Technology Overview

Introduction

The Illumina Genome Analysis System is a groundbreaking new platform for sequence analysis and functional genomics.  Dramatically improving speed and reducing costs, it is suitable for a wide range of applications including whole genome and candidate region sequencing, expression profiling, DNA-protein interactions, and small RNA identification and quantitation.  Leveraging proprietary reversible terminators and Clonal Single Molecule Array technology, the Illumina Genome Analysis System can generate several billion bases of data per run and in the process transform the way many experiments are devised and carried out.

The Illumina Genome Analysis System is ideal for genome-scale as well as targeted sequencing projects.  This platform has the potential to allow researchers to sequence a human genome for under $100,000 and in a matter of weeks, a feat that marks a dramatic improvement over the capabilities offered by traditional technologies.

Sequencing-By-Synthesis (SBS), using proprietary reversible terminators, lets the Illumina Genome Analysis System provide a high degree of sequencing accuracy even through homopolymeric regions and across G-C rich regions.  This allows researchers to sequence complex genomes rapidly, economically, and accurately. The versatile format of the flow cell also enables researchers to tailor the system to meet the specific needs of their application.

Sample Preparation

Sample preparation varies by application; however, each preparation is a variation on a common theme: namely, libraries are prepared and adapters are ligated onto the ends of DNA fragments to generate flow-cell-suitable templates; the adapters are complimentary to the two surface-bound amplification primers located on flow cells.  Please see Protocols and Sample Submission links for more details (via sidebar).

Cluster Station

The Cluster Station is a fluidics device that hybridizes samples onto a flow cell and amplifies them for later sequencing on the Genome Analyzer.  It uses solid support bridge amplification to create an ultra-high density sequencing flow cell with millions of clusters, each containing about 1,000 copies of the same template, in approximately 5 hours. .

The Cluster Station works in conjunction with a dedicated computer and the Illumina Cluster Station software. The open-source software allows either individual subroutines to be run or modification of protocols to meet research needs.

The Cluster Station automatically dispenses reagents and controls reaction times, flow rates, and temperatures.

Genome Analyzer

The Genome Analyzer sequences clustered template DNA using a robust four-color DNA Sequencing-By-Synthesis (SBS) technology that employs reversible terminators with removable fluorophores.  This approach provides a high degree of sequencing accuracy even through homopolymeric regions.

High sensitivity fluorescence detection is achieved using laser excitation and total internal reflection optics.  Short sequence reads are aligned against a reference genome and genetic differences are called using a specially developed data pipeline.  See Figure 1 for a pictoral representation

Figure 1: Sequencing Technology Overview

Workflow

Illumina's simplified and very automated workflow allows researchers to obtain data in just a few weeks.  See Figure 2.

Figure 2: Illumina's Genome Analyzer workflow, from sample preparation to incorporation.