Illumina

Illumina, Inc. is an American company, based in San Diego, that makes DNA sequencers and microarrays. It was founded in 1998 to sell genotyping arrays and became a sequencing company in 2007, when it bought Solexa, a company with origins in Cambridge, England, and a method called sequencing by synthesis.^[1][2] Its instruments read DNA optically, in short pieces, millions at a time, and the company says its sequencing-by-synthesis technology "has been used to generate >90% of the world's sequencing data".^[3]

Illumina's sequencers do not use pores, but the company licensed one: in 2013 it took exclusive worldwide rights to MspA, a protein nanopore developed at the University of Washington and the University of Alabama at Birmingham.^[4] Molecular Reality Corporation, a much smaller nanopore company, cites it as the incumbent form of sequencing, optical and dependent on reagent kits.^[5]

Illumina was incorporated in California in April 1998, around the BeadArray, a technology licensed from Tufts University in which microscopic beads, each carrying copies of a DNA probe, sit in wells on a chip and light up where a sample binds to them.^[1] Its early products were arrays for genotyping, which read hundreds of thousands of known positions in a genome at once.

The company announced the purchase of Solexa in November 2006 and completed it in January 2007.^[2] Solexa's chemistry came from two chemists at the University of Cambridge, and its Genome Analyzer became Illumina's first sequencer. In 2008 a paper in Nature used the method to sequence a whole human genome.^[6] Shipments of the HiSeq 2000, a high-throughput instrument, began in 2010, and the MiSeq, a benchtop machine for smaller laboratories, followed in 2011.^[7] The NovaSeq 6000 arrived in 2017. The iSeq 100, which began shipping in 2018, replaced the camera with a CMOS image sensor.^[8]

On September 29, 2022, Illumina introduced the NovaSeq X series with a new chemistry, XLEAP-SBS. The company said the larger model, the NovaSeq X Plus, could sequence more than 20,000 whole genomes a year. It also changed how the chemistry travels: 15 reagents were reformulated so that they could be shipped at ambient temperature, and the company reported 90% less packaging waste than for the NovaSeq 6000.^[9] The instrument runs the company's DRAGEN analysis software on board, with a compression format that Illumina says makes files five times smaller without loss.^[9]

The largest single project on the platform was the sequencing of UK Biobank. Its 500,000 volunteers' whole genomes were read on Illumina NovaSeq machines between 2018 and 2021 by the Wellcome Sanger Institute and deCODE Genetics, and the data were released to researchers on November 30, 2023.^[10][11]

In sequencing by synthesis, DNA is cut into fragments, and each fragment is copied in place on a glass flow cell into a cluster of identical molecules, so that the signal from one cluster is bright enough to photograph. In each cycle the instrument floods the flow cell with all four nucleotides, each carrying a fluorescent dye and a chemical block, the reversible terminator, that lets only one base be added. Illumina's own description reads: "A fluorescently labeled reversible terminator is imaged as each dNTP is added." The block and dye are then cut off so the next base can follow.^[12] Because all four nucleotides compete at every step, incorporation bias is low.^[12]

The method's limit is length. The molecules in a cluster gradually fall out of step with one another, and the signal blurs after a few hundred cycles, so reads are short, typically 150 to 300 bases from each end of a fragment. Short reads are cheap and very accurate, but they cannot place long repeated stretches of a genome. The first complete, gapless human genome, published in 2022, was assembled from the long reads of Pacific Biosciences and Oxford Nanopore Technologies.^[13] Molecular Reality's quiz game puts the point in one line of commentary: "Long reads solved what short reads couldn't".^[14]

In October 2013 Illumina licensed the nanopore sequencing technology built around MspA, a pore protein from the bacterium Mycobacterium smegmatis engineered by laboratories at the University of Washington and the University of Alabama at Birmingham; the terms were not disclosed.^[4] It has not sold a nanopore sequencer. The Hole World, Molecular Reality's atlas of molecular-sensing groups, nevertheless includes an entry for Illumina among its companies and draws it with the atlas's picture of a protein pore.^[15][a]

Molecular Reality's materials sum up Illumina's technology in six words, "Optical sequencing-by-synthesis with reagent kits", as the incumbent against which nanopores are compared.^[5] Its own instruments measure an electric current through a single pore, and its materials list the reagent for its pores as "Salt".^[5][16]

• Human Genome Project
• Ion Torrent
• List of nanopore companies
• Nanopore sequencing