Illumina HiScanSQ

HiScanSQ is a sequencer released by Illumina in April 2010. It is based on Sequencing by Synthesis (SBS).

Illumina HiScanSQ
Photo of HiScanSQ: by Illumina


Manufacturer Illumina
Technology Sequencing by Synthesis (SBS)
Release date April 2010
Price [2] Discontinued
Type Benchtop
Weight 136 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Illumina HiScanSQ: 1x35bp to 2x100bp
Run time Illumina HiScanSQ: 36 to 204 hours
Reagent cost per Gb [1] Illumina HiScanSQ: Unavailable
Data quality [3] Illumina HiScanSQ: Greater than 85% bases higher than Q30
Maximum output per run (Gb)[4] Illumina HiScanSQ: 150.00
Primary error type [5] Substitutions
Notes about the specifications

  1. Cost per Gb: The cost per Gb is calculated by dividing the costs of sequencing reagents by the manufacturer’s maximum output per run. For these runs, the manufacturer may have included their own controls and used specific library preparation kits. Actual performance may vary based on sample and library type and quality, loading concentration, and other experimental factors. The sequencing reagent costs used for calculations do not include any other costs associated with preparing the samples or running the instrument, including reagents used for extraction, quality control or library preparation, labor, electricity, lab consumables, storage, etc. Performance metrics and prices are subject to change.
  2. Price: The final price may be different depending on the supplier, the region and any discounts provided through bulk orders or negotiation. Other factors that may influence the final price are warranty options, maintenance contracts, possible trade-ins of older instruments, and any financing arrangements chosen.
  3. Data quality: This is the maximum data quality that the instrument can offer based on manufacturer’s specifications and optimizations. The quality of a specific run will depend on multiple factors, including sample quality, sample quantity, library prep protocol, run conditions, etc.
  4. Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
  5. Primary error type: This is the most common type of error that may occur due to sequencing. Other types of error may occur as well.

More about the HiScanSQ

The Illumina HiScanSQ was a powerful next-generation sequencing platform designed for flexibility in mid- to high-throughput sequencing projects. It notably integrated both microarray-based and sequencing-by-synthesis (SBS) technologies within a single system. The HiScanSQ filled a market niche demanding the scalability of sequencing for research projects on diverse sample types. However, Illumina discontinued this instrument, and it has largely been superseded by members of the NextSeq series.

Key Innovations

  • Integration of Sequencing and Arrays: The HiScanSQ was uniquely capable of running both sequencing-based and array-based assays on the same instrument. This offered significant flexibility for researchers who might need to use a combination of approaches depending on the research question.
  • Scalable Throughput: The HiScanSQ employed a modular design enabling users to select between flow cells. This adaptability allowed projects of varying sizes to be run, helping to optimize reagent use and throughput.

Features and Technologies

  • Sequencing-by-Synthesis (SBS) Chemistry: Like other Illumina sequencers, the HiScanSQ used SBS chemistry with reversible terminators for error minimization. This ensured highly accurate DNA sequencing.
  • Autoloader Capability: Hands-free operation was enabled by an autoloader, optimizing laboratory workflow and streamlining processes.
  • High Data Output: Data output capabilities for the HiScanSQ ranged from 50 Gb up to a substantial 150 Gb per run depending on configuration and read length.

Intended Uses and Specific Applications

The Illumina HiScanSQ instrument was suited for:

  • Whole-Genome Sequencing (WGS): Projects demanding extensive genomic coverage at moderate depth.
  • Targeted Sequencing: Investigating specific regions of interest, often with the use of custom panels.
  • RNA Sequencing (RNA-seq): Studies of the transcriptome for exploring gene expression patterns.
  • Microarray (Chip-based) Studies: High-throughput genotyping, ideal for projects like genome-wide association studies (GWAS).

As the HiScanSQ is discontinued, there are no suitable library prep kits from Illumina that are available for purchase.

Comparison with Competing Instruments

  • Illumina NextSeq 550 The NextSeq 550 is a successor instrument, offering slight lower max output but with higher flexibility in read lengths and much faster run times.
  • PacBio Onso: PacBio's Onso platform fills a niche for those needing extremely accurate short reads. Although the max output is similar to the HiScanSQ, the Onso can reach higher read lengths (i.e. 150-200 bp) at much faster speeds and higher accuracy.
  • Complete Genomics DNBSEQ-G99: This platform offers less max output than the HiScanSQ, but it can reach higher read lengths (i.e. 150 bp) at much faster run times and at slightly higher accuracy, especially for the shorter read lengths.

Special Considerations

Since the HiScanSQ is discontinued, researchers considering a similar instrument should evaluate the NextSeq series from Illumina as a more modern alternative. However, pre-owned HiScanSQ instruments could provide a cost-effective option for labs wanting both array and SBS sequencing capabilities, provided suitable support and reagent availability can be secured.

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This information on this page is up-to-date as of April 18, 2024 and based on the spec sheets published by the manufacturer.