454 Sequencing

One Fragment = One Bead = One Read

The complete sequencing workflow of the Genome Sequencer FLX System comprises four main steps, leading from purified DNA to analyzed results. These basic steps include:

Generation of a single-stranded template DNA library

　　Emulsion-based clonal amplification of the library

　　Data generation via sequencing-by-synthesis

　　Data analysis using different bioinformatics tools

For an overview of the entire sequencing workflow, please see the Genome Sequencer FLX Multimedia Presentation.

Sample Input and Fragmentation

The Genome Sequencer FLX System supports the sequencing of samples from a wide variety of starting materials including genomic DNA, PCR products, BACs, and cDNA. Samples such as genomic DNA and BACs are fractionated into small, 300- to 800-basepair fragments. For smaller samples, such as small non-coding RNA or PCR amplicons, fragmentation is not required. Instead, short PCR products amplified using Genome Sequencer fusion primers can be used for immobilization onto DNA capture beads as shown below under "One Fragment = One Bead". 

 Library Preparation

Using a series of standard molecular biology techniques, short adaptors (A and B) - specific for both the 3' and 5' ends - are added to each fragment. The adaptors are used for purification, amplification, and sequencing steps. Single-stranded fragments with A and B adaptors compose the sample library used for subsequent workflow steps. 

One Fragment = One Bead

The single-stranded DNA library is immobilized onto specifically designed DNA Capture Beads. Each bead carries a unique single-stranded DNA library fragment. The bead-bound library is emulsified with amplification reagents in a water-in-oil mixture resulting in microreactors containing just one bead with one unique sample-library fragment. 

emPCR (Emulsion PCR) Amplification

Each unique sample library fragment is amplified within its own microreactor, excluding competing or contaminating sequences. Amplification of the entire fragment collection is done in parallel; for each fragment, this results in a copy number of several million per bead. Subsequently, the emulsion PCR is broken while the amplified fragments remain bound to their specific beads. 

One Bead = One Read

The clonally amplified fragments are enriched and loaded onto a PicoTiterPlate device for sequencing. The diameter of the PicoTiterPlate wells allows for only one bead per well. After addition of sequencing enzymes, the fluidics subsystem of the Genome Sequencer FLX Instrument flows individual nucleotides in a fixed order across the hundreds of thousands of wells containing one bead each. Addition of one (or more) nucleotide(s) complementary to the template strand results in a chemiluminescent signal recorded by the CCD camera of the Genome Sequencer FLX Instrument. 

Data Analysis

The combination of signal intensity and positional information generated across the PicoTiterPlate device allows the software to determine the sequence of more than 400,000 individual reads per 7.5-hour instrument run simultaneously. For sequencing-data analysis, three different bioinformatics tools are available supporting the following applications: de novo assembly up to 120 megabases; resequencing up to 3 gigabases; and amplicon variant detection by comparison with a known reference sequence.