Illumina Inc. v. BGI Genomics Co., Ltd.

Background

Illumina sued BGI, asserting that BGI’s CoolMPS products infringed claims in three Illumina patents concerning sequencing of nucleic acids: U.S. Patent Nos. 7,771,973, 7,541,444, and 10,480,025. Claim construction is the court’s determination of what disputed patent-claim terms mean. The parties asked the court to construe five terms from those patents.

Legal standard

The court explained that claim terms generally receive their ordinary and customary meaning to a person of ordinary skill in the relevant field at the time of the invention. The court primarily considers the claim language, the patent specification, and the patent’s prosecution history. It may consider reliable outside evidence, but that evidence cannot contradict the meaning shown by the patent materials.

Rulings on the disputed terms

1. Removal of the blocking group before the next nucleotide

For the ’973 patent term “wherein the blocking group is removed prior to introduction of the next complementary nucleotide,” the court adopted Illumina’s proposed construction: the blocking group must be removed before the next complementary nucleotide is incorporated into a growing nucleotide strand complementary to the target single-stranded polynucleotide being sequenced.

The court rejected BGI’s proposal that the blocking group must be removed before complementary nucleotides are added to the reaction mixture. The court concluded that “introduction” in this claim is used very similarly to, or interchangeably with, “incorporation.” It found that BGI’s proposed construction would add a limitation unsupported by the patent specification and that the claim does not impose a timing requirement concerning when nucleotides are added to the reaction mixture.

2. Monitoring sequential incorporation

For the ’973 patent term “monitoring the sequential incorporation of complementary nucleotides,” the court concluded that no construction was necessary. It rejected BGI’s proposal to require labeled nucleotides and monitoring over multiple cycles in a sequencing-by-synthesis reaction.

The court reasoned that the patent’s preferred embodiment used labeled nucleotides, but the claims did not require that particular detection method. The court also found that adding the phrase concerning multiple cycles and sequencing by synthesis was unnecessary and potentially confusing.

3. At least one incorporation having a removable blocking group

For the ’973 patent term “wherein at least one incorporation is of a nucleotide having a removable 3’–OH blocking group covalently attached thereto,” the court concluded that no construction was necessary and rejected BGI’s indefiniteness challenge. Indefiniteness is a patent-invalidity argument asserting that the claim does not inform skilled readers about its scope with reasonable certainty.

The court first held that BGI waived the challenge because BGI did not disclose this specific indefiniteness theory in its invalidity contentions and did not show good cause to amend them. The court also addressed the merits and concluded that BGI had not shown the term to be indefinite. The phrase “at least one” could cover a method in which at least one nucleotide had the specified blocking group while other nucleotides had a different blocking group, or the process could end when a nucleotide without the specified group was incorporated.

4. Reaction producing an intermediate in which each R” is exchanged for H

For the ’444 patent term “wherein said molecule may be reacted to yield an intermediate in which each R” is exchanged for H,” the court concluded that no construction was necessary and rejected BGI’s indefiniteness argument.

The court held that the claim clearly lists five alternative chemical structures that may satisfy the “Z” structure. It determined that the disputed limitation does not apply when “Z” is azidomethyl under the more specific listed structure. The existence of another listed structure that can also describe azidomethyl did not make the claim’s scope unclear.

5. Modification or removal to expose a 3’ OH group

For the ’025 patent term “that can be modified or removed to expose a 3’ OH group,” the court concluded that no construction was necessary and rejected BGI’s indefiniteness challenge.

The court held that BGI waived this challenge because BGI had not disclosed the particular theory in its invalidity contentions and had not sought permission to amend them. Even on the merits, the court found that BGI had not shown indefiniteness. The court concluded that statements by Illumina about the expected effectiveness of azidomethyl in an obviousness dispute did not create an unstated “efficiency” requirement in the patent claims.

Disposition and effect

The court entered the five claim constructions described above. The opinion resolved the meaning of the disputed patent terms and rejected BGI’s asserted indefiniteness challenges, but it did not decide whether BGI’s products infringed the patents.