Updates in […] following some feedback and comments!

MGI and Illumina are going head-to-head in a patent battle over the chemistry used to sequence genomes. The battle for sequencing supremacy was won many years ago by Illumina (although @nanopore,@MGI_BGI and a few others still in stealth mode hope to change that). Their market share in WGS, exomes and RNA-Seq is huge, and their purchase of PacBio will extend this to almost a monopoly. This dominance has led to a drop in the cost of sequencing a Human genome from well over $10,000 a decade ago to under $1000 today. However, the price has remained relatively stable since 2014 when the HiSeq X was introduced, and the $100 genome will be waiting in the wings until technical challenges are solved and there is enough customer demand.

MGI announced their latest updates at AGBT’19 (read coverage by Dale and GenomeWeb). This revealed the new “CoolNGS” chemistry on the T7 system, which uses nucleotides that are not fluorescently labeled and may enable them to get around the core SBS patents. Instead of covalently attaching a fluorescently moiety to each base MGI use base-specific-block antibodies. Each of these binds to the blocking chemistry (which stops more than one base bing incorporated in each SBS cycle) and is read similarly to the standard Illumina chemistry.









Patent wars:

Earlier this year Illumina launched litigation against MGI in both Germany and Denmark. These allege that MGI infringe two key patents: EP 3002289 B1 and EP 1530578 B1, both of which describe “MODIFIED NUCLEOTIDES FOR POLYNUCLEOTIDE SEQUENCING”. However, the Illumina patents seem pretty clearly to describe the use of nucleotides with a fluorescent molecule covalently linked to the base. Whilst, MGI’s “CoolNGS” links the base indirectly to the label, via the antibody.

MGI have hit back with their recent lawsuit, which alleges that Illumina infringe their US 9222132 patent. This describes “Methods and compositions for efficient base calling in sequencing reactions”, and clearly describes the use of a two-colour SBS workflow as used on the Illumina NextSeq and NovaSeq instruments. If this stands up in court then expect it to be used as a bargaining chip in negotiations between the two companies.

Unfortunately, for those of us who were hoping to see the $100 genome before 2020, MGI’s announcements on the updated instruments and chemistry on T7 at AGBT’19 come with an $500 per WGS price-tag (MGI are currently approx $700). Coupled to the fact that most groups using NGS don’t quite have faith that MGI/BGI can deliver the same quality as Illumina today, this makes mass adoption unlikely.

“Nobody got fired for buying…”