In a recent article in MIT Technology Review, Francis de Souza, president of Illumina is quoted as saying 228,000 human genomes will be sequenced this year (2014).  He further estimates that this number will double every 12 months to reach 1.6 million genomes by 2017. In a March blog post we extrapolated 400,000 genomes in 2015 by estimating the throughput of Illumina instruments in the market, HiSeq X Ten projects initiated on Genohub and large population sequencing projects starting in the UK and other countries. Pretty close to De Souza’s latest numbers. 

80% of the genomes sequenced this year will be part of scientific research projects, making one wonder when ‘clinical genomes’ will be ready. To get there we’re going to either need greater throughput, higher coverage or lower costs. However, instead on focusing on reducing costs, Illumina is betting on simplified, targeted sequencing. According to De Souza, “It’s not clear you can get another order of magnitude out of this…people are saying the price is not the issue”.  Rather than focusing on selling complex instruments, Illumina wants to become an everyday brand in hospitals. Illumina is actually in the process of simplifying their instruments and developing clinically relevant, targeted panels to be sold as FDA approved kits.

While targeted panels for research purposes are available today, most are not-regulated. Illumina believes regulation is a necessary step the FDA will have to take in order for targeted sequencing to become more popular in the clinic. A fast track way to get there is to work with pharmaceutical companies who are in the business of getting approval from the FDA. Last month, Illumina said it was developing a universal NGS based oncology test with AstraZeneca, Janssen Biotech, and Sanofi for use as a companion diagnostic on it’s MiseqDX platform. Today, Thermo Fisher announced plans to develop NGS based tests for solid tumors on its Ion PGM Dx platform with Pfizer and GSK.  At least in the short term future, it looks like targeted re-sequencing will be a mainstay in the clinic while research based WGS will guide targeted panel design.