Microarray Scanner
Microarray Scanner
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Agilent has redefined microarray scanning with the new Agilent DNA Microarray Scanner with SureScan High-Resolution Technology, which delivers higher-quality data from current microarrays and equally superior output from Agilent’s future generation microarrays planned for introduction later in 2008. Agilent DNA Microarray Scanners provide greater transcript and chromosomal definition, as well as expression measurements that more accurately reflect the range of gene activity in biological systems.
Based on the existing, proven platform—a 48-slide scanning system using Agilent’s SureScan technology—the new DNA Microarray Scanner incorporates innovative new optics, electronics, and software that work together seamlessly to deliver an unprecedented level of performance.
Scanning resolutions of 10, 5, 3, and 2 microns are available, and the instrument can scan a 244,000-feature microarray at maximum resolution in 20 minutes. With a dynamic range up to 20 times greater than other scanners, the new scanner permits high-sensitivity scanning without saturation; this results in enhanced data quality across a broad range of applications such as gene expression, miRNA profiling, array CGH, ChIP, and methylation assays. Laboratories equipped with the previous model scanner can also enjoy this level of performance with a simple on-site retrofit.
Figure 1. Agilent’s SureScan High-Resolution Technology includes a unique dynamic autofocus feature that continually adjusts the scanner’s focus to ensure that features remain in focus at all times. Compared to other commercial scanners that only focus on a few discrete spots on a slide to compensate for glass aberrations, Agilent’s Dynamic Autofocus adjusts thousands of times per second to gracefully flow with any curvature, warpage, or other common glass slide imperfections; it also allows for high-speed, high-resolution scanning of both legacy and new higher density microarrays. The end result is highly sensitive and confident results that researchers can trust for their downstream data analyses.
As an integrated platform including PC, barcode reader, and image analysis software complete with QC reporting features, the new DNA Microarray Scanner offers walk-away operation for scanning, image analysis, and array quality assessment. Extracted data are easily collected and linked to downstream analysis packages such as Agilent’s GeneSpring Software.
Figure 2. A comparison between the G2565BA scanner and the new G2565CA high-resolution scanner shows equivalent results as indicated by the identical array scanned on both scanners. The data are displayed both in linear (left) and log scale (right) and maintain linearity over 5 orders of magnitude.
Figure 3. Various parameters were examined for the same array scanned on both scanners. The results are compared with the notation “B,” indicating the prior revision G2565BA scanner, while “C” indicates the results from the new G2565CA scanner. The summary results indicate that results are quite comparable on both scanners.
Figure 4. Detection of DNA aberrations on chromosome 4 with DNA Analytics 4.0 using the ADM-1 algorithm with a 1Mb moving average shows a very similar result when the same array is scanned on both scanners. Blue: G2565BA-scanner. Gold: G2565CA-scanner (new scanner).
Figure 5. Detection of DNA aberrations on chromosome 11 with DNA Analytics 4.0 using the ADM-1 algorithm on a 5.56Mb zoom-in show the same amplification with the same start and end points observed when the same array is scanned on both scanners. Blue: G2565BA-scanner. Gold: G2565CA-scanner (new scanner)
Figure 6. Detection of DNA aberrations on chromosome 9 with DNA Analytics 4.0 using the ADM-1 algorithm 1Mb moving average shows that small aberrations are consistently detected between the same array scanned on both scanners. Blue: G2565BA-scanner. Gold: G2565CA-scanner (new scanner).
Figure 7. Detection of DNA aberrations on chromosome 2 with DNA Analytics 4.0 using the ADM-1 algorithm on a 1.09Mb zoom-in show the same amplification with the same start and end points observed when the same array is scanned on both scanners. Blue: G2565BA-scanner. Gold: G2565CA-scanner (new scanner).
Agilent laboratory testing examined methods for quantifying the performance of a microarray scanner and applied those techniques to assess the capabilities of our DNA microarray scanner. The method for quantifying DNA microarray scanning performance offered a simple and effective way of assessing the impact of scanner noise on experimental uncertainty. Using standard microarray metrics, namely signal-to-noise, detection limit, and log(Ratio), this method was used successfully to quantify the performance of three different commercial microarray scanners. The results show that these performance metrics varied significantly among the scanners tested and had a measurable and dramatic impact on image quality. The study also described the measurement of the total experimental error introduced by the complete Agilent microarray system, including the scanner, microarray, sample preparation, labeling, hybridization, and data extraction components. The results clearly demonstrate that even when all components were included, variability with the Agilent microarray-based Gene Expression system was minimal, underscoring the variability in performance among the three microarray scanners used in the study.
Figure 8. Discover what you’ve been missing in microarray scanning. The Agilent Microarray Scanner is able to detect the low abundant genes or weak features, where other scanner brands (Y and Z) fail when analyzing the same weak feature from the same area of the microarray being scanned.
Reference: Agilent’s Microarray Platform: How High-Fidelity DNA Synthesis Maximizes the Dynamic Range of Gene Expression Measurements.
Agilent Publication Number 5989-9159EN.
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Reference:
Title: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
Journal: Nat. Biotechnol. 24(9), 1151-61.
Authors: MAQC Consortium, Shi, L., et al. (2006)
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DNA Microarray Scanner
For detailed specifications and ordering information visit agilent.com
DNA Microarray Scanner Accessories
For detailed specifications and ordering information visit agilent.com
For research use only and not for use in diagnostic procedures.