Source: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-cand-3_05-cv-04158/USCOURTS-cand-3_05-cv-04158-15/pdf.json

Nature of Suit Code: 830
Nature of Suit: Patent
Cause of Action: 35:271 Patent Infringement

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UNITED 

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For the Northern District of California

NITED 

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UNITED STATES DISTRICT COURT

NORTHERN DISTRICT OF CALIFORNIA

BOARD OF TRUSTEES OF THE LELAND

STANFORD JUNIOR UNIVERSITY

Plaintiff,

v.

 ROCHE MOLECULAR SYSTEMS, INC.,

ET AL.

Defendants.

_____________________________________/

No. C 05-04158 MHP

MEMORANDUM & ORDER

Claim Construction Memorandum and

Order for United States Patent Nos.

5,968,730; 6,503,705; and 7,129,041.

On October 14, 2005 plaintiff Board of Trustees of the Leland Stanford Junior University

(“plaintiff” or “Stanford”) brought this action against Roche Molecular Systems, Inc., Roche

Diagnostics Corporation, Roche Diagnostics Operations, Inc., and Roche Diagnostic Systems, Inc.1

(collectively “defendants” or “Roche”) alleging infringement of U.S. Patents Nos. 5,968,730 (“the

‘730 patent”) and 6,503,705 (“the ‘705 patent”). On November 17, 2005 Roche filed a counterclaim

against Stanford, naming Dr. Thomas Merigan as an additional counterclaim defendant. In June

2006, Roche amended its counterclaim without objection to add Dr. Mark Holodniy as a

counterclaim defendant. On March 26, 2007, Stanford amended its complaint to also allege

infringement of U.S. Patent No. 7,129,041 (“the ‘041 patent”). Now before the court are the parties’

claim construction briefs, filed pursuant to Patent Local Rule 4-5. Having considered the parties’

arguments and submissions, and for the reasons set forth below, the court construes the disputed

terms as follows.

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BACKGROUND

This patent dispute concerns the application of Polymerase Chain Reaction (“PCR”)

technology in the context of research related to the Human Immunodeficiency Virus (“HIV”) and

the Acquired Immunodeficiency Syndrome (“AIDS”). Stanford currently owns three patents titled

“Polymerase Chain Reaction Assays for Monitoring Antiviral Therapy and Making Therapeutic

Decisions in the Treatment of Acquired Immunodeficiency Syndrome.” The patents involve

correlating measurements of HIV nucleic acids obtained via a PCR assay with determining whether

or not a therapy is effective. The results can also be helpful in determining whether the patient has

developed a strain of HIV that is resistant to the particular therapy the patient is undergoing.

Claims 1, 5-9, 13-14, 18-19, and 23 of the ‘730 patent; Claims 1 and 5-10 of the ‘705 patent;

and Claims 1-4 and 8 of the ‘041 patent are asserted in this litigation. In general, there are two types

of method claims in these patents. The first type includes a step for measuring the HIV copy

number. See ‘730 patent, Claims 9, 14, and 19; ‘705 patent, Claims 1 and 8. Claim 9 of the ‘730

patent reads:

9. A method of evaluating the effectiveness of anti-HIV therapy of a patient

comprising

(i) collecting a plasma sample from an HIV-infected patient who is being

treated with an antiretroviral agent;

(ii) amplifying the HIV-encoding nucleic acid in the plasma sample using

HIV primers in about 30 cycles of PCR; and

(iii) measuring the HIV RNA copy number using the product of the PCR,

in which an HIV RNA copy number greater than about 500 per 200 ul of

plasma correlates positively with the conclusion that the antiretroviral agent is

therapeutically ineffective.

Similarly, Claim 1 of the ‘705 patent reads:

1. A method of evaluating the effectiveness of anti-HIV therapy of an HIV-infected

patient comprising:

a) collecting statistically significant data useful for determining whether or

not a decline in plasma HIV RNA copy numbers exists after initiating

treatment of an HIV-infected patient with an antiretroviral agent by:

(i) collecting more than one plasma sample from the HIV infected

patient at time intervals sufficient to ascertain the existence of a

statistically significant decline in plasma HIV RNA copy numbers;

(ii) amplifying the HIV-encoding nucleic acid in the plasma samples

using HIV primers via PCR for about 30 cycles;

(iii) measuring HIV RNA copy numbers using the products of the PCR

of step (ii);

(iv) comparing the HIV RNA copy numbers in the plasma samples

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collected during the treatment; and

b) evaluating whether a statistically significant decline in plasma HIV RNA

copy numbers exists in evaluating the effectiveness of anti-HIV therapy of a

patient.

The other type of method claims do not include a measuring step, but instead include a step

testing for the presence or absence of detectable HIV-encoding nucleic acid. See ‘730 patent,

Claims 1, 6, 7, and 8; ‘041 Patent, Claim 1. Claim 1 of the ‘041 patent reads:

1. A method of evaluating the effectiveness of anti-HIV therapy of a patient

comprising correlating the presence or absence of detectable HIV-encoding nucleic

acid in a plasma sample of an HIV infected patient with an absolute CD4 count,

wherein the presence or absence of said detectable HIV-encoding nucleic acid is

determined by

(i) collecting a plasma sample[] from an HIV-infected patient who is being

treated with an antiretroviral agent;

(ii) amplifying HIV-encoding nucleic acid that may be present in the plasma

sample using HIV primers via PCR and;

(iii) testing for the presence of HIV-encoding nucleic acid sequence in the

product of the PCR.

The present dispute boils down to four specific terms which are used in various contexts

throughout the patents. The terms are: 1) “therapeutically effective” or “therapeutically ineffective”;

2) “an antiretroviral agent”; 3) “measuring the HIV RNA copy number”; and 4) “presence of

detectable HIV-encoding nucleic acid” or “absence of detectable HIV-encoding nucleic acid.”

LEGAL STANDARD

I. Claim Construction

Under Markman v. Westview Instruments, Inc., 517 U.S. 370, 389–90 (1996), the court

construes the scope and meaning of disputed patent claims as a matter of law. The first step of this

analysis requires the court to consider the words of the claims. Teleflex, Inc. v. Ficosca N. Am., 299

F.3d 1313, 1324 (Fed. Cir. 2002). According to the Federal Circuit, the court must “indulge a

‘heavy presumption’ that a claim term carries its ordinary and customary meaning.” CCS Fitness,

Inc. v. Brunswick Corp., 288 F.3d 1359, 1366 (Fed. Cir. 2002). To determine the ordinary meaning

of a disputed term, the court may review a variety of sources including the claims themselves, other

intrinsic evidence such as the written description and prosecution history, and dictionaries and

treatises. Teleflex, 299 F.3d at 1325. The court must conduct this inquiry not from the perspective

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of a lay observer, but rather “from the standpoint of a person of ordinary skill in the relevant art.” 

Id. (citing Zelinski v. Brunswick Corp., 185 F.3d 1311, 1316 (Fed. Cir. 1999)).

Among the sources of intrinsic evidence, the specification 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). By expressly defining terms in the specification, an inventor may “choose[] to be his or her

own lexicographer,” thereby limiting the meaning of the disputed term to the definition provided in

the specification. Johnson Worldwide Assocs., Inc. v. Zebco Corp., 175 F.3d 985, 990 (Fed. Cir.

1999). In addition,“[e]ven when guidance is not provided in explicit definitional format, ‘the

specification may define claim terms ‘by implication’ such that the meaning may be ‘found in or

ascertained by a reading of the patent documents.’” Irdeto Access, Inc. v. Echostar Satellite Corp.,

383 F.3d 1295, 1300 (Fed. Cir. 2004) (quoting Bell Atl. Network Servs., Inc v. Covad Commc’ns

Group, Inc., 262 F.3d 1258, 1268 (Fed. Cir. 2001)). “The specification may also assist in resolving

ambiguity where the ordinary and accustomed meaning of the words used in the claims lack

sufficient clarity to permit the scope of the claim to be ascertained from the words alone.” Teleflex,

299 F.3d at 1325. At the same time, the Federal Circuit has cautioned that the written description

“should never trump the clear meaning of the claim terms.” Comark Comms., Inc. v. Harris Corp.,

156 F.3d 1182, 1187 (Fed. Cir. 1998) (citations omitted); see also Tate Access Floors, Inc. v.

Maxess Techs., Inc., 222 F.3d 958, 966 (Fed. Cir. 2000) (“Although claims must be read in light of

the specification of which they are part, . . . it is improper to read limitations from the written

description into a claim . . . .”).

Likewise, the prosecution history may demonstrate that the patentee intended to deviate from

a term’s ordinary and accustomed meaning. Teleflex, 299 F.3d at 1326. “Arguments and

amendments made during the prosecution of a patent application and other aspects of the

prosecution history, as well as the specification and other claims, must be examined to determine the

meaning of terms in the claims.” Southwall Techs., Inc. v. Cardinal IG Co., 54 F.3d 1570, 1576

(Fed. Cir. 1995), cert. denied, 516 U.S. 987 (1995). “In particular, ‘the prosecution history (or file

wrapper) limits the interpretation of claims so as to exclude any interpretation that may have been

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disclaimed or disavowed during prosecution in order to obtain claim allowance.’” Teleflex, 299

F.3d at 1326 (quoting Standard Oil Co. v. Am. Cyanamid Co., 774 F.2d 448, 452 (Fed. Cir. 1985)).

Dictionary definitions and other objective reference materials available at the time that the

patent was issued may also provide evidence of the ordinary meaning of a claim. Phillips v. AWH

Corp., 415 F.3d 1303, 1322 (Fed. Cir. 2005) (en banc); Texas Digital Sys., Inc. v. Telegenix, Inc.,

308 F.3d 1193, 1202 (Fed. Cir. 2002). A dictionary “has the value of being an unbiased source,

accessible to the public in advance of litigation.” Phillips, 415 F.3d at 1322 (internal quotation

omitted). Thus, district courts “are free to consult such resources at any time in order to better

understand the underlying technology and may also rely on dictionary definitions when construing

claim terms, so long as the dictionary definition does not contradict any definition found in or

ascertained by a reading of the patent documents.” Vitronics, 90 F.3d at 1584 n.6. A court should

be cautious, however, not to place too much reliance on dictionaries, as the resulting construction

may be too broad. Phillips, 415 F.3d at 1321.

Federal Circuit decisions take a less favorable view of other forms of extrinsic evidence,

such as expert testimony and prior art not cited in the specification or the prosecution history, noting

that “claims should preferably be interpreted without recourse to extrinsic evidence, other than

perhaps dictionaries or reference books, and that expert testimony should be received only for the

purpose of educating the judge.” EMI Group N. Am., Inc. v. Intel Corp., 157 F.3d 887, 892 (Fed.

Cir. 1998), cert. denied, 526 U.S. 1112 (1999). Although “extrinsic evidence in general, and expert

testimony in particular, may be used . . . to help the court come to a proper understanding of the

claims[,] it may not be used to vary or contradict the claim language . . . . Indeed, where the patent

documents are unambiguous, expert testimony regarding the meaning of a claim is entitled to no

weight.” Vitronics, 90 F.3d at 1584.

The Federal Circuit recently revisited the basic approach to claim construction in Phillips. 

Although Phillips consists largely of an affirmation of ten years of claim construction jurisprudence,

it provides at least two pieces of additional guidance. First, the Federal Circuit rejected a line of

cases suggesting that claim interpretation must begin with a dictionary definition of the disputed

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terms. Phillips, 415 F.3d at 1320–21. Second, the Federal Circuit emphasized that claim terms must

be interpreted in light of their context, especially the language used in other claims and the

specification. Id. at 1321. Taken as a whole, Phillips appears to signal a small retreat from

formalism and bright-line rules in claim construction. As a result, the court will focus primarily on

the intrinsic record before it. Cases cited by the parties in support of fixed “rules” of claim

construction will accordingly be given somewhat less weight.

DISCUSSION

I. Level of Ordinary Skill

“Factors that may be considered in determining level of ordinary skill in the art include: (1)

the educational level of the inventor; (2) type of problems encountered in the art; (3) prior art

solutions to those problems; (4) rapidity with which innovations are made; (5) sophistication of the

technology; and (6) educational level of active workers in the field.” Envtl. Designs, Ltd. v. Union

Oil Co., 713 F.2d 693, 696 (Fed. Cir. 1983) (citing Orthopedic Equip. Co. v. All Orthopedic

Appliances, Inc., 707 F.3d 1376, 1381–82 (Fed. Cir. 1983)). These factors are not exhaustive and

merely provide guidance when determining the level of ordinary skill in the art.

Stanford claims that a person of ordinary skill in the art is a medical doctor working on

clinical HIV research involving antiretroviral agents or a Ph.D. researcher working on molecular

methods relating to clinical HIV research involving antiretroviral agents. Roche claims that a person

of ordinary skill in the art is one with a medical degree or graduate degree in biochemistry or a

related field and who has had at least two years of relevant laboratory bench experience conducting

PCR assays.

The art involved in these patents is the use of PCR assays to determine HIV viral load in a

sample so that the information may be used to determine the effectiveness of the antiretroviral

therapy regimen that the sample is undergoing. There does not seem to be a significant difference

between the parties’ competing formulations except for Stanford’s requirement that one of skill have

experience with antiretroviral agents. A medical doctor without experience with antiretroviral

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agents would not have the level of ordinary skill required because the patents in question relate

directly to the effectiveness or ineffectiveness of antiretroviral agents.

The individuals included in Stanford’s definition will certainly have experience with

antiretroviral agents, but may or may not be experienced in conducting PCR assays. The patents at

issue, however, all relate to the use of PCR assays used to generate data for the purpose of

evaluating the effectiveness of anti-HIV therapy. Since knowledge of PCR assays is a prerequisite

to understand, let alone practice, the patents in question, the court is convinced that knowledge of

PCR assays is required.

The person of ordinary skill is thus defined as: A medical doctor working on clinical HIV

research involving antiretroviral agents or a Ph.D. researcher working on molecular methods relating

to clinical HIV research involving antiretroviral agents. Any person of ordinary skill in the art must

have conducted numerous PCR assays in conjunction with his research.

II. Discovery Abuses

Roche claims two instances of discovery abuse by Stanford, each related to one of Stanford’s

two experts. First, that Stanford improperly failed to make its expert Dr. Kramer available for

deposition, and second, that Stanford improperly instructed its expert Dr. Volberding not to answer

certain questions during his deposition.

On August 2, 2007 the court issued an order regarding expert depositions in conjunction with

claim construction. See Docket No. 175. The court stated that the expert’s deposition could be

canceled if either party did not intend to rely upon the testimony of that expert in its briefing. Id.

Soon thereafter, Stanford informed Roche that Dr. Kramer’s August 15, 2007 deposition was being

cancelled because it did not intend to use his testimony in its opening brief. See Docket No. 184,

Exhs B & D; Rhyu Supp. Dec., Exh. 32. Nonetheless counsel for Roche traveled to Boston to take

the deposition. See generally Kramer Dep. On August 15, 2007 this court ruled that if Stanford

intended to rely on Dr. Kramer’s testimony, it would have to make him available for deposition if

requested by Roche. See Docket No. 186. Stanford did not use Dr. Kramer’s testimony in any of its

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briefing and thus its actions were proper.

Stanford, however, did rely on Dr. Volberding’s opinion. Specifically, Dr. Volberding

opined on the meaning of “therapeutically effective” and “therapeutically ineffective.” Volberding

Dec., ¶¶ 7–12. Thus, in accordance with the court’s order, Mr. Volberding’s deposition was taken

by Roche on August 19, 2007. At this deposition, counsel for Stanford did not let Mr. Volberding

answer questions regarding which other parties, if any, currently make recommendations about HIVtherapy or its effectiveness for a particular patient. See Cannon Dec., Exh. A at 83:5–88:8. Roche

requests, as a remedy, that the court strike Dr. Volberding’s declaration and that Stanford be

precluded from challenging Roche’s construction of the terms “therapeutically effective” and

“therapeutically ineffective.”

Roche claims that one hotly contested issue in this litigation is who performs the assay and

who makes evaluations about effectiveness. It relies upon Wilson Sporting Goods Co. v. Hillerich

& Bradsby Co., 442 F.3d 1322, 1326–27 (Fed. Cir. 2006), to claim the appropriateness of raising

infringement issues during claim construction. Wilson, however, did not allow infringement issues

to be raised or decided during claim construction. Instead, it allowed infringement issues to identify

claims that needed construction. Id. (“While a trial court should certainly not prejudge the ultimate

infringement analysis by construing claims with an aim to include or exclude an accused product or

process, knowledge of that product or process provides meaningful context for the first step of the

infringement analysis, claim construction.”). Providing context is not the same as raising

infringement issues for resolution. In fact, “[a] claim is construed in light of the claim language, the

other claims, the prior art, the prosecution history, and the specification, not in light of the accused

device.” SRI Int’l. v. Matsushita Elec. Corp. of Am., 775 F.2d 1107, 1118 (Fed. Cir. 1985). Roche

also argues that Stanford initially put this particular issue in contention. Again, if the questions

during discovery did not pertain to claim construction, who put the issue into contention is

irrelevant.

Roche’s proposed construction relies on its argument that it is the physician, and nobody

else, that makes evaluations about the overall effectiveness of an antiretroviral therapy. This, they

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claim, has been the case since May 1992. Since the objected to questions were within the scope of

this construction, they were properly asked of Dr. Volberding. The court, with respect to claim

construction, will therefore assume that Stanford has waived any argument regarding who makes

decisions about whether a particular therapy is effective overall. Namely, for the purposes of claim

construction, it will be considered admitted that the physician generally makes the decision

regarding a particular therapy’s overall effectiveness.

III. Claim Construction

The following chart summarizes the court’s construction of the disputed terms.2 The full

analysis supporting each construction is below.

Term Construction 

“therapeutically effective” or

“therapeutically ineffective”

No construction necessary.

“an antiretroviral agent” “At least one substance having or capable of having

an effect against a retrovirus, such as HIV”

“measuring the HIV RNA copy number” No construction necessary.

“presence of detectable HIV-encoding

nucleic acid” or “absence of detectable

HIV-encoding nucleic acid”

No construction necessary.

A. “Therapeutically effective” or “therapeutically ineffective”

Stanford claims that these terms need not be construed because the plain meaning of these

terms is sufficiently clear. As stated above, the court must “indulge a ‘heavy presumption’ that a

claim term carries its ordinary and customary meaning.” CCS Fitness, Inc. v. Brunswick Corp., 288

F.3d 1359, 1366 (Fed. Cir. 2002). Specifically, the Federal Circuit has held that if commonly

understood words are used, then the “ordinary meaning of claim language as understood by a person

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of skill in the art may be readily apparent even to lay judges, and claim construction in such cases

involves little more than the application of the widely accepted meaning of commonly understood

words.” Phillips v. AWH Corp., 415 F.3d 1303, 1314 (Fed. Cir. 2005) (en banc). The terms

“therapeutically effective” or “therapeutically ineffective” are commonplace—a juror can easily use

these terms in her infringement fact-finding without further direction from the court. 

These terms do not need to be construed because they are neither unfamiliar to the jury,

confusing to the jury, nor affected by the specification or prosecution history. See United States

Surgical Corp. v. Ethicon, Inc., 103 F.3d 1554, 1568 (Fed. Cir.1997) (“Claim construction is a

matter of resolution of disputed meanings and technical scope, to clarify and when necessary to

explain what the patentee covered by the claims, for use in the determination of infringement. It is

not an obligatory exercise in redundancy.”). First, the terms will not be unfamiliar to the jury since

“therapeutic,” “effective,” and “ineffective” are all familiar words. The court will only rely on

extrinsic evidence if the totality of the intrinsic evidence is insufficient to construe the claims. Here,

it is clear that the patents in suit were designed to determine whether or not the anti-retroviral

therapy was assisting in decreasing the amount of HIV in the sample (“the viral load”). The court,

therefore, need not resort to dictionary definitions. Second, these terms are not confusing. 

Conducting this inquiry from the perspective of a person of ordinary skill in the art, the court is

convinced that the meanings of these words would be clear to her. Third, there is no evidence that

the specification or the prosecution history intended a different meaning be attached to these terms. 

In sum, the court is not persuaded that the terms are ambiguous.

Roche’s proposed constructions for “therapeutically effective” and “therapeutically

ineffective” are: “elicits the medical effect intended by the treating physician such that the course of

treatment is not modified” and “fails to elicit the medical effect intended by the treating physician as

a result of drug resistance such that the course of treatment is modified.” These constructions do not

address the ordinary and customary meaning of these terms and fail due to two specific flaws. First,

Roche integrates a physician’s mental or subjective state, namely an intended medical effect into the

construction. Roche also limits the construction to a particular physician—the “treating” one—not

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just any physician. Second, Roche requires a particular course of action by the physician.

Roche’s arguments combine three facts that are generally not in dispute. First, the only

person who evaluates whether anti-HIV therapy for a patient is therapeutically effective or

ineffective is the treating physician. Second, the patents in question relate to a decision about the

effectiveness of the therapy. See Title of ‘730 patent. Third, the patent is silent as to what is

therapeutically effective and ineffective. Thus, Roche contends, one of ordinary skill in the art

would consider these terms to refer to the medical effect intended by the treating physician with

respect to the prescribed treatment. Each premise is discussed below followed by a discussion of

Roche’s conclusion.

First, Roche makes great attempts, both in its brief and its expert declarations, to demonstrate

that the treating physician is the one who makes decisions regarding the patient’s drug regimen. 

There is little doubt that it is the treating physician who usually makes determinations regarding a

patient’s treatment regimen and whether it is therapeutically effective. Neither Stanford nor the

court disputes this. Indeed, the patent itself states that “[i]f a patient being treated with an

antiretroviral therapeutic agent exhibits an increase in plasma HIV RNA copy number, a physician

should consider altering the patient[’]s treatment regimen.” ‘730 patent at 2:45–49. The patent,

however, does not limit itself to the treating physician. Therefore, the decision does not necessarily

have to be made by the treating physician and could be made by other medical professionals.

Second, the patents are clear regarding their purpose—to determine if the given antiretroviral regimen is aiding in the decrease of HIV viral load. The physician is told by the

specification what should or should not be considered therapeutically effective. See, e.g., ‘730

patent Claim 1 (“the absence of detectable HIV-encoding nucleic acid correlates positively with the

conclusion that the anti-retroviral agent is therapeutically effective.”). It is clear that physicians take

multiple factors into account when determining whether a particular antiretroviral therapy is

effective or not and the result of the patented method would be but one of those factors.

Third, the patent is indeed silent as to what is to be considered therapeutically effective or

ineffective. As discussed above, this ordinarily would be within the purview of the physician. The

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patents merely aid the physician in that determination by pointing her in the right

direction—correlating certain results with effectiveness or ineffectiveness.

Roche wants the court to insert the physician’s state of mind into the construction. State of

mind has been discussed by the Federal Circuit. See Amazon.com, Inc. v. Barnesandnoble.com,

Inc., 239 F.3d 1343 (Fed. Cir. 2001). The Amazon court was “not prepared to assign a meaning to a

patent claim that depends on the state of mind of the accused infringer.” Id. at 1353. The court

there refused to “inject[] subjective notions into the infringement analysis.” Id. Here, however, the

physician’s ex-ante state of mind does not determine if the patent was infringed or not. Specifically,

a physician’s intent is nowhere mentioned in the patents or prosecution history. The patent is

infringed if the particular method is practiced, not by the physician’s eventual determination of the

effectiveness or ineffectiveness of the therapy. The court is thus unwilling to incorporate that

limitation into the claim terms. Furthermore, even if the physician’s intended effect was taken into

account, there can be but one ex-ante intended effect of antiretroviral therapy—to lower the patient’s

HIV viral load. This intended effect is already taken into account and incorporated into the patent

specifications, which positively correlate a reduction with therapeutic effectiveness and vice versa.

Roche attempts to distinguish Amgen Inc. v. Hoechst Marion Roussel, Inc., 457 F.3d 1293,

rehearing denied, 469 F.3d 1039 (Fed. Cir. 2007), with its broad definition of “therapeutically

effective amount” because the patents in question there specifically listed the intended medical

effects. The Federal Circuit rejected the reasoning that listing the uses of the invention restricted the

scope of the invention. Id. at 1303. Roche argues that “therapeutically effective” may be limited in

this scenario because the intended medical effects are not listed. There are two flaws with this

rationale. First, if listing the uses does not restrict the scope of the invention, it is unclear how not

listing the uses would restrict the scope. And even if it did, it is unclear how the scope would in fact

be restricted. Second, the patents do list markers of therapeutic effectiveness—determination of

viral load count, CD4 count, and amenability to drug resistance. ‘730 patent at 2:14–52; 2:64–3:6;

7:50–8:14; 12:57–13:32. Finally, the fact that the patent prompts the physician to consider altering

the treatment if an increase in HIV RNA copy number is detected does not inject the physician’s

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intended effect into the definition of “therapeutically ineffective” because, as stated above, the result

of the patented method is but one input into the physician’s calculus when determining whether to

alter the patient’s drug regimen.

Furthermore, the patent may be practiced by others not physicians. For instance, the method

described in the patent may be practiced on old samples to track a patient’s viral load over time. 

They may even be practiced after patients are deceased in order to gather data regarding the

effectiveness of a particular regimen on a large sample. Neither of these instances would require a

physician’s ex-ante intent or the physician’s participation. The patents also describe identifying

patients whose infection has become resistant to a particular anti-retroviral regimen. See, e.g., ‘730

patent at 1:21–25. The myriad ways in which the methods described in the patent can be practiced

cautions against limiting the patent to the physician’s intent.

Roche’s construction would also require that the course of treatment be modified or not

modified for the treatment to be considered therapeutically effective or not. Physicians, however,

may choose to modify a course of treatment even if they consider the treatment to be effective. 

Similarly, a physician may choose not to modify a course of treatment even if it is not effective. For

instance, the physician may want to wait and see if the treatment might become effective over a

longer period of time. Roche itself states that physicians analyze multiple factors when determining

a particular course of treatment. Bartlett Dec., ¶ 28 (listing baseline resistance of patient’s HIV

strain, side effects, concurrent conditions, and patient preference as factors); see also Opp. Br. at 8. 

Thus, whether the treatment is modified or not does not necessarily demonstrate whether the

treatment is therapeutically effective or not. This rationale applies equally as forcefully to the

intended medical effect limitation because achieving or not achieving the intended medical effect

does not necessarily determine whether a treatment is effective or not.

Reading the terms in context, it is clear that the terms are being used to describe the

effectiveness of antiretroviral agents as defined by the viral load, not by subsequent actions, such as

treatment modification. See ‘730 patent, Claim 9 (“A method of evaluating the effectiveness of

anti-HIV therapy of a patient . . . in which an HIV RNA copy number greater than about 500 per 200

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ul of plasma correlates positively with the conclusion that the antiretroviral agent is therapeutically

ineffective.”). Treatment modification may or may not occur depending upon the methods described

in the patents, but neither treatment modification nor non-modification based upon the results of the

presence or absence of HIV-encoding nucleic acid are taught by the patents. The methods described

serve as one factor, albeit an important one, to consider when the physician is evaluating which antiretroviral therapy to prescribe. The patents help determine the efficacy of anti-retroviral agents and

do not dictate a course of action for the attending physician, if any. Id.

Finally, as discussed above, the patent’s suggestion that the physician may alter treatment is

but one embodiment of the innovation and the court refuses to limit the patent’s scope to that one

embodiment.

In sum, the court holds that no construction is necessary for “therapeutically effective” and

“therapeutically ineffective.”

B. “An antiretroviral agent”3

Roche argues that “an antiretroviral agent” should be defined as “antiretroviral agents

available to doctors for the treatment of AIDS/HIV infected patients in 1992.” This construction is

based on two arguments: 1) the specification defines the term to be those antiretroviral agents

“known” at the time; and 2) that the terms must be given their meaning as of the time of the

invention. Each argument is discussed below, followed by the three independent and fatal flaws that

mar Roche’s construction.

Roche argues that the statement: “Antiretroviral agent, as used herein, includes any known

antiretroviral agent including, but not limited to, dideoxynucleosides” limits the patent only to

agents known at the time of the patent. ‘730 patent at 8:39–41. The plain meaning of the phrase,

however, is the opposite. The statement is inclusive and seeks to include, without limiting the

scope, agents known at the time. The specific inclusion of known agents presupposes the existence

of agents unknown at the time that may also be considered to be antiretroviral agents. See Amgen,

457 F.3d at 1302. Kopyake Enterprises, Inc. v. Lucks Co., 264 F.3d 1377, 1382–83 (Fed. Cir. 2001)

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is not on point because it discussed which forms of screen printing were “conventional” forms of

screen printing at the time of the patent—the patent itself limited its scope to “conventional” forms. 

Id. at 1380. The method of printing in question existed at the time of the patent application was filed

but was only later adapted for use as screen printing. Thus, the Kopyake court declined to consider

it “conventional.” See id. at 1383 (“[W]hen a claim term understood to have a narrow meaning

when the application is filed later acquires a broader definition, the literal scope of the term is

limited to what it was understood to mean at the time of filing.”); see also PC Connector Solutions

LLC v. Smartdisk Corp., 406 F.3d 1359, 1364 (Fed. Cir. 2005) (finding that claim language

referring to an “standard input/output port” that is “traditionally connectable to a computer” or an

I/O port “normally connect[a]ble to a conventional computer input/output port” is a “port that was in

common use at the time of filing in 1988”). In contrast, there are no limiting words in the patents in

question here.

Roche relies on Phillips v. AWH Corp., 415 F.3d 1303, 1313 (Fed. Cir. 2005), for the

proposition that there is a temporal context to claim construction. The language of the opinion states

that “the ordinary and customary meaning of a claim term 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.” Id. Thus, Roche

argues, claims cannot be construed to cover later developed technology that was unknown at the

time of the invention.

The term “antiretroviral agents” describes a category of pharmaceuticals. This is clear

because Roche itself uses the term antiretroviral agents to describe new drug therapies that were

unveiled in 1995. Opp. Br. at 8. In May 1992, when Stanford applied for the patents in question,

those antiretroviral agents that had been developed were of the type that inhibited reverse

transcription. After 1995, this category expanded to include protease inhibitors. For instance,

Highly Active Antiretroviral Therapy (“HAART”) combination therapy was not available until

1995-96. However, this new type of antiretroviral therapy was anticipated. Articles published in

1990 and 1991 discussed protease inhibitors, indicating they were known. It just took three or four

years for their development and availability.

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Roche’s reliance on Phillips misses the mark because the temporal context espoused by

Phillips is the meaning of the term to a person of ordinary skill at the time of the invention. The

term in question may be a category, the contents of which expand over time. It is clear that the term

“antiretroviral agents” describes a category of pharmaceuticals because Roche itself uses the term

antiretroviral agents to describe new drug therapies that were unveiled in 1995. Opp. Br. at 8. It is

clear from the publication history and the prolific research being conducted by HIV researchers on

protease inhibitors, that a person of ordinary skill in the art would have known that the category of

“antiretroviral agents” would only expand over time to include these new agents.

SuperGuide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870 (Fed. Cir. 2004) is instructive. 

The SuperGuide court, when construing a system claim, had to decide whether “regularly received

television signal” included digital signals that were not in regular use when the patentee applied for

the patent. The court held that since the “claim language does not limit the disputed phrases to any

particular type of technology or specify a particular type of signal format” the term should be

construed as “video data that is customarily received by the television viewing public . . . [t]he form

of the television signal is irrelevant.” Id. at 878–81. Thus, the Federal Circuit declined to limit the

claim to what was actually broadcast for mass consumption at the time. Roche attempts to

distinguish SuperGuide by arguing that SuperGuide only extended to technology that was known

and available to skilled artisans with knowledge when the patent was granted. Thus, they argue, the

patents in question here must be limited because only agents that inhibit reverse transcription were

known or available before May 1992.

The SuperGuide opinion focuses only on the knowledge of one skilled in the art.

Specifically, “[i]t appears indisputable that it was known to those skilled in the art during the

pendency of the ‘578 patent application that video data could be communicated in either analog or

digital format. Although analog may have been the dominant format of video data when the ‘578

patent application was filed, we have little doubt that those skilled in the art knew of the existence of

digital video data at the time.” Id. at 879. In addition, the court stated that it found “no reason here

to limit the scope of the claimed invention to analog technology, when ‘regularly received television

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signals,’ i.e., video data, is broad enough to encompass both formats and those skilled in the art

knew both formats could be used for video.” Id. at 880. The situation here is indistinguishable. 

Although agents that inhibit reverse transcription may have dominated the category of antiretroviral

agents in May 1992, the court has no doubt that those skilled in the art anticipated antiretroviral

agents that were protease inhibitors and other inhibitors yet to be developed. See Bartlett Dec., Exh.

B. The conceptual work for identifying antiretroviral agents other than those that had been federally

approved had begun as of May 1992. See id. Thus, even if they were not available, these afterdeveloped technologies were certainly known in May 1992. See Rhyu Supp. Dec., Exh. 27 at

28:5–24 (persons of skill in 1992 knew the steps of the HIV replication cycle and that inhibiting any

of the steps could inhibit replication of HIV). Furthermore, the law “does not require that an

applicant describe in his specification every conceivable and possible future embodiment of his

invention.” SRI, 775 F.2d at 1121. Since the ordinary and customary meanings of the words are not

dependant on time, the court finds no reason to limit the scope of “antiretroviral agents” to those

agents available when the patentee applied for the patent. The claims can therefore be construed to

cover later developed technology that was unavailable but known at the time of the invention. In

sum, even if specific agents were not available in May 1992, the conceptual framework for them had

been laid and they were reasonably known to those skilled in the art.

This case is distinguishable from Schering Corp. v. Amgen Inc., 222 F.3d 1347, 1354 (Fed.

Cir. 2000), where the court concluded that the claim reference to “polypeptide of the IFN-a type”

did not include later-discovered species of “IFN-a” that were unknown at the time of the application. 

Schering defined “IFN-a,” originally used to refer to a particular type of interferon but ultimately

understood to refer to several categories of proteins, of which the patentee was only concerned with

one. See Mark A. Lemley, The Changing Meaning of Patent Claim Terms, 104 Mich. L. Rev 101,

104 n.12 (2005). The court held that “the [claim] term as used in the . . . patent . . . did not and

could not enlarge the scope of the patent to embrace technology arising after its filing.” Schering,

222 F.3d at 1353. Here, there is no evidence that the patentee intended to limit the patent

“antiretroviral agents” to known and available technologies, nor is there evidence that the

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categorical term, antiretroviral agents, was ever used to refer only to agents that inhibit reverse

transcription.

Turning from the principles of claim construction that govern the temporal issues to Roche’s

construction, the court notes that first of all, it is self-referential. The purpose of claim construction

is to resolve disputed meanings and technical scope in order to aid the fact-finder. See United States

Surgical Corp. v. Ethicon, Inc., 103 F.3d 1554, 1568 (Fed. Cir.1997); see also Opp. Br. at 2 (“claim

construction is intended to . . . provide meaning to a lay juror who may not be familiar with

technical terms.”). Roche’s construction does not help the lay juror. Defining “an antiretroviral

agent” as “antiretroviral agents” available for HIV treatment in 1992 does nothing to elucidate the

meaning of the disputed term. Roche’s proposed construction, therefore, only seeks to insert further

limitations into the term “antiretroviral agent” without defining the term itself.

Second, Roche seems to have admitted what the definition of “an antiretroviral agent” ought

to be, even though it proposes that the court adopt a different construction. Roche states that

“[a]ntiretroviral agents are drugs that are effective in reducing or stopping replication of

retroviruses.” Opp. Br. at 2, 22; Bartlett Dec., ¶¶38–41. Roche’s clear and succinct definition of

“an antiretroviral agent” undercuts all of their other arguments regarding any alternate construction. 

Furthermore, this construction is very close to Stanford’s proposed construction.

Third, Roche seeks to include three limitations that are not present in the term. Specifically,

Roche seeks to limit the scope of antiretroviral agents to: 1) those available to doctors; 2) those

available for the treatment of AIDS/HIV infected patients; and 3) those available in 1992. Each of

these limitations fails for the same reasons described above regarding after-developed

technologies—they all attempt to limit the scope of “antiretroviral agents” when there is no evidence

that the patentee intended the same.

Stanford, in turn, argues that “an antiretroviral agent” should be construed as “at least one

substance having or capable of having an effect against a retrovirus, such as HIV.” This effect may

be either positive or negative. Roche does not argue that the construction may include more than

one substance as its own definition construes the term in the plural. The plain language of the term

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is not limited to monotherapy. Indeed, the patents in suit specifically refer to combination therapy. 

‘730 patent at 7:63–8:14; 9:46–48; 13:9–11. This demonstrates that the inventors and those of

ordinary skill in the art were aware of combination therapy.

The rest of Stanford’s construction describes antiretroviral agents using generally accepted

dictionary definitions. The construction closely matches the definition given by Roche, that

“[a]ntiretroviral agents are drugs that are effective in reducing or stopping replication of

retroviruses.” Opp. Br. at 2; id. at 22; Bartlett Dec., ¶¶38–41. Roche’s construction requires that the

agent be effective in reducing or stopping replication of retroviruses. The same, however, goes

against the patent construed as a whole. The patent is designed to measure the effectiveness of

antiretroviral agents and therefore the construction must include the fact that the agent may or may

not be effective in reducing or stopping replication of the retrovirus. Thus, Stanford’s construction

is superior because it allows for the possibility that the agent may not in fact be effective against the

retrovirus. The court therefore adopts the following construction for “an antiretroviral agent”: “at

least one substance having or capable of having an effect against a retrovirus, such as HIV.”

C. “Measuring the HIV RNA copy number”

Roche seeks to define this term as “techniques available in May 1992 to quantify HIV RNA

copy number using PCR, specifically the assay in the 1991 JID article as set forth in the

specifications.” Stanford, on the other hand, argues that no construction is necessary because the

plain meaning suffices to guide the jury in its fact-finding.

Roche argues that Stanford’s patents enable no more than the five-step end point PCR assay

set forth in the 1991 JID paper and that “[t]he scope of the claims must be less than or equal to the

scope of the enablement.” Nat’l Recovery Techs., Inc. v. Magnetic Separation Sys., Inc., 166 F.3d

1190, 1196 (Fed. Cir. 1999). Although the foregoing is true, the same confuses invalidity with claim

construction. Questions as to whether the disclosure is sufficient to enable a person skilled in the art

to practice the invention are best reserved for arguments alleging invalidity. As the Federal Circuit

has stated, unambiguous claim terms “can be construed without the need to consider whether one

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possible construction would render the claim invalid while the other would not.” Phillips, 415 F.3d

at 1328. The ordinary and customary meaning of “measuring the HIV RNA copy number” is

unambiguous and allows for any measuring technique. Since the claim terms are unambiguous, the

invalidity analysis is premature.

Roche also seeks to limit the measuring steps used to determine the HIV RNA copy number

to the techniques available in May 1992 because after-developed technologies such as real-time PCR

and internal standards were not taught by the patents and unknown when Stanford applied for the

patents. Specifically, Roche claims that what one of skill in the art today would understand by a

method using PCR is different than it would have been in May 1992. That argument is not related to

the definition of “measuring the HIV RNA copy number” because the copy number is measured

using the product of the PCR. Roche is again confusing claim construction issues with infringement

issues. Roche may well argue, at the summary judgment stage or later, that its product does not

infringe upon Stanford’s patents based upon the claim limitations, but it may not inject the end point

PCR limitation into the definition of “measuring the HIV RNA copy number.” It is settled patent

law that the claims of a patent must not be construed as being limited to the embodiment if the

patent describes only one embodiment. Phillips, 415 F.3d at 1323. In fact, it is improper to read

limitations from the specifications into the claim term because the same can “restrict[] the claims to

coverage of a single embodiment.” Callicrate v. Wadsworth Mfg., Inc., 427 F.3d 1361, 1368 (Fed.

Cir. 2005).

Nevertheless, the claims that state “about 30 cycles” must be limited to end-point PCR. The

court can, as part of claim construction, construe the scope of “about 30 cycles.” The claims’

specific reference to the number of cycles of PCR must limit those claims to end-point PCR as a

specific number of cycles is only germane within the context of end-point PCR. The fact that the

number of cycles is irrelevant in real-time PCR further buttresses this finding.

Some of the patent claims, however, do not limit themselves to “30 cycles of PCR,” but use

the more generic term “PCR.” See ‘041 patent, Claims 1–3, 5–8. This categorical term is

distinguishable from the categorical anti-retroviral agents because there is no evidence in the record

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that, as of 1992, one of ordinary skill in the art knew of real-time PCR or of its conceptual

framework. Thus, based on SuperGuide, the term “PCR” cannot include real-time PCR. Mass. Inst.

of Tech. v. Abacus Software, 462 F.3d 1344, 1353 (Fed. Cir. 2006), is also instructive. Abacus held

that at the time of the patent application, a person of ordinary skill in the art would have known of

two general types of scanners, drum scanners and flatbed scanners. Since both those scanners

required close proximity between the color original and the scanner, the court defined the term

scanner by what was known in the art at the time and included a requirement of close proximity. Id.

Similarly, in 1992, a person of ordinary skill in the art did not know of real-time PCR. Defining

PCR by what was known in the art at the time requires that real-time PCR be excluded.

In sum, the court holds that no construction is necessary for “measuring the HIV RNA copy

number,” but limits the claims stating “about 30 cycles” to end-point PCR and excludes real-time

PCR from the scope of the term “PCR.”

D. “Presence of detectable HIV-encoding nucleic acid” and “absence of detectable HIVencoding nucleic acid”

Roche argues that these terms be construed as a “qualitative result indicating greater than or

less than 40 copies of HIV RNA per 200 ul of sample.” Stanford argues that no construction in

necessary because the plain meaning is sufficient to guide the jury’s fact finding.

Roche seeks to construe this term as a qualitative yes or no test based upon the lowest

detection level taught by the patent, 40 copies per 200 micro-liters of sample, because these terms

are in direct contrast to the claims that include a specific measuring step. Roche again attempts to

interject a specific copy number limitation into the construction. This attempt fails for the same

reasons as above, where a construction including a temporal limitation or particular assay limitation

was rejected. The plain and ordinary meaning of “detectable” has to be an amount of substance that

is higher than the lowest level of sensitivity of whatever assay is actually used in practicing the

claimed methods. Furthermore, the patent demonstrates that the patentee inserted specific numerical

limitations when desired. See ‘730 patent, Claim 9. The court refuses to integrate numerical

limitations into the construction where none was contemplated by the patentee.

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Roche argues that different terms in different claims must have different meaning and that

Stanford’s construction reduces “presence” and “absence” to “measuring.” Roche is correct in its

contention that a difference in meaning is presumed. Nystrom v. Trex Co., 424 F.3d 1136, 1143

(Fed. Cir. 2005). The presumption, however, may be overcome, as in the case here. Even though

the presence or absence of a substance is indeed a yes or no test, determining whether a compound is

present or not is not fundamentally different from measuring the amount of compound. Presence or

absence is merely a specific manifestation of measuring for the compound where the actual amount

of the compound present is not of any import if the compound is indeed present.

In addition, there is no basis for Roche’s claim that the detection process be a qualitative

process. In fact, there is evidence to the contrary—that a quantitative process was envisioned. See,

e.g., ‘730 patent at 5:53–57, 10:34–40, 12:58–60. This is further buttressed by Stanford’s statements

made while prosecuting the patents, which distinguish an article by Ottoman based on the fact that

the article described using non-quantitative PCR assays. See Rhyu Dec., Exh. 25 at STAN 1435,

1458. This evidence may be relied upon in spite of Honeywell Int’l v. ITT Indus., Inc., 452 F.3d

1312 (Fed. Cir. 2006). Honeywell only disallows the patentee’s own statements if they are “broad

and vague statement[s]” that “contradict the clear statements in the specification describing the

invention more narrowly.” Id. at 1318–19. That is not the case here.

A quantitative process is necessary because a minimum amount of the compound must be

present for any detection method to test for the presence or absence of the compound. Thus testing

for the “presence” or “absence” is really the same as “measuring,” except that if the measurement

reveals any amount greater than zero (or the minimum amount necessary to be detectable), the actual

amount of the compound is irrelevant.

Stanford’s neglect in failing to define the terms is of no import and consequently the terms

will not be construed against Stanford. Though the patentee may choose to be his own

lexicographer, he does not have to be. In general, the claim terms will carry their ordinary and

customary meaning and this court will not import limitations from the specifications into the claims

unless it is clear from the specifications that the same was intended.

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Finally, for reasons described above, Roche’s enablement arguments are just as misplaced

here as they were with respect to the other claim terms.

In sum, the court holds that no construction is necessary for “presence of detectable

HIV-encoding nucleic acid” and “absence of detectable HIV-encoding nucleic acid.”

CONCLUSION

For the foregoing reasons, the court construes the disputed claims in the manner described

above.

Dated: November 26, 2007 _______________________________

MARILYN HALL PATEL

United States District Court Judge

Northern District of California

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1. Roche Diagnostic Systems, Inc. was dismissed as a defendant without prejudice by

stipulation of the parties entered on November 17, 2005.

2. Roche has agreed to Stanford’s proposed definitions of “collecting statistically significant

data useful for determining whether a decline in HIV RNA copy numbers exists,” “statistically

significant data,” and “statistically significant decline.”

3. The definition of “anti-HIV agent,” consistent with “anti-retroviral agent,” is thus “at least

one substance having or capable of having an effect against HIV.”

ENDNOTES

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