Illumina Cambridge Ltd v Latvia MGI Tech Sia
| Jurisdiction | England & Wales |
| Judge | Mr Justice Birss,Birss J |
| Judgment Date | 20 January 2021 |
| Neutral Citation | [2021] EWHC 57 (Pat) |
| Date | 20 January 2021 |
| Docket Number | Case No: HP-2019-000052 |
| Court | Chancery Division (Patents Court) |
[2021] EWHC 57 (Pat)
IN THE HIGH COURT OF JUSTICE
BUSINESS AND PROPERTY COURTS OF ENGLAND AND WALES
INTELLECTUAL PROPERTY LIST (ChD)
PATENTS COURT
Royal Courts of Justice
The Rolls Building
7 Rolls Buildings
Fetter Lane
London EC4A 1NL
THE HON. Mr Justice Birss
Case No: HP-2019-000052
Iain Purvis QC, Piers Acland QC and Kathryn Pickard (instructed by Powell Gilbert LLP) for the Claimant
Thomas Mitcheson QC, Thomas Hinchliffe QC, Miles Copeland, Isabel Jamal and Alice Hart (instructed by Allen & Overy LLP) for the Defendants
Hearing dates: 9 th – 13 th, 16 th–20 th, 25 th, 26 th November and 9 th December 2020
Approved Judgment
THE HON. Mr Justice Birss
| Topic | Paragraph |
| Introduction and the issues | 1 |
| The witnesses | 23 |
| The modified nucleotide patents 578, 289 and 433 | 39 |
| The skilled person | 58 |
| The common general knowledge | 101 |
| The specifications of the modified nucleotide patents | 131 |
| Claim construction | 153 |
| Obviousness | 179 |
| Priority | 233 |
| Insufficiency | 243 |
| Added matter — amendment | 302 |
| Infringement | 307 |
| The 412 patent – ascorbate | 347 |
| The 415 patent – labelled nucleotide | 424 |
| Conclusions | 515 |
| Annexes: | |
| Modified nucleotide patent claim sets A, B and C | |
| Lists of issues provided at closing: | |
| Illumina MNP Issues | |
| MGI MNP Issues | |
| MGI FP Issues (412 and 415) (no list from Illumina) |
Introduction
This is a patent action about DNA sequencing technology. The patentee (Illumina) holds patents which derive from work by Solexa, a spin out company from Cambridge University which Illumina bought in 2007. The defendants (MGI) are all companies in the Beijing Genomics Institute group. MGI seeks to sell DNA sequencing systems in the UK. Illumina contends that these systems infringe various of its patents. In general, MGI denies infringement of any valid claim and contends the patents are invalid. Following a launch last year, MGI gave undertakings limiting UK sales until this trial.
It is convenient to take three Illumina patents together. They are EP (UK) No. 1 530 578, EP (UK) No. 3 002 289 and EP (UK) No. 3 587 433. These three patents are divisionals. The first two are entitled “Modified Nucleotides for Polynucleotide Sequencing” and 433 is entitled “Modified Nucleotides”. They based on an application filed on 22 nd August 2003. Although the earliest claimed priority is a US filing on 23 rd August 2002, in this case Illumina relied on the second priority document with a priority date of 23 rd December 2002. The three patents were granted on 13 th March 2013, 22 nd February 2018 and 22 nd April 2020 respectively. The 578 patent was opposed at the EPO but those proceedings ended with the patent upheld as granted. Opposition proceedings relating to the 289 continue and the opposition period for 433 has not yet ended. These patents all relate to an azidomethyl group as a reversible chain terminator in sequencing by synthesis.
EP (UK) 1 828 412 is entitled “Improved Method of Nucleotide Detection”. It was filed on 13 th December 2005 with its earliest claimed priority being a UK filing on 13 th December 2004. It was granted on 28 th November 2012. Opposition proceedings were commenced but have now been finally concluded. The patent was upheld in an amended form. The patent relates to the use of ascorbic acid (or a salt thereof) as a component in the fluorescent imaging buffer. Ascorbic acid is an anti-oxidant.
EP (UK) 2 021 415 is entitled “Dye Compounds and the use of their Labelled Conjugates”. It was filed on 16 th May 2007 claiming priority from a US UK filing on 18 th May 2006. It was granted on 15 th March 2017. There was no EPO opposition. As proposed to be amended the patent relates to a conjugate molecule consisting of a nucleotide, a particular cleavable linker and a particular fluorescent dye compound.
The modified nucleotide patents — issues
In terms of validity, MGI pleaded that the modified nucleotide patents are obvious over four pieces of prior art:
i) International patent application WO 91/06678 (Tsien) filed by SRI International and published on 16 th May 1991;
ii) International patent application WO 02/ 29003 (Ju) filed by a group at Columbia University and published on 11 th April 2002;
iii) A paper entitled “ 1-Alkythioalkylation of Nucleoside Hydroxyl Functions and Its Synthetic Applications: A New Versatile Method in Nucleoside Chemistry”, Zavgorodny et al., Tetrahedron Letters (1991) Vol. 32, No. 51, pp 7593–7596; and
iv) A paper entitled “ S,X-acetals in nucleoside chemistry. III1. Synthesis of 2'- and 3'-O-azidomethyl derivatives of ribonucleosides”, Zavgordony et al., Nucleosides, Nucleotides and Nucleic Acids (2000) Vol. 19, Issue 10–12, pp1977–1991.
The written evidence covered all four citations, however shortly before trial MGI abandoned its case on Tsien and on Ju. By closing it became clear that there was no need to dwell on Zavgorodny 2000. MGI's case can be made over Zavgorodny 1991 and if that does not succeed then the case over Zavgorodny 2000 would not succeed either.
There is also an issue of priority. If the modified nucleotide patents are not entitled to the December 2002 priority date then a further citation is prior art and is relied on for obviousness: US patent application no. 2003/0104437 A1, published on 5 th June 2003. This was a Solexa application and has been called “Barnes”, after the first named inventor.
Another validity question is whether particular claims of 578 and 433 are obvious for lack of technical contribution and/or insufficient. The issue is the same for both claims. Illumina advances an amendment which (it is not disputed) would cure that invalidity but does not agree those unamended claims are invalid and so the point falls to be decided. The relevant claims are 12 (as granted) of 578 (now claim 7 of claim set A) and claim 6 of 433 (as granted and in claim set C).
There were two added matter objections to the claim amendments. The one which remains live relates to claim 9 of 289 (claim set B). The one which was dropped was a challenge to claim 1 of 578 (claim set A). MGI dropped it after Illumina changed the amendments it was seeking to 578 by deleting granted claim 8. Both added matter issues are referred to at Illumina MNP Issue 6 but as explained only one is live.
Finally there is an insufficiency squeeze in relation to a number of the relevant claims of the modified nucleotide patents such that, if they are not obvious, they are insufficient, in part having regard to the recent Supreme Court decision in Regeneron v Kymab [2020] UKSC 27.
In terms of infringement, MGI has various systems alleged to infringe. One system is called StandardMPS and the other is called CoolMPS. Both use the azidomethyl group on the deoxyribose as a reversible chain terminator. In StandardMPS the four nucleobases carry a different fluorescent dye molecule covalently linked to the base via a linker. In CoolMPS the nucleobase is not covalently linked to a dye, rather detection uses four different antibody molecules, each linked to a different dye and each of which binds to a different nucleobase and the azidomethyl group. There are various detailed infringement issues, including allegations based on the doctrine of equivalents.
MGI also has two further azidomethyl based systems. They are the “two colour variant” and something called DNBSEQ E. In the two colour variant instead of four different dyes linked to the four nucleotides as in Standard MPS, only two dyes are used and detection occurs in two colours. Just as two binary bits can encode four numbers, so two dyes can distinguish four nucleotides by putting one dye on one nucleotide, the other dye on another nucleotide, both dyes on a third nucleotide, and no dye on the fourth nucleotide.
In the DNBSEQ E variant there are no fluorescent dyes at all. The nucleotides are linked to two types of non-fluorescent label. This method uses the same kind of encoding scheme as the two colour variant to distinguish four nucleotides.
All four of StandardMPS, CoolMPS, the two colour variant and the DNBSEQ E are alleged to infringe some claims of the modified nucleotide patents. Some of those points are admitted and others are not. The very useful lists of issues provided in closing naturally only list the points which are in dispute, but to get a full picture one needs to see the admitted aspects as well. A useful summary of the whole position was provided by Illumina. I have adjusted the claim numbers in it. In summary the position is:
StandardMPS, the two colour variant and the DNBSEQ E variant
i) Claims 1, 7, 12, 20 and 24 of the 578 patent (claim set A) are alleged to be infringed by all three systems. MGI does not admit infringement of claim 20 (claim set A) by the two colour or DNBSEQ E variants. The other allegations are admitted.
ii) Claims 1, 4, 5 and 6 of the 289 patent (claim set B) are alleged to be infringed by all three systems. MGI does not admit infringement of claim 4 by the two colour variant kit or the DNBSEQ E variant kit. The other allegations are admitted.
iii) Claims 1 and 6 of the 433 patent (claim set C) are admitted to be infringed by all three systems.
Cool MPS
iv) It is alleged that the CoolMPS system infringes claims 1, 7, 12, 20 and 24 of the...
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