intensity difference[s]
between the fluorophores” for sequencing. In the context of SBS,
the specification teaches that “four bases in one position may be read
with two colors using two different intensities of the two colors.”
And it teaches that the differing intensities “could be achieved with
dyes with the same emission wavelength but with different
brightnesses.” This tracks what claim 1 recites regarding the
The prosecution history similarly supports my conclusion
that no additional construction of the claim words is needed. In a
post-allowance amendment, the Applicant modified the language of
claim 27 (issued as claim 1). Claim 27 originally recited a first and
second “portion” of the third nucleotide, instead of a first and second
(’473 Patent at 42:42-43:31).
(Id. at 43:15-24).
(Id. at 42:58-60:22).
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“type.” The Applicant amended the claim to remove each
reference to “portions” and to instead “recite there are two ‘types’
of third nucleotides.” By replacing “portion” with “type,” the
Applicant sought to convey that the pool comprises two “differently
labeled” types of the recited third nucleotide.
The seventh term is “amplicons” in claim 3 of the ’473
Patent. Complete Genomics proposes the construction “products of
one or more polynucleotide amplification reactions.” Illumina
proposes “a nucleic acid concatemer that is the product of a
polynucleotide amplification reaction.”
Each side asserts that its proposal is based on a definition in
the ’473 Patent. Here I agree with Complete Genomics. The ’473
Patent defines “amplicon,” stating that “‘[a]mplicon’ means the
product of a polynucleotide amplification reaction.” It goes on
to say “[t]hat is, it is a population of polynucleotides that are
replicated from one or more starting sequences.” That is in the
section of the patent offering definitions for many terms.
Although the ’473 Patent also states that concatemers are
referred to as amplicons, I do not see that as a definition.
Concatemers may be amplicons, but that does not mean that all
amplicons are concatemers.
Those are my constructions for the Complete Genomics
patents. Now for the one remaining term of the Illumina patents
“irradiating.” Illumina proposes that no construction is necessary.
Complete Genomics proposes that it means “repeatedly or
prolongedly exposing to intense illumination.”
Here, I agree with Illumina that the term need not be
construed. The parties don’t really dispute the standard meaning of
irradiating. The issue is Complete Genomics’ attempts to add
additional concepts from the specification and the prosecution
history into the standard definition. The specification does not
define “irradiating,” but states that “[m]ethods for detecting
fluorescently labelled nucleotides generally require use of incident
(D.I. 106-1, Ex. 13 at CGI000049203 (Amendment After Allowance Under 37 C.F.R. §
(Id. at CGI000049208).
(’473 Patent at 9:1-4).
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light (e.g. laser light) of a wavelength specific for the fluorescent
label, or the use of other suitable sources of illumination, to excite
the fluorophore. Fluorescent light emitted from the fluorophore may
then be detected.”
As to the first part of Complete Genomics’ proposal, both
claim 1 of the ’178 Patent and claim 2 of the ’290 Patent require that
the claimed steps (a)-(d) be repeated at least ten times. The
irradiating step is step (b) of the claimed method, and therefore the
claim already requires repetition in irradiation by way of the last
Similarly, importing “intense” into the construction injects
unnecessary ambiguity into this term’s meaning. Although the
specification does explain that the claimed method “includes a
detection step which requires repeated or prolonged exposure to
intense illumination,” this is insufficient support for importing
this concept into the construction of “irradiating.”
The Honorable Maryellen Noreika
United States District Judge
(’178 Patent at 4:19-23).
(Id. at 2:20-22).
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