AGBT16 day 3 plenary part 1 - Jay Flatley

Friday, February 12, 2016 09:40 (updated to improve the description of the chemistry and applications)

Jay Flatley, Illumina “Beyond the $1000 Genome-What’s next for NGS?”. He spent his time describing some of the key ingredients that have driven the sequencing tech at Illumina, and gave us a little historical overview of Illumina (see this 2004 presentation from Solxea).

1. the best technology, estimated about 3 million hours in development of SBS (around 350 years).
2. the best team
3. an engaged community (many applications developed by customer, ChIP-Seq, cancer genomes, single-cell genomes), showed the wonderful methods poster by Jaques Retief. An estimated 2000 analysis methods.

Jay went through some of the major breakthroughs: 2007 GA; 2010 line scan imaging (HiSeq 2000); 2011 LED optics and basespace (MiSeq); 2012 rapid run mode, faster fluidics and scanning (HiSeq 2500); patterned flowcells (HiSeq X); 2014 2 colour SBS, dry flowcells and consumer optics (NextSeq).

Firefly - What has Illlumina been doing with Avantome: Jay described this as a development plan - not available till Christmas 2017!

The original Avantome sequencing on CMOS required emulsion PCR, which was too limiting so Illumina never brought to market, Jay showed the sequencer that was built but never sold! However Illumina kept working on this technology and have implemented SBS on CMOS. "Other implementations to date have sacrificed accuracy" - I think Jay may be refering to Ion Torrent. Semindcondutor is a one channel device. He showed an image of the CMOS chip tech but no photos are allowed at AGBT so you'll have to find one somewhere else. Briefly nanowells  are fabricated over each photodiode and clusters are built directly on top of the CMOS sensors. Unlike the 4-colour HiSeq or 2-colour NextSeq the new Firefly implements an innovative 1-colour SBS  solution: A (removable fluor), T (permanently labelled), G (initially unlabelled) and C (unlabelled). After incorporation (and initial imaging) a chemistry cycle allows separation of the bases, the A fluor is removed, and G is now tagged with a fluor. A raw read accuracy of 99% is achievable and is roughly comparable to HiSeq X.

The systems uses an integrated digital fluidic library prep and sequencing instruments with a very small footprint. It uses the NeoPrep fluidics (is this going ot slow it down).

Firefly Specs: Run times are just from 3.5 to 13 hours for up to 2x150PE, 1Gb per run, 4M reads at $100 per sample and about $30,000 capital costs. The applications Illumina are aiming Firefly at are: targeted sequencing, infectious disease, inherited disease, and reproductive and genetic health.

Why is Illumina talking about it so far out from launch? The reality is that it is going to be difficult to keep this quiet with so many 3rd parties involved. Also Illumina are opening up the microfluidics apps to 3rd parties.

Recent collaborations and new ventures from Illumina: BioRad, 10X, Helix (consumer genomics from Illumina), Grail; which aims to detect cancer early by monitoring cell-free circulating tumour DNA. Screening asymptomatic individuals is challenging as you are right at the limits of detection in many cancers. may need to sequence up to 300,000 genomes at 60X by 2019.