Helicos Biosciences Corp. v. Illumina, Inc.

• Decision Date: 28 August 2012
• Docket Number: Civil No. 10–735–SLR.
• Parties: HELICOS BIOSCIENCES CORPORATION, Plaintiff, v. ILLUMINA, INC., Defendant.
• Court: U.S. District Court — District of Delaware

888 F.Supp.2d 519

HELICOS BIOSCIENCES CORPORATION, Plaintiff,

v.ILLUMINA, INC., Defendant.

Civil No. 10–735–SLR.

United States District Court, D. Delaware.

Aug. 28, 2012.

Richard D. Kirk, Esquire and Stephen B. Brauerman, Esquire of Bayard, P.A., Wilmington, DE, for Plaintiff. Of Counsel: Douglas J. Kline, Esquire, Daniel M. Forman, Esquire, Brian A. Fairchild, Esquire, Sheryl Koval Garko, Esquire and Kurt M. Kjelland, Esquire of Goodwin Procter LLP.

Steven J. Balick, Esquire and Lauren E. Maguire, Esquire of Ashby & Geddes, Wilmington, DE, for Defendant. Of Counsel: Jeffrey N. Costakos, Esquire and Rebecca Jan Pirozzolo–Mellowes, Esquire of Foley & Lardner LLP.

MEMORANDUM OPINION

SUE L. ROBINSON, District Judge.

I. INTRODUCTION

Plaintiff Helicos Biosciences Corporation (“Helicos”) filed a patent infringement complaint against Pacific Biosciences of California (“PacBio”) on August 27, 2010, alleging infringement of its U.S. Patent Nos. 7,645,596 (“the '596 patent”), 7,037,687 (“the '687 patent”), 7,169,560 (“the '560 patent”), and 7,767,400 (“the '400 patent”). (D.I. 1) Prior to PacBio's answer, Helicos amended its complaint adding allegations of infringement of the '596, '687 and '560 patents by Life Technologies Corporation (“Life”) and of the '687, '560 patents by Illumina, Inc. (“Illumina”); Illumina is also alleged to infringe Helicos's U.S. Patent No. 7,593,109 (“the '109 patent”). (D.I. 9) PacBio answered and asserted counterclaims for declaratory judgment of noninfringement, invalidity, and unenforceability of the '596, '687, '560 and '400 patents. (D.I. 14) Life also brought counterclaims for declaratory judgment of noninfringement and invalidity of the patents asserted against it. (D.I. 21) Illumina brought counterclaims for declaratory judgment of noninfringement and invalidity of the '560, '687 and '109 patents asserted against it, and for a declaratory judgment that the '560 patent is unenforceable. (D.I. 22)

In December 2011, the court denied PacBio's motion to stay the litigation pending reexamination of the '596, '687, '560 and '400 patents, and also denied Life's motion to “drop it from this suit or, in the alternative, sever and stay the claims against Life.” (D.I. 170; D.I. 175) By agreement of the parties and the court, Helicos filed a second amended complaint adding plaintiff Arizona Science and Technology Enterprises LLC d/b/a Arizona Technology Enterprises (“AZTE”), the exclusive licensee of the '596 and '687 patents, to the suit. (D.I. 157, ex. 1; D.I. 159, ex. 1; D.I. 163; D.I. 171) On February 15, 2012, Helicos, AZTE and Illumina entered a stipulation of dismissal with respect to these parties' claims regarding the '560 patent. (D.I. 213)

On May 3, 2012, 858 F.Supp.2d 367 (D.Del.2012), following an evidentiary hearing, the court denied a motion to transfer venue to the Northern District of California filed by PacBio, Life and Illumina. (D.I. 251) PacBio was dismissed from the suit on May 10, 2012. (D.I. 255) The '596, '687 and '560 patents have been finally rejected by the examiner in concurrent reexamination proceedings; the PTO issued notices of right to appeal on April 26 and May 9, 2012. (D.I. 262 at 1) On June 14, 2012, Helicos and AZTE executed a covenant not to sue Life on the '596, '687 and '560 patents. (D.I. 302) On June 15, 2012, Helicos and AZTE stipulated to the dismissal of their claims of infringement of the '687 patent against Illumina, and Illumina stipulated to the dismissal of its related counterclaims. (D.I. 301) A stipulation of dismissal was filed with respect to Life on June 28, 2012. (D.I. 336)

Remaining are Helicos's claims that Illumina infringes the '109 patent. ¹ Currently pending before the court are several motions: (1) Illumina's motion for summary judgment of invalidity of the ' 109 patent (D.I. 266); ² (2) Helicos's motion for summary judgment of infringement of claims 1–4, 6–7, 9–10 and 13 of the ' 109 patent (D.I. 272); ³ and (3) Illumina's motion for summary judgment of noninfringement (D.I. 291). The court has jurisdiction over these matters pursuant to 28 U.S.C. § 1338.

II. BACKGROUNDA. The Parties

Helicos is a Delaware corporation with its principal place of business in Cambridge, Massachusetts. (D.I. 171 at ¶ 2) Founded in 2004, Helicos is a life science company in the business of developing genetic analysis techniques for the research, discovery, and clinical diagnostics markets. ( Id. at ¶ 3)

Illumina is a Delaware corporation with its principal place of business in San Diego, California. (D.I. 178 at ¶ 8) Illumina is also a life science company has been developing products for use in analyzing genetic variation and function since 1998. (D.I. 267 at 2)

B. The '109 Patent

The '109 patent, entitled “Apparatus and Methods for Analyzing Samples,” was issued September 22, 2009. One inventor, Kevin Ulmer, is named. The ' 109 patent is a continuation of the application now issued as U.S. Patent No. 7,276,720; priority is claimed to a provisional application filed July 19, 2004. Helicos is listed as the assignee.

The abstract of the '109 patent characterizes the invention as “related to apparatus, systems and methods for analyzing biological samples.” There are two general components to the foregoing: the use of a vacuum source to pull microfluidic volumes through analytical equipment; and the use of “optical equipment in conjunction with analytical equipment to analyze samples and control the operation thereof.” ('109 patent, abstract) The latter is at issue on the present motions.

The background section describes certain disadvantages of prior art, vacuum-driven systems for analyzing samples in a flow cell. For example, leaks, contaminants, and air bubbles are all of concern. ('109 patent at col. 1:25–57) “In analyzing microfluidic volumes and related biological materials using a light source, it is desirable for the light source to hit the sample in such a way that results in total internal reflection flourescence (‘TIRF’),” or “an optical phenomenon that occurs when light propagating in a dense medium, such as glass, meets an interface with a less dense medium such as water.” ( Id., col. 1:58–64) At a certain angle, called the “critical angle,” all of the light is refracted through the interface into the dense medium. ( Id. at col. 1:64–col. 2:1) Some of the beam's energy “propagates a short distance,” or “about 100 nm,” “into the less dense medium, generating an evanescent wave.” ( Id., col. 2:1–4) This energy can either be absorbed back into the dense medium or, if present, absorbed by a flourophore molecule within the evanescent wave, where it can absorb photons. ( Id. at col. 2:4–10) Excited flourophores can be observed using an intensified CCD camera. ( Id.) “Accurately maintaining the critical angle to obtain TIRF in a dynamic system is difficult.” ( Id.)

The court focuses on the lighting system aspect of the invention, which includes “a first light source for analyzing a sample of interest and a second light source. The first light source defines a first optical path that intersects a sample of interest and the second light source operates with the first light source for determining a position of the first optical path.” ( Id., col. 2:22–27) That is, the “first beam of light is for analyzing the sample of interest.” ( Id., col. 2:66–67) The second beam “may be used to continuously monitor the position of the first optical path.” ( Id. at col. 2:50–51)

In various embodiments, “[t]he first beam of light is at least partially coaxial with the second beam of light.” ( Id. at col. 2:65–66) The second light source may be “directed to a position sensor for sensing an angle of reflection of the first optical path relative to the sample of interest,” generating a signal which will cause the position of the first optical path to be adjusted to vary the angle of reflection. ( Id. at col. 2:30–39) The beams generally work simultaneously, with the goal of maintaining substantially total reflection of the first light source relative to the sample of interest. ( Id. at col. 2:28–39) Optionally, a third light source may be included, defining a third optical path at least partially coaxial with the first optical path, and operating simultaneously. ( Id. at col. 2:45–50)

In other aspects, the invention relates to a system for analyzing a sample, including a flow cell, passive vacuum source, lighting system (as described above) and optical instrument. ( Id. at col. 3:7–33) An apparatus for handling microflouridic volumes (“such as biological samples for analysis”) is also disclosed, which includes a passive vacuum source and flow cell. ( Id. at col. 3:34–46) The specification goes on to detail how the apparatus and system of the invention can be used for detecting single molecules, for example, a flow cell including a bound nucleotide and an attached primer ( id., col. 3:47–56) and applying a vacuum to “a flow cell that defines a channel that is treated to identify specific molecules” ( id. at col. 4:14–19). Another method involves “attaching template nucleic acids to a flow cell in the presence of a primer for template-dependent nucleic acid synthesis.” That is, individual template nucleic acids are positioned on the flow cell so that each is individually optically resolvable, “dye-labeled primers [are] hybridize[d] to individual templates,” the label is excited, and the emission spectrum is detected and compared to known spectra to identify the sequence. ( Id. at col. 4:36–67)

Finally, the '109 patent discloses a “flow cell for analyzing single molecules such as nucleotides,” and a slide to use in such a flow cell, which can include “at least one nucleotide bound to a surface of the slide.” ( Id. at col. 5:5–22) A coverslip embodiment is also described. ( Id. at col. 5:22–36)

C. Claims at Issue

Helicos originally asserted claims 1, 2–4, 6–7, 9–10 and 13 of the '109 patent against Illumina. As noted above, Helicos disclaimed claims 1 and 6...