Genomics technology company and sequencing platform · BEGINNER LESSON
Illumina
Illumina is a genomics technology company whose sequencing platforms use sequencing-by-synthesis, a method that reads DNA by adding labeled nucleotides one cycle at a time. In these systems, many DNA copies are made into clusters on a solid surface so the instrument can measure fluorescent signals from each cycle.
What it is and what is measured
Illumina is a company that sells second-generation sequencing systems for studying genetic variation and biological function. Its instruments measure signal intensity from fluorescent labels during each sequencing cycle, which is then used to call the DNA bases that were added. This makes the output a large set of short DNA reads used in research and related testing. [0,1,2]
[1] Bioinformatics and Computational Tools for Next-Generation ... [2] Innovation at Illumina: The road to the $600 human genome [3] Overview of Next Generation Sequencing Technologies - PMC
How the method works
The Illumina workflow begins with DNA or complementary DNA (cDNA, DNA made from RNA). The sample is fragmented and adapters, which are short added sequences, are attached to both ends. The fragments bind to matching oligonucleotides, short DNA pieces on a flow cell surface, and bridge amplification copies each fragment many times into a cluster of identical molecules. Sequencing then uses sequencing-by-synthesis (SBS), meaning DNA is read while new bases are copied onto the growing strand. Each incoming base carries a fluorescent label and acts as a reversible terminator, so only one base is added per cycle before detection and the block is removed for the next cycle. [0,2]
[1] Bioinformatics and Computational Tools for Next-Generation ... [3] Overview of Next Generation Sequencing Technologies - PMC
Why clusters and short reads matter
Making many identical copies in one place raises the signal enough for imaging. The instrument reads millions to billions of short sequences in parallel, and the many reads can be combined to build a consensus sequence, meaning an agreed-upon sequence supported by the data. Short-read instruments like Illumina work best when libraries contain shorter fragments of similar size. Illumina supports many applications, including whole-genome, exome, targeted, RNA, metagenome, and methylome sequencing. [1,2]
[2] Innovation at Illumina: The road to the $600 human genome [3] Overview of Next Generation Sequencing Technologies - PMC
Limits and sources of error
Illumina is considered accurate and robust, but several limitations remain. Fluorescent dyes can lose activity, and overlapping emission signals can make base calling harder. The chemistry also needs the copies in a cluster to stay synchronized; if they drift out of step, the consensus becomes less reliable. Too much DNA on the flow cell can cause overclustering, which also reduces performance. These limits matter because the system depends on clean fluorescent measurements from each cycle. [0,2]
[1] Bioinformatics and Computational Tools for Next-Generation ... [3] Overview of Next Generation Sequencing Technologies - PMC
SEE THE IDEA
Illumina sequencing in simple steps
Cut DNA or cDNA into pieces and add adapters to both ends.
Fragments attach to matching oligos on a solid surface.
Repeated copying creates dense clusters of identical molecules.
One fluorescent, reversible-terminator base is added and imaged each cycle.
Signal intensity is converted into DNA sequence reads.
Each step prepares the next: attachment enables amplification, clusters enable imaging, and imaging enables sequence reading.
Illumina reads DNA by building fluorescent clusters on a flow cell and measuring one synthesis cycle at a time.
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.