Illumina's HiSeq X Five Sequencing System.
Illumina's HiSeq X Five Sequencing System.

Illumina, Inc. announced it has expanded the world’s most comprehensive next-generation sequencing (NGS) portfolio with the launch of the HiSeq X Five System and HiSeq 3000/4000 Systems. Over the last five years, the HiSeq Sequencing System family has been established as the platform of choice for high-throughput, production-scale sequencing laboratories. The new systems bring to market technology innovations and cost reductions that enable high-throughput laboratories to significantly increase their productivity.

Additionally, during its presentation at the J.P. Morgan Healthcare Conference today, Illumina introduced the NextSeq 550 System, the first NGS system enabled for array scanning. The system’s initial applications are for cytogenetics and prenatal genetic diagnosis (PGD). The company also unveiled a roadmap for further market expansion in the areas of reproductive health and oncology.

“Illumina technology has broken down barriers in genomics by increasing data throughput at an astounding rate, while at the same time dramatically reducing the price per data point,” said Jay Flatley, Illumina’s Chief Executive Officer. “These advancements enable us to deliver the industry’s simplest, most efficient sequencing experience to our research and clinical customers as they work to forever transform our understanding of genomics and medicine.”

HiSeq X Five System

Illumina delivered the world’s first $1,000 genome in 2014 with the HiSeq X Ten System, a set of 10 HiSeq X instruments, which enables a single laboratory to sequence approximately 18,000 high-quality, high-coverage human whole genomes per year. For laboratories wanting to take advantage of HiSeq X technology for human whole genome sequencing (WGS) at a smaller scale, Illumina now offers the HiSeq X Five System.

The HiSeq X Five, which consists of five individual HiSeq X instruments, allows production centers to adopt high-throughput WGS with a lower capital investment and at an attractive price per genome. At full utilization, the five instruments provide the throughput to sequence more than 9,000 genomes a year. The HiSeq X Five makes high-throughput human WGS more accessible, enabling production-scale sequencing to be performed in more laboratories.

HiSeq 3000/4000 Sequencing Systems

Building on the proven performance of the HiSeq 2500 System and leveraging patterned flow cell technology originally developed for the HiSeq X Ten System, the HiSeq 3000/4000 Systems provide unparalled speed and performance for the full range of high-throughput sequencing applications.

The innovative patterned flow cell technology enables the HiSeq 3000 (using a single flow cell) and the HiSeq 4000 (using dual flow cells) to deliver an exceptional level of throughput, at a lower price per data point than the HiSeq 2500. With the ability to process one or two flow cells simultaneously, the HiSeq 4000 can sequence up to 12 genomes, 100 whole transcriptome samples, or 180 exomes in 3.5 days or less. Using a single flow cell, the HiSeq 3000 can produce half the throughput at the same price per sample as the HiSeq 4000. These capabilities set a new standard for cost-effective, high-throughput production-scale sequencing across multiple applications.

NextSeq 550

The NextSeq 550 System combines microarray scanning with the proven and robust NextSeq 500 Sequencing System. By leveraging microarray scanning on the NextSeq 550, researchers have access to a powerful, complementary technology for further exploration or confirmation of copy number variants detected through sequencing. The initial arrays qualified for the system are for cytogenetics and PGD applications. Illumina’s BlueFuse software is integrated into the system, creating a streamlined workflow for data management and analysis. The NextSeq 550 will enable a broad range of applications in reproductive health, genetic health, and oncology-related research.

The HiSeq X Five, HiSeq 3000/4000, and NextSeq 550 Systems are now available for order.

Market Expansion

Today, Illumina also shared the following strategies and innovations for market expansion.

  • In reproductive health, Illumina will launch the VeriSeq NIPT Solution in Europe in Q2’15. The 48-sample non-invasive prenatal test (NIPT) assay, based on paired-end sequencing, offers significant workflow and cost benefits by eliminating the need for PCR. Paired-end sequencing enables high performance, while allowing the estimation and reporting of fetal fraction ranges as an additional quality control metric. The new method is ideally suited for decentralized NIPT.

    The company also provided an update on its regulatory plan, including a change in focus from a submission of the HiSeq 2500 and an existing NIPT assay to the U.S. Food and Drug Administration (FDA). Instead, it will continue with CE-IVD marking of NIPT software in Europe in early 2015, as well as with CE-IVD marking of the new VeriSeq NIPT assay and associated software in 1H’15. In the U.S., Illumina is working with the FDA to determine the appropriate claims and required datasets for an NIPT assay for use in the high risk and average risk populations. Further announcements on timing of a submission will follow.

  • In oncology, Illumina announced a circulating tumor DNA development program to address the significant research and clinical opportunity for better understanding and improving cancer treatment and drug response. The company plans to release research use only kits in 2015, and operate a laboratory developed test to gather clinical evidence for regulatory submission and work with key partners. It is also planning to update the intended use for the MiSeqDx for use with FFPE samples. These innovations complement the company’s recent announcements regarding a universal NGS-based oncology test system and the Actionable Genome Consortium, which is working to define and standardize genomic testing for cancer tumors.