The geneatlas wt expression kit assay is not compatible with affymetrix array strips designed to focus on the 3 ends of transcripts. The 10k array, which is a piece of glass about the size of a thumbnail, has over 400,000 squares. The cytoscan hd cytogenetics solution from affymetrix enables. Cytoscan assay manual workflow thermo fisher scientific. Venkatraman es, olshen ab 2007 a faster circular binary segmentation algorithm for the analysis of. Faq, cytoscan assay and cytoscan hd array pdf, 169 kb manuals. The surface of the affymetrix array is like a giant checkerboard. An example of it is affymetrix cytoscan family, that includes a highdensity array. Affymetrix gene profiling reagents offer unparalleled convenience by simplifying assay workflow, decreasing handson time, and reducing quality control testing compared to researchuseonly. Affymetrix support by product for cytoscan hd array kit. How is the cytoscan assay different from the assay used with the affymetrix genomewide human snp. Both blood and cell line sample sources have been tested by affymetrix with the cytoscan assay. Aug 02, 2016 amplified dna was labeled and further fragmented using an affymetrix cytoscan hd array kit and reagent kit bundle cat.
Jan 31, 2014 working with cychp files from affymetrix cytoscan hd. Use of affymetrix arrays genechip human transcriptome 2. The cytoscan 750k cytogenetics solution is a complete cytogenetic microarray solution that includes the new. The tool aptcopynumbercyto 1 from the suit affymetrix power tools 2 generates a cychp file for each raw cel file.
Affymetrix cytoscan hd array is the property of its rightful owner. Affymetrix, according to the manufacturers protocol. Evaluation of the affymetrix cytoscan dx assay for developmental. Cytoscan assay manual workflow supports processing of as little as. Note that elosa wells must be coated with dna spotting oligos and incubated overnight before the elosa assay may be run. Jul, 2015 use of affymetrix arrays gene chip human transcriptome 2. Affymetrix nimbus target preparation instrument automate your workflow. Test the discrimination scoresagainst the userdefinable threshold tau. The assay and the associated reagents are for use with affymetrix gene 1. Cytoscan dx assay provides genomewide coverage for the detection of chromosomal. 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 array kit and reagent kit bundle zip, 500 kb package inserts. Materials needed for the elosa qc assay are listed in appendix a.
How to can analyze the affymetrix cytoscanhd array data. Affymetrix developed the cytoscan hd array by empirically selecting probes from a pool of over 20 million probes and then further screening them with greater than 3,000 samples to choose the highest performing probes for wholegenome cytogenetic applications. Jul 21, 2015 snp genotyping using the affymetrix axiom genomewide panafrican panafr array set 1. See the troubleshooting section of the cytoscan assay user manual part number 703038 for more information about under fragmentation. Working with cychp files from affymetrix cytoscan hd. An example of it is affymetrix cytoscan family, that includes a highdensity array cytoscan hd and a light version array. Syndrome agreement was compared between clinical interpretation based upon rpc and cytoscan dx assay, with an overall interpretation positive agreement of 80. Fdacleared cytoscan dx assay for postnatal use only. 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. Affymetrix, biodiscovery launch cancer research software.
Assay warnings and precautions 8 cytoscan assay manual workflow user guide 1 do use 250 ng of doublestranded genomic dn a gdna that is not degraded size 10 kb by gel analysis, not contaminated, and free of pcr inhibitors. Jun 06, 2014 the cytoscan platform is used extensively for research on hematological cancer nexus copy number for affymetrix has a set of tools that help uncover key genomic events in these projects. The cytoscan xon assay is intended to be used with genomic dna from postnatal peripheral blood samples. The content and the organization of these files is described in 3. Oncoscan microarray analysis is a reliable assay to assess human cancers for genomewide copy number changes. The easiest, most userfriendly and free solution is affymetrix power tools. Aug 05, 20 affymetrix launches new oncoscan ffpe assay kit breakthrough assay provides genome wide solid tumor copy number analysis in only 48 hours from only 80ng input dna santa clara. Affymetrix developed the cytoscan 750k cytogenetics array to. Thus far ive played around with birdseed and clrmm. The cytoscan assay manual worflow supports processing of as little as eight samples, two of which are a positive and negative control. By way of comparison, a human hair is about 50 microns wide. Hd array, an optimized and streamlined assay, an allinclusive.
Pdf high fidelity copy number analysis of formalinfixed. This assay circumvents previous obstacles by combining a unique target generation system with microarrays so that almost all types of solid cancer samples can be analyzed in less than 48 h. The features on affymetrix arrays are incredibly small about 8 microns across. Specimens are processed according to cytoscan dx assay instructions.
Affymetrix cytoscan hd platform the cca assay in the clinical cytogenetics laboratory uses the affymetrix cytoscan hd platform which has approximately 2. Affymetrix cytoscan dx assay, global developmental. Starting quantity of rna input for mirna input for mirna. The central nontechnical difference between the affymetrix cytoscan dx assay and other similar microarray platforms is the recent fda approval for use of the affymetrix cytoscan dx assay in the diagnosis of children with developmental delay, intellectual disability, congenital anomalies, andor dysmorphic features. Display oschp data from affymetrix oncoscan ffpe assay arrays. Chromosome analysis suite chas was developed with input from leading experts and is customized for copy number and cytogenetics research analysis and reporting.
Snp genotyping using the affymetrix axiom genomewide pan. User, guide, genechip scanner 3000 targeted genotyping system. Robust manual or automated assay workflowsdna to result in less than three days. Cytoscan hd suite was designed to provide the most comprehensive coverage and highest performance for detecting chromosomal aberrations in a broad range of sample. Affymetrix created the cytoscan hd array by empirically selecting probes from a pool of over 20 million probes and then further screening them with greater than 3,000 samples to choose the highest performing probes for wholegenome cytogenetic applications. Test the discrimination scoresagainst the user definable threshold tau. Affymetrix inc 20112012 affymetrix cytoscan assay user manual.
The purpose of this manual is to provide users with a comprehensive description of different terms used in genechip expression analysis, to present users with information on assessing sample and array quality, and to supply instructions on how to use the affymetrix microarray suite mas software to analyze expression data. Seragnoli university of bologna, italy finding and implementing the right clinically actionable cancer biomarker. Dna samples were digested with nspi restriction enzymes, ligated to adapters and to universal primers that recognize. The kit contains enough reagents to prepare 400 pcr reactionsequivalent to 96100 samples processed with the cytoscan assay. All protocols included in this manual have been used successfully by scientists at affymetrix, or have been recommended by our collaborators during the development of particular. Affymetrix launches new oncoscan ffpe assay kit aol finance. Noncoding rnas play major roles in the translational control of gene expression. This section provides short videos that demonstrate each step of the cytoscan assay as described in the cytoscan user manual pn 703038. 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. This manual is a technical guide for using genechip expression analysis probe arrays. This family of arrays was designed to provide a genomewide overview of the whole genome since they include markers for constitutional and cancer genes and omim and refseq genes.
It can read affymetrix chp files associated with affymetrix genechip arrays for expression assays only. Chromosome analysis suite chas thermo fisher scientific us. Affymetrix inc 20112012 the cytoscan hd cytogenetics solution. Data sheet josep carreras leukaemia research institute. A total of 43 different clinical syndromes were represented in the prospective clinical study. The ambion wt expression kit enables you to prepare rna samples for affymetrix whole. Later, the function aptparam creates a required object that indicates the correct system call to deal with aptcopynumbercyto from apt. Instructions for use ifu and assay limitations can be found at. Exceptional performancecoverage without compromisecy. Affymetrix was followed to obtain biotinlabeled dna. In order to identify diseaseassociated mirnas in precursor lesions of lung cancer, rna extracts from lungs of either craf transgenic or wildtype wt mice were hybridized to the agilent and affymetrix mirna microarray platforms, respectively.
The cytoscan platform is used extensively for research on hematological cancer nexus copy number for affymetrix has a set of tools that help uncover key genomic events in these projects. The cytoscan assay manual worflow is optimized for processing 8 to 24 samples at a time to obtain whole genome copy number and snp information from cytoscan arrays. Access and download the latest technical resources online, including product documentation, manuals, msdss, product support resources, faqs, videos, software. Affymetrix support by product for cytoscan hd array kit and. Jan 10, 2017 oncoscan microarray analysis is a reliable assay to assess human cancers for genomewide copy number changes. Materials needed for affymetrix genechip mirna arrays are listed on page 6.
The user needs to download the files corresponding to their own datas technology. Cytoscan hd suite includes cytoscan hd array, cytoscan reagent kit, the easytouse chromosome analysis suite chas, and the proven genechip instrument system. There are two steps to process the data from affymetrix cytoscan arrays with affy2sv. The probes on these arrays have been selected to be distributed throughout the entire length of each transcript. Evaluation of automatic class iii designation for affymetrix. Oncoscan ffpe assay kit, based on molecular inversion probe mip technology, offers. In a hypothetical assay failure in which pcr fragment size distribution observed on the pcr gel is. Ppt affymetrix cytoscan hd array powerpoint presentation. Affymetrix cytoscan dx assay is manufactured by affymetrix, inc. Genechip mirna array target protocol 1 protocol performed using the flashtag biotin hsr rna labeling kit affymetrix 901910 user manual pn 703095 rev. Chas enables you to view and summarize chromosomal aberrations across the genome.
Target snps yri snps from three snp discovery projects n y 2. Genetic landscape of a case of extraovarian peritoneal serous. Affymetrix launches new oncoscan ffpe assay kit aol. An example of it is affymetrix cytoscan family, that includes a highdensity array cytoscan hd and a light version array cytoscan 750k 23, 24. Genotype calling for affymetrix cytoscan hd array and cytoscan 750k array results. The elosa qc assay plate must be coated with dna spotting oligos the night before starting the labeling protocol.
This resulted in the detection of a range of mirnas varying between. Welcome to the affymetrix genechip expression analysis technical manual. Setting the argument textoutput to true the acii text format of these files is also generated. Affymetrix achieves first fda clearance of microarray. An r package to preprocess affymetrix cytoscan hd and 750k arrays for snp, cnv, inversion and mosaicism calling article pdf available in bmc bioinformatics 161 may 2015 with 382 reads. A crossplatform comparison of affymetrix and agilent. In january 2014, the food and drug administration approved affymetrix s postnatal blood test, cytoscan dx assay, looking at wholegenome correlates of congenital abnormalities and other causes of childhood developmental delay.
Cytoscan hd suite is the unrivaled standard in cytogenetics research and delivers with. See the troubleshooting section of the cytoscan assay user manual part number 703038 for more information. Evaluation of the affymetrix cytoscan dx assay for. Cytoscan hd suite is a complete cytogenetic microarray solution that includes cytoscan hd array, reagent kit, and the simple, userfriendly software, chromosome analysis suite chas.
Affymetrix created the cytoscan hd array by empirically selecting probes from a pool of over 20 million probes and then further. Contact the webmaster terms of use privacy policy terms of use privacy policy. Working with cychp files from affymetrix cytoscan hd lambda. If so, share your ppt presentation slides online with. Cytoscan 750k array, an optimized and streamlined assay, an allinclusive reagent kit, the proven genechip system 3000 instrumentation platform, stateoftheart affymetrix chromosome analysis suite chas software for data. Genetic landscape of a case of extraovarian peritoneal. Fda authorized for marketing the affymetrix cytoscan dx assay, which can detect chromosomal variations that may be responsible for a childs developmental delay or intellectual disability. Cytoscan 750k array, an optimized and streamlined assay. Once a fresh or freshfrozen sample is received in the laboratory, genomic dna is extracted. Affymetrix launches new oncoscan ffpe assay kit breakthrough assay provides genome wide solid tumor copy number analysis in only 48.
Affymetrix offers an expanding portfolio of customer support and. Novel genes associated with colorectal cancer are revealed. An example of it is affymetrix cytoscan family, that includes a highdensity array cytoscan hd and a light. Affymetrix achieves first fda clearance of microarraybased. The cytoscan dx assay consists of five reagent modules, wash buffers ws, a microarray kit, and analysis software. Affymetrix also claims that their cytoscan hd copy number values do not need paired samples, because they use an internal reference to determine copy number. Fda authorized for marketing the affymetrix cytoscan dx assay, which can detect chromosomal variations that may be responsible.
Cytoscan dx assay is a qualitative assay intended for the postnatal detection of chromosomal copy number variants cnv in genomic dna gdna obtained from peripheral whole blood in patients referred for chromosomal testing based on clinical presentation. Read microarray data from affymetrix genechip file. These arrays are excellent tools to perform gwas not only with snps but also with common and rare svs. Utilization of the oncoscan microarray assay in cancer. Amplified dna was labeled and further fragmented using an affymetrix cytoscan hd array kit and reagent kit bundle cat. All other trademarks are the property of their respective owners. The discrimination scoredescribes the ability of a probe pair to detect its. High fidelity copy number analysis of formalinfixed and paraffinembedded tissues using affymetrix cytoscan hd chip. See how easy it is to visualize expression data, alternative splicing, and mirnamrna networks.
405 1271 155 1254 696 1273 854 341 1441 673 738 545 1053 399 1207 1273 140 1315 1399 619 243 680 50 1239 383 328 557