The cytoscan 750k cytogenetics solution is a complete cytogenetic microarray solution that includes the new. Affymetrix microarray solutions include necessary components for a microarray experiment, from arrays and reagents to instruments and software, enabling scientists and clinicians to understand, identify, create, and improve genetic markerassisted breeding programs in. Affymetrix support by product for cytoscan hd array kit and. Affymetrix genechip fluidics station 450 users guide for agcc. The cytoscan hd cytogenetics solution is a complete. Novel genes associated with colorectal cancer are revealed. Cytoscan hd suite was designed to provide the most comprehensive coverage and. The 10k array, which is a piece of glass about the size of a thumbnail, has over 400,000 squares.
How to can analyze the affymetrix cytoscanhd array data. Affymetrix inc 20112012 the cytoscan hd cytogenetics solution. In addition to identifying copy number changes, cytoscan dx assay is capable of detecting allelic imbalances and copy number neutral abnormalities such as aohloh that can be associated with uniparental disomy upd or. For problems with the fluidics station or scanner, especially under any of the following conditions, unplug the instrument from the power source and contact affymetrix technical support. Dna is analyzed for copy number alterations using affymetrix cytoscan hd assay as per manufacturers instructions. By way of comparison, a human hair is about 50 microns wide. Affymetrix is dedicated to developing stateoftheart technology for acquiring, analyzing, and managing complex genetic information for use in biomedical research. Affymetrix hereby grants to buyer a nonexclusive, nontransferable, nonsublicensable license to affymetrix core product ip to use the products, but only in accordance with the product labels, inserts, manuals and written instructions provided by affymetrix. Chromosome analysis suite chas was developed with input from leading experts and is customized for copy number and cytogenetics research analysis and reporting. The procedures of washing and scanning of cytoscanhd chips followed the manuals provided by affymetrix, inc. In order to carry out an analysis in bioconductor i am following the tutorial at. The features on affymetrix arrays are incredibly small about 8 microns across. High fidelity copy number analysis of formalinfixed and.
Subject to the affymetrix terms and conditions that govern your use of affymetrix products, affymetrix grants you a nonexclusive, nontransferable, nonsublicensable license to use this affymetrix product only in accordance with the manual and written instructions provided by affymetrix. This section provides short videos that demonstrate each step of the cytoscan assay as described in the cytoscan user manual pn 703038. Affymetrix is dedicated to developing stateoftheart technology for acquiring, analyzing, and managing. The cytoscan cytogenetics suite that includes cytoscan arrays and cytoscan reagents, along with the genechip system 3000 and chromosome analysis software chas enable you to perform highresolution genomewide copy number analysis. Data sheet josep carreras leukaemia research institute. Thus far ive played around with birdseed and clrmm.
Cytoscan hd array kit and reagent kit bundle support materials. Venkatraman es, olshen ab 2007 a faster circular binary segmentation algorithm for the analysis of array cgh data. Seragnoli university of bologna, italy finding and implementing the right clinically actionable cancer biomarker. Cytoscan assay manual workflow thermo fisher scientific. Genotype calling for affymetrix cytoscan hd array and cytoscan 750k. Manuals that are relevant will depend on your system configura tion. For the ht array system configuration, refer to the following documents. Cel files were generated from agcc software from affymetrix, inc. Hi, is there a pipelinepacakage that can easily get me genotypes eg in aa, ag, gg type format from affy genome wide snp cel files. Cytoscan hd suite includes cytoscan hd array, cytoscan reagent kit, the easytouse chromosome analysis suite chas, and the proven genechip instrument system. Affymetrix support by product for cytoscan hd array kit.
The record is updated if the fda identifies a violation and classifies the action as a recall, and it is updated for a final time when the recall is terminated. The fetal thymus has a unique genomic copy number profile resulting from physiological t cell receptor gene rearrangement. Cytoscan assay automated workflow site preparation guideapplied biosystems nimbus instrument 5 1 introduction about cytoscan automated target preparation solution on the nimbus instrument cytogenetics research studies are performed to identify structural changes in dna, such as copy number changes cnv, loss of heterozygosity loh, and mosaicism. All other trademarks are the property of their respective owners. Discordant mirna expression in lung cancer as determined by the agilent and affymetrix microarray platforms.
The surface of the affymetrix array is like a giant checkerboard. Cytoscan microarray for genomewide copy number assessment for. Affymetrix is dedicated to developing stateoftheart technology for acquiring, analyzing, and managing complex genetic. User guide, genetitan instrument thermo fisher scientific. A shown is the venn diagram of detected mirnas by the two different microarray platforms in male and female wildtype mice, respectively. Affymetrix inc 20112012 affymetrix cytoscan assay user manual. Im trying to read some cel files from cytoscan hd arrays with the r. Affymetrix microarray solutions include necessary components for a microarray experiment, from arrays and reagents to instruments and software, enabling scientists and clinicians to understand, identify, create, and improve genetic markerassisted breeding programs in agriculture for human health and wellness. Cytoscan hd suite is the unrivaled standard in cytogenetics research and delivers with.
The easiest, most userfriendly and free solution is affymetrix power tools. If the instrument is not working correctly, please contact your affymetrix technical support. Venkatraman es, olshen ab 2007 a faster circular binary segmentation algorithm for the analysis of. The combined high resolution dna copy number data and the ability to detect gains. Access and download the latest technical resources online, including product documentation, manuals, msdss, product support resources, faqs, videos, software. The cytoscan xon assay is intended to be used with genomic dna from postnatal peripheral blood samples. Cytoscan assay automated workflow on applied biosystems. Evaluation of the affymetrix cytoscan dx assay for developmental. Chas enables you to view and summarize chromosomal aberrations across the genome. Watch the videos before you start working in the lab to familiarize yourself with the setup and best practices for a successful cytoscan assay run. Specimens are processed according to cytoscan dx assay instructions.
High fidelity copy number analysis of formalinfixed and paraffinembedded tissues using affymetrix cytoscan hd chip. Package rcgh march 29, 2020 type package title comprehensive pipeline for analyzing and visualizing arraybased cgh data version 1. The fetal thymus has a unique genomic copy number profile. Affymetrix created the cytoscan hd array by empirically selecting probes from a pool of over 20 million probes and then further. A crossplatform comparison of affymetrix and agilent. Cytoscan assay manual workflow supports processing of as little as. View all available support material by product name. The dependence on tkwidgets only concerns few convenience functions. B shown is the venn diagram of detected mirnas by the different microarray platforms in male and female craf transgenic mice, respectively.