Intelligent Bio-Systems, Inc. v. Illumina Cambridge Ltd.

821 F.3d 1359, 119 U.S.P.Q. 2d (BNA) 1171, 2016 U.S. App. LEXIS 8481, 2016 WL 2620512
CourtCourt of Appeals for the Federal Circuit
DecidedMay 9, 2016
Docket2015-1693
StatusPublished
Cited by168 cases

This text of 821 F.3d 1359 (Intelligent Bio-Systems, Inc. v. Illumina Cambridge Ltd.) is published on Counsel Stack Legal Research, covering Court of Appeals for the Federal Circuit primary law. Counsel Stack provides free access to over 12 million legal documents including statutes, case law, regulations, and constitutions.

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Intelligent Bio-Systems, Inc. v. Illumina Cambridge Ltd., 821 F.3d 1359, 119 U.S.P.Q. 2d (BNA) 1171, 2016 U.S. App. LEXIS 8481, 2016 WL 2620512 (Fed. Cir. 2016).

Opinion

O’MALLEY, Circuit Judge.

Illumina Cambridge Ltd. (“Illumina”) owns U.S. Patent No. 7,566,537 (“the '537 patent”), which is directed to a method of labeling nucleotides in a deoxyribonucleic acid (“DNA”) strand. Intelligent Bio-Systems, Inc. (“IBS”) filed a revised petition to the • Patent Trial and Appeal Board (“Board”) requesting inter partes review of claims 1-6 and 8 of the '537 patent on August 30, 2013. The Board instituted review of the challenged ' claims on the basis that they were invalid as obvious under 35 U.S.C. § 103 in view of certain prior art references. In its Final Written Decision, issued February 11, 2015, the Board found that IBS failed to satisfy its burden of demonstrating the obviousness of the challenged claims by a preponderance of the evidence. IBS appeals. Because we find that the Board’s judgment was supported by substantial evidence, we affirm.

Background

A. Technology

By way of background, DNA is comprised of two strands of nucleotides, which bind to each other to form a double helix structure. “A nucleotide is made up of a sugar molecule, a phosphate, and a ‘base.’ It is the ‘base’ — adenine (A), cytosine (C), guanine (G), or thymine (T) — that provides the code for the genetic information in DNA.” Appellant Br. 4. The bases of two nucleotide strands pair predictably: A with T, and G with. C. In this way, if one knows the identity of a nucleotide in one strand, the identity of the corresponding nucleotide in the other strand is easily inferred. Identification of the sequence of nucleotides in DNA is important, ;as “the sequence of nucleotides in DNA determines the traits of living organisms/’ Id.

The invention of the '537 patent “relates to labelled nucleotides.” '537 patent, col. 1 1. 14. • The' labels, used to identify the nucleotides, are removable and are intended for “use in’ polynucleotide sequencing methods.” ’ Id. at col. 1 11. 14-16. The polynucleotide sequencing method at issue is the so-called sequencing by synthesis (“SBS”) method. SBS “is a process used to identify the sequence of nucleotides in DNA by synthesizing a single strand of DNA using nucleotides that are complementary to the nucleotides in a sample single strand of DNA.” Appellee Br. 3.

The claimed method in the '537 patent is directed to labelling nucleotide bases to determine their identity. The 3'-OH (“three prime hydroxyl”) position of the sugar components of the labeled nucleotides áre furth’ér modified with a blocking group (also referred to as a protecting group). The blocking group (or protecting group) attached to the sugar molecule “prevent[s] the natural linking process between nucleotides.” Appellant Br. 4. By stopping the linking process, one can de *1363 tect the label on the nucleotide base and determine its identity (A, C, G, or T). The blocking group is cleavable, which allows the linking process to continue after the label is detected.

The SBS method starts with a single strand of unknown nucleotides and adds complementary nucleotides one-by-one. to form the complete, double-helix structure. “The protecting groüp allows the polymerase to incorporate only one nucleotide at a time into the complementary strand.” Intelligent Bio-Sys., Inc. v. Illumina Cambridge Ltd., IPR2013-00517, 2015 WL 996355, at *3 (PTAB Feb. 11, 2015) (Final Written Decision of the Board). "By incorporating such modified nucleotides one-by-one into á growing DNA chain, researchers are able to first detect the label to determine the base of each nucleotide, before another nucleotide (with its own label attached to its owii base) is added.” Appellant Br. 4-5. The identity of the attached label is determined “by any suitable method, including fluorescence spectroscopy or by other optical means.” '537 patent, col. 5 11. 21-23.

The claims require that “the protecting group comprises an azido group.” Id. at col. 19 11. 58-59 (claim 1). According to Illumina, “the inventors of the '537 patent were the. first to identify the azidomethyl group (CH2N3) as a protecting group that would meet the rigorous requirements of SBS.”'Appellee Br. 9.

Claim 1, the only independent claim under review, is reproduced below:

1. A method of labeling a nucleic acid molecule, the method comprising incorporating into the nucleic acid molecule a nucleotide or nucleoside molecule, wherein the nucleotide or nucleoside molecule has a base that is linked to a detectable label via a cleavable linker and the nucleotide or nucleoside molecule has a ribose or deoxyribose sugar moiety, wherein the ribose or deoxyri-bose sugar moiety comprises a protecting group attached via the 2' or 3' oxygen atom, and said protecting group can be modified or removed to expose a 3' OH- group and the protecting group comprises an azido group.

Id. at col. 19 11. 49-59 (emphases added).

B. Prior Art

There are three articles of prior art at issue in this appeal: (1) Roger Tsien et al., WO 91/06678 (May 16, 1991) (“Tsien”); (2) Jingyue Ju et al., U.S. Patent No. 6,664,079 (Dec. 16, 2003) (“Ju”); and (3) Zavgorodny et al., 1-Alkylthioalkylation of Nucleoside. Hydroxyl Functions and Its Synthetic Applications: A New, Versatile Method in. Nucleoside Chemistry, 32 Tetrahedron Letters 7593 (1991) (“Zavgorodny”).. IBS argued to the Board that Ju in combination with Zavgorodny or Tsien in., combination with Zavgorodny render the patent invalid as obvious pursuant, to 35 U.S.C. § 103. 1 IBS relied on Tsien and Ju for similar purposes.

In its Decision to Institute, the Board determined that both Ju and Tsien “describe [] a process of labeling, and ultimately sequencing, a nucleic acid molecule” by 'a polymerase; J.A. 166, 169. Both Ju. and Tsien disclose a method of sequencing unknown DNA involving the SBS' method, including the labeling of nucleotides for detection and the use of a protecting group at the 3'-OH position of *1364 the nucleotide. Neither Ju nor Tsien disclose a protecting group that comprises an azido group, however.

Regarding Zavgorodny, the Board found that it teaches that an “azidomethyl moiety is a suitable protecting group for the 3' OH position of nucleosides, precisely the position requiring protecting in Ju’s [or Tsien’s] process, as well as the fact that the- azidomethyl group is cleavable from the nucleoside under specific and mild conditions.” J.A, 167, 172. As Zavgorodny notes, the “[a]zidomethyl group is of special interest, since it can be removed under very specific and mild conditions, viz. with triphenylphosphine in aqueous pyridine at 20 °C.” J.A. 861.

Of particular importance to this appeal, Tsien teaches'that one of “[t]he criteria for the successful use of 3'-blocking groups” is “the availability of mild conditions for rapid and quantitative deblocking.” J.A. 1010 (emphasis added).

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821 F.3d 1359, 119 U.S.P.Q. 2d (BNA) 1171, 2016 U.S. App. LEXIS 8481, 2016 WL 2620512, Counsel Stack Legal Research, https://law.counselstack.com/opinion/intelligent-bio-systems-inc-v-illumina-cambridge-ltd-cafc-2016.