Agilent Oligonucleotide Array-Based CGH on the Agilent DNA Microarray Platform Brochure
Contents
1. in duplicate Sample Dilutions 30 m GO m 0 mu hetevozygous Aeletion AetectedA even at 30 purity CA TECT T ARRANG T ATHIC TA TA AT Validate Your Results with CGH Analytics Identify statistically significant variations Remove the quandary of subjective analysis Integrate data analysis seamlessly Agilent s CGH analytics software offers a sophisticated set of analytical tools for assessing chromosomal aberrations helping you place results into biological context Once you have identified key areas analyze specific regions of interest for common gains and losses across cohorts Powertul Data Representation e Visualize complex genetic patterns at varying levels of detail Optimized Statistical Tools e Make reliable variation calls based on a choice of multiple sophisticated algorithms Harness robust quality control metrics and filters to remove outliers An Integral Component of the GeneSpring Analysis Platform e Synthesize results trom multiple genomic applications e g gene expression genotyping or ChIP on chip alternative technologies BAC spotted arrays and genomic annotations look closev with i GENE VIEW f a4 s Get Started Today Find out more about the platform that s open to what you need Agilent offers world class support to provide both organizations and individual scientists all of the technical solutions they need to succ2. of interest Experience unmatched data clarity Agilent s Oligo aCGH tools offer increased sensitivity and reduced noise for more accurate analysis Me of genetic gains and losses When coupled with high definition options Agilent s platform enables identification of target regions with greater sensitivity and less noise than other tools Our HD CGH Chro MOS arrays enable you to identify objectively the critical regions for your research focus using CGH 7 specific 60 mer probes significantly improving resolution partis Improve Signal to Noise Ratios e Use CGH specific parameters for background subtraction and other calculations small hetevozygous Reliably Identify Single Copy Changes Aeletion e Characterize specific areas of interest with an overall median probe spacing of 8 9 kb even in samples that are diluted or only 30 pure Look Closely For High Definition Analysis e Visualize data at multiple levels for in depth analysis of target regions wmicroabevvation Auplication lt 100 KB cytobanmd qll 22 Expevimental Conditions M MOCK cells derived from a leukemia patient were processed following standard Agilent aCGH protocols Pub No G4410 90010 v4 0 and analyzed using 1 5 ug of labeled DNA at 30 60 and 100 purity The plots for each degree of purity are based upon wmicvoabervvation Auplication collective data from four separate microarrays each dye flip pair in opposite polarity performed
3. DEVELOPING CANCER REGIONS AN CHANGES WE DO NOT YET UNDERSTAND DO YOU NEED THE ABILITY TO SCAN WIDE AND THEN ZOOM OBSTACLE IN TIGHT Discover the Comprehensive Platform with Optimized CGH Tools Identity copy number changes Characterize molecular aberrations Map genomic breakpoints Designed for discriminating resolution the Agilent DNA Microarray Platform provides a comprehensive workflow with products and related technical support to take you through every step of analysis From whole genome to high definition HD targeted oligo aCGH microarrays Agilent s platform provides the sensitivity to allow you to identify regions of interest and the flexibility to look in closer for validation and more in depth investigation SCAN genome wide No Zoom in fov A closev look TT aT Alle ei ke TT aT Arlt ei P Choose trom a Wide Range of Flexible Microarrays Optimize your experiments with efficient custom manufacturing Design your own CGH specitic arrays Multiplex for maximum efficiency and reduced cost per experiment The Agilent platform offers global coverage of native DNA with CGH specific probes to identify regions of interest as well as the resources to design targeted arrays upon discovery of anomolous regions Agilent s SurePrint inkjet technology ensures high precision feature placement through base by base synthesis and a robust QC process resulting in superior quality microarrays Catalog e Prede
4. SCANNING ADVANCED DATA ANALYSIS Analyze total genomic DNA with no Take advantage of our integrated Use software specifically designed for complexity reduction using two color hybridization tools and award winning genomic aberration analysis to gain a hybridization Cyanine 3 and Cyanine 5 scanning technology for seamless workflow more complete perspective of the entire and normal reference DNA eliminating integration Built upon dependable chromosome delineate aberration experimental bias Agilent s Oligo aCGH engineering and years of experience in boundaries and make statistically arrays are compatible with tissues fresh or the industry Agilent s DNA microarray relevant variation calls Analyze CGH and frozen cell lines whole blood and other scanner is a powerful research tool Gene Expression data jointly validating challenging samples the relationship between transcriptional and genetic regulation _ i fiddtcdied H vad Cee ee wU Homo Fi oP PU iy PUNE gi E Ei 7 j i f a ee Tirno C O cosa Es z alofleaeal ad fiona ll peaQaatals Quality Control Hybridization Analysis amp Statistics Labeling Kits Array Processing Visualization scanning Pathway Integration AG TICS A G A ri ALT AT T ARYOT G TIFICAT CA FEGT T C T A G A T T A C CAT Detect and Analyze Even the smallest Chromosomal Alterations Quantify chromosomal gains and losses Dive deeper into your regions
5. croarray platform that provides the CGH specific probe coverage you need for genome wide scanning while providing the flexibility to zoom in to regions of interest You need a platform that s optimized for CGH yet capable of integrating with other genomics applications To fully explore the options offered by oligo aCGH technology you need a platform that can go wherever your research takes you References 1 Barrett MT Scheffer A Ben Dor A Sampas N Lipson D Kincaid R Tsang P Curry B Baird K Meltzer PS Yakhini Z Bruhn L Laderman S Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA Proc Natl Acad Sci U S A 2004 Dec 21 101 51 17765 70 2 Brennan C Zhang Y Leo C Feng B Cauwels C Aguirre AJ Kim M Protopopov A Chin L High resolution global profiling of genomic alterations with long oligonucleotide microarray Cancer Res 2004 Jul 15 64 14 4744 8 DO YOU NEED TOOLS THAT GO WHERE YOUR RESEARCH TAKES YOU TO KEEP UP WITH YOU INSTEAD OF DEFINING YOU ARE TRYING TO TACKLE DO YOU NEED AN OPEN PLATFORM TO HELP YOU TO ELUCIDATE THE IMPACT OF Open Up to High Resolution Copy Number Detection The Agilent Oligo aCGH microarray combines flexibility and sensitivity in an array designed specifically for CGH letting you study aberrations and copy number variations with total confidence Engineered for flexibility Agilent s SurePrint inkjet technology prints oligonucleotides on demand e
6. e se I ei i S T p i T Open to Change Oligonucleotide Array Based CGH on the Agilent DNA Microarray Platform Agp Agilent Technologies Where Are You Taking Your Chromosome Analysis Microarrays are revolutionizing comparative genomic hybridization CGH Are you ready to take advantage of new research opportunities Do you have the tools you need to dive deeper into the genome Scientists studying genetics have long investigated global changes in chromosomal balance Traditional comparative genomic hybridization CGH and other microscopy methods provide opportunities for rough chromosome investigation but are fraught with challenges that hinder precise analysis Shortcomings in spatial resolution low throughput methods and weak analytical tools pose major challenges to researchers The use of BAC and cDNA microarrays for CGH research improves resolution and throughput but these microarrays are still compromised by nonspecific hybridization potential inconsistent quality limited commercial availability and suboptimal resolution Now oligonucleotide microarrays can enable you to detect large or focal amplifications and deletions elucidate copy number boundaries within the genome and characterize chromosomal variations 2 To take advantage of the promise of microarrays for CGH you need a platform that gives you the resolution you need to pinpoint chromosomal changes with confidence You need a mi
7. essfully incorporate aCGH into their research Agilent s DNA Microarray Platform offers technical solutions from beginning to end providing everything you need to achieve success in your research Visit www OpenGenomics com or contact an Agilent customer center at 1 800 227 9770 T Chart a Path into the Future of Genomics Investigate the latest in peer science Discover the potential of Agilent s oligo aCGH tools Connect and learn more today As genomics moves towards a systems approach novel techniques such as oligo aCGH will enable cytogeneticists and oncologists alike to examine familiar questions from fresh and innovative perspectives New genomics applications are enabling scientists to define innovative approaches to challenging research problems Agilent is committed to providing you with novel tools to define this path and connecting you with others asking similar questions To hear from researchers who are charting their own course in Genomics visit www OpenGenomics com i ae e Find an Agilent customer center in your country a emng www agilent com chem contactus U S and Canada 1 800 227 9770 agilent_inquiries agilent com me on lm Asia Pacific a e adinquiry_aplsca agilent com Europe info_agilent agilent com For research use only and not for diagnostic procedures Information descriptions and specifications in this publication are subject to change without notice Agilent Technologies s
8. hall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing performance or use of this material Agilent Technologies Inc 2006 Printed in the U S A September 20 2006 5989 5475EN afte Agilent Technologies
9. nabling total control over array content with no compromise in cost data quality or scalability The power of oligo aCGH stems from enhanced design flexibility and high definition capabilities combined with full genome representation by aCGH specific optimized probes You now have the capability to scan genome wide then focus on regions of interest for high definition analysis Design your own arrays with eArray our web based portal for custom design and receive your unique arrays in weeks rather than months Focused on sensitivity Agilent s microarrays provide superior sensitivity over traditional and other array based methods enabling a clear path from data to decisions Our 60 mer oligonucleotide probes are synthesized in situ resulting in highly reproducible features This enables you to work with complex mixtures analyze heterogeneous samples and detect biological changes that cannot be seen with other techniques Designed for integration From sample preparation to data analysis Agilent provides an integrated experimental workflow for aCGH specific applications Furthermore Agilent s CGH Analytics software integrates with our GeneSpring Software Platform enabling analysis comparison and visualization of data across multiple applications improving your confidence when making close aberration calls Introducing Agilent s Oligo aCGH Microarray Optimized Integrated Open Agdient HETEROGENEOUS SAMPLES FROM
10. signed high resolution microarrays enable genome wide survey and chromosomal profiling Oligo aCGH probes are selected based on proprietary CGH optimized algorithms delivering increased data quality and reproducible aberration detection Custom e High definition HD CGH microarrays offer the highest resolution tiling based on Agilent s database of over 8 million CGH probes This design process is coupled with world class technical support offering insights into design options and processing Multiplexed Arrays e Multiple arrays on a single slide reduce costs and can reduce experimental variability Obtain high quality microarrays in your choice of 1 2x 4x or 8x formats for maximum efficiency eArray e Our online array design tool puts you in control of your array designs SurePrint inkjet technology ensures rapid Iteration allowing you to print and receive arrays in weeks anywhere in the world Consider the Workflow that s Open to Your Needs Adopt an end to end CGH solution Integrate the CGH specific components you need Optimize your workflow for CGH analysis To take full advantage of opportunities for CGH research your genomics workflow must be flexible enough to allow you to experiment on your own terms while providing broadly compatible comprehensive tools From sample preparation to data analysis identify chromosomal gains and losses while controlling your own experimental direction SAMPLE PREPARATION PROCESSING AND
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Agilent Oligonucleotide Array Based CGH on the Agilent DNA Microarray Platform Brochure