More than ones million probes analyse the expression of almost50 000 RNA transcripts and variants on a single array the sizeof a dime the transcribed human genome is now available ona single chip.
Affymetrix has launched its new GeneChip brand Human Genome U133 Plus 2.0 Array, offering researchers the transcribed human genome on a single commercially available catalogue microarray.
The HG-U133 Plus 2.0 Array analyses the expression level of nearly 50 000 RNA transcripts and variants with 22 independent probes per transcript. This, says the company, provides superior data quality unmatched by technologies using a just single probe per transcript.
"With over one million probes on a commercial chip the size of a human thumbnail, the Human Plus array represents a leap in array technology data capacity, and further demonstrates the unique power and potential of our technology to explore vast areas of the genome,“ said chief commercial officer Trevor J Nicholls. "Using multiple independent measurements for each transcript ensures that our data quality remains industry standard even as our data capacity increases dramatically.“
The HG-U133 Plus 2.0 Array combines the content of the previous HG-U133 two-array set with nearly10 000 new probe sets for a total of nearly 50 000 RNA transcripts and variants. This new information, verified against the actual genome map, provides researchers the most comprehensive and up-to-date genome-wide gene expression analysis (Fig.1).
The probe design strategy of the HG-U133 Plus 2.0 Array is identical to the previous HG-U133 set and there is a very strong data concordance between the two arrays. With more than double the data capacity of the previous-generation Affymetrix human array, the HG-U133 Plus 2.0 Array can significantly cut processing and analysis time for scientists in the lab, freeing up valuable resources and accelerating research.
The company says that the HG-U133 Plus 2.0 Array offers the most genes and transcripts on any commercially available single array for human gene expression analysis, while maintaining its unrivalled data quality. It uses 22 independent data points to measure the hybridisation of each transcript on the array, more than a million data points in all and more than 30 times that of any other microarray technology. Using multiple measurements provides optimal sensitivity and specificity, and the most accurate, consistent and statistically significant results possible.
"More data points produce more reliable results and ultimately, better science,“ added Nicholls. "Our powerful probe set strategy gives our customers the assurance that what they see on the array reflects what is happening in their sample.“
Affymetrix is also launching an updated 11-micron version of its popular HG-U133A Array called the GeneChip HG-U133A 2.0 Array. By reducing the feature size from 18 microns to 11 microns, the new array will enable researchers to use smaller sample volumes while maintaining industry-standard performance. The new array represents over 14 000 well-characterised human genes that can be used to explore human biology and disease processes. All probe sets represented on the original GeneChip HG-U133A Array are identically replicated on the GeneChip HG-U133A 2.0 Array.
Portable DNA detection
Meanwhile, in Tokyo, Toshiba Corporation has applied its chip-based DNA detection and analysis methodology to a portable system that can provide accurate DNA analysis in environments as diverse as hospital laboratories and food inspection lines.
Genelyzer introduces a simple accurate, platform that makes DNA analysis a practical tool in applications as diverse as developing personalised medicine and testing for genetically modified crops.
Other DNA-chip-based systems for gene analysis use fluorescence detection. Each of the five processes necessary for detection and analysis -- DNA extraction, amplification, hybridisation reaction, detection and identification requires dedicated, expensive equipment and complex manual handling, all of which confine testing to special facilities, such as clinical laboratories. Moreover, the high degree of complexity and high costs of fluorescence-based detection are not matched by the accuracy of the analysis. The overall result is to limit the effectiveness and application of DNA testing.
Toshiba's new system is based on the company's breakthrough work and basic patents in DNA current detection method. At the heart of a system is an electrochemical DNA chip that is able to analyse and type single nucleotide polymorphisms (SNPs), common DNA sequence variations that can be used to identify genes.
Genelyzer integrates this chip into a system that automates all procedures from hybridisation on, and does so in a single piece of equipment that is only 45cm wide, 50cm deep and 23cm in height. Typical analysis of SNPs in a sample takes only one hour.
The fundamental reliability of Toshiba's electrochemical DNA chip has already been tested and proved in its application to a system for providing personalised drug therapies for people suffering from hepatitis C. While interferon is the preferred therapy for flushing hepatitis C from the liver, some individuals do not respond to this medication. The electrochemical DNA chip was successfully applied to a system for screening patients to assure they received appropriate medication.
Genelyzer builds on this success to provide a portable, easy to use automated DNA detection system, a practical, accurate platform that can be applied to a wide range of applications and multiple analyses. Toshiba now proposes to provide leading research institutes in Japan and overseas with Genelyzer, so that they can conduct a wide range of beta testing that will support its refinement as a multi-purpose platform.
One notable programme will be launched soon at the Institute of Human Virology, a centre of the University of Maryland Biotechnology Institute, which will apply Genelyzer to gene analysis relating to the effects and side-effects of anti-HIV drugs in order to develop tailor-made treatment regimes for patients undergoing antiretroviral therapy.
