Ladatech, LLC v. Illumina, Inc.

• Decision Date: 24 January 2012
• Docket Number: Civil No. 09–627–SLR.
• Citation: 841 F.Supp.2d 860
• Parties: LADATECH, LLC, Plaintiff, v. ILLUMINA, INC. and Solexa, Inc., Defendants.
• Court: U.S. District Court — District of Delaware

841 F.Supp.2d 860

LADATECH, LLC, Plaintiff,

v.ILLUMINA, INC. and Solexa, Inc., Defendants.

Civil No. 09–627–SLR.

United States District Court, D. Delaware.

Jan. 24, 2012.

Jack B. Blumenfeld, Esquire, Maryellen Noreika, Esquire, Derek Fahnestock, Esquire and Jeremy A. Tigan, Esquire of Morris, Nichols, Arsht & Tunnell LLP, Wilmington, DE, for Plaintiff.

Steven J. Balick, Esquire, Tiffany Geyer Lydon, Esquire and Lauren E. Maguire, Esquire of Ashby & Geddes, Wilmington, DE, for Defendants. Of Counsel: Jeffrey N. Costakos, Esquire, Kimberly K. Dodd, Esquire and Rebecca J. Pirozzolo–Mellowes, Esquire of Foley & Lardner LLP.

MEMORANDUM OPINION

SUE L. ROBINSON, District Judge.

I. INTRODUCTION

Plaintiff LadaTech, LLC (“plaintiff” or “LadaTech”) brought this action on August 21, 2009 alleging direct and indirect infringement of U.S. Patent No. 6,107,023 (“the '023 patent”) by defendant Illumina, Inc. (“Illumina”). (D.I. 1) Plaintiff filed an amended complaint on February 2, 2010 adding allegations of infringement of the '023 patent against defendant Solexa, Inc. (“Solexa”). (D.I. 7) Illumina and Solexa (collectively, “defendants”) answered on February 19, 2010, asserting defenses of noninfringement, invalidity, and unenforceability, and related counterclaims. (D.I. 9) Discovery is now complete and the parties have briefed several claim construction issues. Currently pending are defendants' motions for summary judgment of noninfringement (D.I. 126) and invalidity and patent expiration (D.I. 119) and plaintiff's motion for summary judgment of no anticipation by certain references (D.I. 124). The court held a hearing on these issues November 4, 2011 and a jury trial is scheduled to commence on February 21, 2012. The court has jurisdiction over these matters pursuant to 28 U.S.C. § 1338.

II. BACKGROUNDA. The Parties

LadaTech is a Delaware limited liability company with its principal place of business in Larchmont, New York. (D.I. 7 at ¶ 1) When it was formed, LadaTech was jointly owned by Genelabs Technologies (“Genelabs”), which has since been acquired by GlaxoSmithKline Plc, and IP–Finance Holdings, LLC. (D.I. 9 at 9–10, ¶ 3; D.I. 14 at ¶ 3) LadaTech owns the '023 patent, but has not commercialized the technology described therein. (D.I. 120 at 2)

Illumina is a Delaware corporation with its principal place of business in San Diego, California. (D.I. 9 at ¶ 2) Solexa, a wholly owned subsidiary, was a Delaware corporation with its principal place of business in Hayward, California as of the date of the first amended complaint, but has since merged into Illumina (as of February 8, 2010). (Id. at ¶ 3) Illumina has developed and markets an array of DNA sequencing products used by academic, government, pharmaceutical, biotechnology and other institutions globally.¹ While Illumina also sells DNA sequencing instruments, the present litigation concerns Illumina's sample preparation kits and cluster generation instruments, discussed infra.

B. Technology Overview²

This litigation involves DNA sequencing technology. DNA, or deoxyribonucleic acid, is a hereditary material that contains the genetic instructions used in the development and functioning of living cells. DNA is made of nucleotides, or chemical building blocks, made of three parts: a phosphate group, a 2'-deoxyribose sugar and four nitrogen bases (deoxyadenosine monophosphate, or adenine (“A”), deoxyguanosine monophosphate, or guanine (“G”), deoxycytosine monophosphate, or cytosine (“C”) and thymidine monophosphate, or thymine (“T”)). DNA is a linear molecule analogous to a chain, and nucleotides are akin to “links” in this chain. Nucleotides are arranged in two long strands that are anti-parallel (that is, they are oriented in opposite directions to each other) and form a spiral called a double helix.

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Each single DNA strand is a polymer of nucleotides joined by covalent (phosphodiester) bonds between the phosphate group at the “5'-end” position of the deoxyribose sugar of one nucleotide and a hydroxyl (-OH) group at the “3'-end” position of the deoxyribose sugar of the next nucleotide. This configuration allows for the two strands to be held together by hydrogen bonds formed by base pairing A with T and C with G nucleotides. Two single strands of DNA that come together by way of hydrogen bonding between stretches of complementary (or substantially complementary) bases are said to be “hybridized” or “annealed” to one another.

Genes contain information needed to make proteins, which play many critical roles in the body. The process whereby proteins are made is complex, but may be summarized as consisting of two major steps: transcription and translation (which, together, are known as gene expression). During transcription, information stored in a gene's DNA is transferred to a ribonucleic acid (or RNA) molecule in a cell's nucleus. RNA is similar to DNA insofar as both are nucleic acids, but RNA is a shorter and (typically) single-stranded nucleotide chain. RNA also differs by its sugar (ribose, rather than DNA's 2'-deoxyribose) and base pairs (RNA utilizes uracil (“U”) rather than the thymine (T) of DNA).

The type of RNA that contains protein-making information is called messenger RNA (or mRNA). mRNA leaves the cell's nucleus and enters the cytoplasm, where translation occurs. The mRNA's sequence of bases is “read” by a complex called a ribosome. Each sequence of three base pairs is called a codon, and usually codes for one particular amino acid, the building blocks of proteins. Protein is assembled by transfer RNA (or tRNA) one amino acid at a time, until the ribosome encounters a “stop” codon, or a codon that does not code for an amino acid.

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As explained in the '023 patent, the ability to identify and isolate unique nucleic acid sequences has become an important facet of medicinal research. The presence or absence of a particular mRNA is indicative of disease. For example, an absent or altered mRNA coding for a specific protein in a specific cell type may cause a hereditary disease, while the presence of an added mRNA (such as a virus-specific mRNA) may be indicative of the beginning of a malignant transformation or the latent presence of an otherwise undetectable infectious agent. ('023 patent, col. 1:41–col. 2:2)

“Cloning” is a process used to produce identical copies of a desired DNA sequence. A common method of cloning involves inserting a DNA fragment ³ into a “vector,” or a nucleic acid sequence that can be replicated in a host organism such as the bacteria E. coli. There are several types of vectors. A plasmid is a small, circular DNA molecule found in bacteria and other cells. A desired DNA fragment may be inserted to create a plasmid vector, as generally depicted below.

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Once introduced into a suitable host cell (most commonly, Escherichia coli) (or “E. coli”), the foreign DNA (of the plasmid vector) is replicated along with the host's DNA each time the cell divides. By contrast, another type of vector, called a bacteriophage (or a “phage” for short), is a type of virus that infects E. coli. Bacteriophages use the infected cell's enzymes to replicate their genomes and package the DNA into new viral particles.

The polymerase chain reaction (or “PCR”) is a technique for amplification of DNA across several orders of magnitude.⁴ In PCR, the complementary strands of the double-helix are denatured, or separated, by heating. Two pieces of synthetic DNA, or “primers,” each complement a specific sequence of DNA. The primers are each hybridized to the 3' end of the sequence of interest within the single-stranded DNA. Following primer hybridization, polymerase (enzyme) replicates the template strand from the primer in a 5' to 3' direction, synthesizing a complement strand to the template strand. In subsequent cycles, double-stranded molecules of both the original DNA and the copies are separated; primers again bind to the complementary sequences; and the polymerase replicates them. At the end of many cycles, exponential replication has been achieved (in theory, 2 ⁿ, where n = the number of cycles) and this amplified genetic information is available for further analysis, such as for cloning.

C. The '023 Patent

The '023 patent was filed as U.S. Patent Application No. 07/208,512 on June 17, 1988 and issued on August 22, 2000. The '023 patent names as inventors Greg Reyes and Jungsuh Kim; Genelabs (plaintiff's predecessor) is the named assignee. A request for ex parte reexamination of the '023 patent was filed by Illumina on January 18, 2008. The United States Patent and Trademark Office (“PTO”) issued an ex parte reexamination certificate on November 17, 2009, confirming the patentability of the reexamined original claims (nos.12–14), as well as one newly added claim (no. 15). Plaintiff asserts infringement of these four claims in the present litigation.

By way of background, the '023 patent explains that many hereditary diseases⁵ are likely to be caused by the absence or alterations of low-abundance mRNAs. A major problem in detecting and isolating such mRNAs (among 10,000 to 30,000 types of distinct mRNA species that may be present in a given cell type) is interference from other, higher-abundance species in the source material. ('023 patent, col. 2:9–18) High background levels require high sensitivity, which is not achieved by the number of nucleic acid hybridization techniques in the art, for example, cDNA probing,⁶ filter hybridization to a conventional cDNA library, and nucleic acid subtraction techniques. ( Id., col. 2:19–56)

The specification and claims of the '023 patents are directed to two distinct (but related) inventions: a method of amplifying a mixture of different sequence duplex DNA fragments; and a method of isolating complex DNA fragments. The inventors provide a method “for isolating RNA...