Illumina’s Next Big Pivot

President of Illumina

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. 

Next Generation Sequencing Applications in the Clinic Today

clinical sequencing carcinoma

Every year an increasing number of next-generation sequencing based diagnostic assays are validated and enter into clinical practice. Hundreds more are developed for pre-clinical research purposes. NGS applications being used in the clinic today include pre-implantation genetic screening (PGS) for in vitro fertilization, chromosomal aneuploidy detection, mutation analysis of patient samples, and sequence driven chemotherapeutics.

Comprehensive assays that identify single base substitutions and fusion events are commonly performed to establish a diagnosis or to help in deciding what drug treatment is best. While routine implementation of clinical NGS in oncology is still in it’s infancy, several assays are currently being performed in CLIA-certified environments: amplicon-based gene panels (1, 2), targeted capture based gene panels (3, 4), full exome and transcriptome-seq (5, 6), whole genome and RNA-seq (7-9). Some patients are even being treated with drugs for off-label indications, based on NGS tests (of all chemotherapeutic prescriptions, 33-47% are off-label (10)). As assays are standardized and confirmed by orthogonal platforms, we expect see an increase in the number of these clinical applications.

NGS-based pre-implantation genetic screening has significantly changed prenatal testing and screening. Currently only ~ 25% of invitro-fertilization procedures are successful. This low rate of success is due to an increasing maternal age and chromosomal aneuploidy.  PGS is performed to select chromosomally balanced embryos during the IVF process, ensuring only euploid embryos are implanted. This NGS based assay has been shown to improve implantation success rates and is being used in clinics today.

Non-invasive prenatal testing using cell-free fetal DNA circulating in maternal blood allows for the detection of genetic diseases and common chromosomal aneuploidies such as trisomies 13, 18, and 21. Fetal DNA, comprising about 10% of the DNA in maternal circulation becomes detectable between 5-10 weeks after conception. The method allows for an early assessment of aneuploidy without the risk of harming the fetus. Sequenom, Verinata Health, Ariosa Diagnostics and Natera each offer CAP and CLIA certified tests and are available at OB/GYN offices.

In November 2013, the FDA cleared the Illumina MiSeqDx platform as a class II device and a cystic fibrosis carrier screening assay. The assay detects 139 variants in the cystic fibrosis transmembrane conductance regulator gene (CFTR) gene.

These are highlights of assays one could expect to receive if visiting a clinic today. We’d like to hear from you about others in development or those currently in practice.


1)    Committee on a Framework for Development a New Taxonomy of Disease & the National Research Council. Toward Precision Medicine: Building a Knowlege Network for Biomedical Research and a New Taxonomy of Disease (National Academies Press, 2011).

2)    Beadling, C. et al. Combining highly multiplexed PCR with semiconductor-based sequencing for rapid cancer genotyping. J. Mol. Diagn. 15, 171–176 (2013).

3)    Dagher, R. et al. Approval summary: imatinib mesylate in the treatment of metastatic and/or unresectable malignant gastrointestinal stromal tumors. Clin. Cancer Res. 8, 3034–3038 (2002)

4)    Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature 417, 949–954 (2002).

5)    Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotech. 27, 182–189 (2009).

6)    Roychowdhury, S. et al. Personalized oncology through integrative high-throughput sequencing: a pilot study.Sci. Transl. Med. 3, 111ra121 (2011).

7)    Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.Cancer Discov. 2, 82–93 (2012).

8)    Matulonis, U. A. et al. High throughput interrogation of somatic mutations in high grade serous cancer of the ovary. PLoS ONE 6, e24433 (2011).

9)    Weiss, G. J. et al. Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma. PLoS ONE 7, e37029 (2012).

10) Conti, R.M. et al. Prevalence of Off-Label Use and Spending in 2010 Among Patent-Protected Chemotherapies in a Population-Based Cohort of Medical Oncologists. J. Clin. Oncol. 31, 1134–1139 (2013).