Illumina GAIIx

GAIIx is a sequencer released by Illumina in January 2006. It is based on Sequencing by Synthesis (SBS).

Illumina GAIIx
Photo of GAIIx: by Illumina


Manufacturer Illumina
Technology Sequencing by Synthesis (SBS)
Release date January 2006
Price [2] $250,000
MSRP as of release date
Type Benchtop
Weight 187 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Illumina GAIIx: 1x35bp to 2x150bp
Run time Illumina GAIIx: 48 hours to 336 hours
Reagent cost per Gb [1] Illumina GAIIx: Unavailable
Data quality [3] Illumina GAIIx: Greater than 85% bases higher than Q30
Maximum output per run (Gb)[4] Illumina GAIIx: 95.00
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 GAIIx

The Illumina Genome AnalyzerIIX (GAIIx) was a powerful next-generation sequencing (NGS) instrument known for its high throughput and accuracy. While now discontinued, it played a significant role in advancing genomics research in the early 2010s. The GAIIx was a significant upgrade over its predecessor, the Illumina Genome Analyzer (GA), and was ultimately succeeded by Illumina's HiSeq series. It was particularly successful in the whole-genome sequencing and resequencing markets.

Key Innovations

  • Enhanced Optics and Detection: The GAIIx incorporated refined optics, lasers, and a more sensitive CCD camera than earlier models. These improvements increased signal-to-noise ratios, thus improving accuracy.
  • Increased Cluster Density: Illumina achieved higher cluster densities on the flow cell surface. This denser packing enabled a massively higher sequencing output per run.
  • Pared-End Sequencing Capability: The GAIIx introduced paired-end sequencing, generating reads from both ends of a DNA fragment. Paired-end reads substantially improve genome assembly and structural variant detection.

Features and Technologies

  • Sequencing by Synthesis (SBS): Like other Illumina platforms, the GAIIx employed SBS chemistry. Fluorescently labeled nucleotides are sequentially incorporated, with images captured after each flow cycle to determine the added base. High-quality image data is crucial in this process.
  • Bridge Amplification: Illumina’s proprietary bridge amplification created dense clusters of identical DNA templates on the flow cell. This signal amplification was key to achieving a detectable output when sequencing single molecules.
  • Data Quality: The GAIIx achieved base call accuracy exceeding 99% for more than 85% of bases, with the ability to produce up to 150 gigabases of sequencing data per run.

Intended Uses and Specific Applications

The Illumina GAIIx was well-suited to numerous applications:

  • Whole Genome Sequencing: For both human and model organism research.
  • Resequencing: Targeting and sequencing specific genomic regions of interest.
  • Transcriptome Sequencing (RNA-Seq): Analyzing gene expression patterns
  • As Illumina has discontinued support, there are no official library prep kits available for purchase that are suitable.

Comparison with Competing Instruments

  • Illumina NextSeq 550: The NextSeq 550 offers higher max output per run than the GAIIx at faster run times and similar read lengths, although the NextSeq 550 offers much more flexibility with the different output modes.
  • DNBSEQ-G99: Although the DNBSEQ-G99 can offer less max output, it has significantly faster run time and has slightly higher accuracy, especially for the shorter read lengths.
  • Ion Torrent Genexus: The Genexus can produce less max output than the GAIIx, but its run times are much faster and then read lengths are also longer (up to 400 bp).

Special Considerations

Since the GAIIx is discontinued, researchers considering it would likely be looking at the secondary market. Key considerations include:

  • Availability and Cost: Used GAIIx instruments may present a cost-effective option, but availability can be limited.
  • Support and Maintenance: Illumina no longer supports the GAIIx. Researchers would need to secure third-party maintenance and reagents or be capable of in-house troubleshooting.
  • Data Output: If high throughput is not a top priority, the output of a GAIIx may be sufficient compared to the investment in newer platforms.

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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.