Initial units of the 'supported oligo ligation detection' (SOLiD) DNA sequencing system have been shipped to leading research institutes and has already been used by researchers at Stanford University, US to create a high resolution map of the tightly wound packing units of DNA, known as nucleosomes, in the model organism C.elegans .
The early access program allows Applied Biosystems to develop applications for the instrument in collaboration with these institutes and marks the beginning of the commercialisation of the SOLiD next-generation sequencing system.
"The next generation technologies do the upfront chemistry in a massively parallel manner, doing close to a billion reactions at the same time.
This means that one next generation instrument could replace between 50 and 100 of the current instruments," Dr Dennis Gilbert, chief scientific officer and vice president for research at Applied Biosystems, told LabTechnologist.com in a previous interview .
The instrument will compete against Roche Diagnostics / 454 Life Sciences' Genome Sequencer FLX system and Illumina's 1G Genome Analyser.
"We have made rapid progress in developing the SOLiD System, which we believed had the best commercial viability among more than 40 next-generation sequencing technologies we evaluated," said Mark P. Stevenson, president for Applied Biosystems' molecular and cell biology division.
"We will continue to work with our customers and collaborators to further refine the system and develop the breadth of applications for what we believe will be the life-science community's platform of choice for both current and future DNA analysis projects."
Institutes including Stanford UIniversity, US, the Broad Institute of MIT and Harvard, US, Baylor College of Medicine, US, the DOE Joint Genome Institute, US, the Wellcome Trust Sanger Institute, UK and the University of Queensland in Australia have all received their early access instruments and have been assisting in the application development process.
Contractual arrangements for the early access instruments involve payment for the system once 'specification standards for the instruments have been achieved' .
The list price for the complete SOLiD system is $600,000 (€450,000) which includes the instrument, a computing cluster, a high capacity data storage centre and ancillary equipment for upfront sample preparation.
Applied Biosystems acquired the technology from Agencourt Personal Genomics in 2006 and has since increased the sample throughput by five times and the base read length by 66 per cent.
The system generates over 1 gigabase of data per run which is equivalent to about one third of the human genome.
This has helped Dr Arend Sidow of Stanford University to analyse 282 megabases of aligned sequence data to create a high-resolution map of nucleosome positioning in the C.elegans round worm that is often used a model organism in the study of biological processes.
The location of these nucleosomes is thought to affect gene expression and and provide insights into DNA transcription.
"I believe the SOLiD System technology has the potential to deliver real breakthroughs in any application of sequencing aimed at understanding biological functions in complex genomes," said Sidow.
The system features 2-base encoding which interrogates each base twice during sequencing, removing measurement errors resulting in high accuracy sequence data allowing detection of sequence variation including single nucleotide polymorphisms (SNPs), gene copy number variation, single base duplication, inversion, insertion and deletion.
When combined with mate pair analysis, a sample preparation method that allows highly accurate sequence assembly, the system can perform gene expression studies on low-expression genes that cannot be identified using hybridisation arrays.
"The mate-pair technology in the SOLiD System will enable us to generate highly accurate sequence data for infectious disease pathogens and other microbes," said Dr George Weinstock co-director at the Human Genome Sequencing Center at Baylor College of Medicine.
The system identified a large duplication in the genome of Escherichia coli ( E.Coli ) that had been missed by Sanger sequencing techniques.
"In our future efforts, we will continue to correlate phenotypes with genotypes of bacteria that have closely related genomes.
For this research, we look forward to next-generation sequencing technologies capable of identifying all kinds of genetic variation that may occur between different species," continued Weinstock.