Our innovative patterned flow cell technology offers an exceptional level of throughput for diverse sequencing applications. Patterned flow cells use distinct nanowells for cluster generation to make more efficient use of the flow cell surface area. This advanced flow cell design contributes to increased data output, reduced costs, and faster run times.
Patterned flow cells contain billions of nanowells at fixed locations across both surfaces of the flow cell (Figure 1). The structured organization provides even spacing of sequencing clusters to deliver significant advantages over non-patterned cluster generation.
Patterned flow cells are produced using semiconductor manufacturing technology. Starting with a glass substrate, patterned nanowells are etched into the surface for optimal cluster spacing. Each nanowell contains DNA probes used to capture prepared DNA strands for amplification during cluster generation. The regions between the nanowells are devoid of DNA probes.
The process ensures that DNA clusters only form within the nanowells, providing even, consistent spacing between adjacent clusters and allowing accurate resolution of clusters during imaging. Maximal use of the flow cell surface leads to overall higher clustering.
Our proprietary exclusion amplification clustering method further increases data output. Exclusion amplification allows simultaneous seeding (landing of the DNA strand in the nanowell) and amplification during cluster generation, which reduces the chances of multiple library fragments amplifying in a single cluster. This method maximizes the number of nanowells occupied by DNA clusters originating from a single DNA template, increasing the amount of usable data from each run.
Patterned flow cell technology, pioneered on the HiSeq X Ten System, makes data-intensive applications more cost-effective, including the $1000 human genome. The HiSeq 3000/HiSeq 4000 Systems were the first Illumina sequencers to use patterned flow cells for diverse genomic applications.
The NovaSeq 6000 System unites the latest high-performance imaging with the next generation of Illumina patterned flow cell technology. The updated NovaSeq flow cell design further reduces the spacing between nanowells, significantly increasing cluster density and data output.
Watch Illumina scientists discuss how over- and underclustering can affect your sequencing data. Learn about common clustering issues and ways to prevent them.View Video
On nonpatterned flow cells, cluster density has a significant impact on run performance, specifically data quality and total data output.Read Technical Bulletin