Affymetrix support by product for cytoscan hd array kit and. I am currently analyzing copy number variant data from affymetrixs cytoscan hd platform on 45 cancer tumor samples. Cytoscan dx microarrays and reagents were each randomly selected from 3 design validation lots and 12 replicates of the gdna samples were tested with cytoscan dx. The cytoscan 750k array contains probes which are empirically selected from the cytoscan hd array, for more than 750,000. It outlines various features within the analysis workflow module including normal. Microarray hybridization and analysis were performed according to the manufacturers instructions, unless otherwise noted. Cytoscan hd suite is the unrivaled standard in cytogenetics research and delivers with. Evaluation of automatic class iii designation for affymetrix. The applied biosystems cytoscan hd suite, which comprises microarrays, reagents, and analysis software, is a comprehensive, highresolution wholegenome solution designed to assist in the understanding and characterization of biomarkers in hematological malignancies. Rare copy number variants analysis identifies novel candidate. Chromosome analysis suite chas software for data visualization and analysis, and full service and support.
Id like to do cnv analysis on tumor samples frozen tissue to detect large arm level cnv as well as focal loh, amplification, homozygous deletion. Chromosome analysis suite chas software support materials. Home products microarray solutions instruments and software software 2. Cel files are analyzed using the chromosome analysis suite chas software thermo fisher scientific, inc and converted to cychp files. By using the highresolution cytoscan hd array with chas software, it is easy to distinguish between aberrations and artifacts. The full cytoscan dx assay, including the cytoscan dx array, the testing reagents, analysis software, and hardware platform, was approved for the specified indications. Cytoscan hd array kit and reagent kit bundle zip, 500 kb library files. Jul 20, 2015 this video walks through converting cel files to cychp or oschp files using the chas analysis workflow module. A snp array analysis cytoscan hd snp affymetrix confirmed this hypothesis. Affymetrix support by product for chromosome analysis suite.
We describe rawcopy, an r package for processing of. An example of it is affymetrix cytoscan family, that includes a high density array cytoscan hd and a light version array cytoscan 750k 23, 24. To investigate whether ffpe tissues are suitable for cytoscan hd analysis, dna from the matched ffpe tissue samples was extracted. Affymetrix cytoscan hd for autism spectrum disorder in.
Download the agcc cytoscan hd array software plugin zip, 91. Current array cgh based patient reference dna required two color utilizes cy dyes. The study demonstrated that rare cnvs play an important role in the pathogenesis of htx in patients. Cytoscan 750k suite is a complete cytogenetic microarray solution that includes cytoscan 750k array, reagent kit, and the simple, userfriendly software, chromosome analysis suite chas. The recent use of cma platforms that combine classic copy number analysis with singlenucleotide polymorphism snp genotyping has increased the diagnostic yields. We used chromosomal microarray analysis cma a cytoscan hd affymetrix, santa clara, ca, usa to. 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. Microarray handson training on the entire microarray assay workflow, from experimental design and target preparation through instrument use, quality control, and data analysis.
Exceptional performancecoverage without compromisecy. Affymetrix cytoscan hd kit bundle microarray analysis. Cytoscan hd suite has greater than 99% sensitivity and can reliably detect 2550kb copy number changes across the genome at high specificity with singlenucleotide polymorphism snp allelic corroboration. The cytoscan hd cytogenetics solution is a complete. The most common software to analyze cytoscan data is called chromosome analysis suite chas 25. Abstractdetection of human genome copy number variation cnv is one of the most important analyses in diagnosing human. Chromosome analysis suite is a software offering intuitive analysis tailored for. 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.
Ppt affymetrix cytoscan hd array powerpoint presentation. Data sheet josep carreras leukaemia research institute. However, balanced chromosomal rearrangements such as inversions or balanced translocations could be potentially missed on the cytoscan hd microarray. Highthroughput free fulltext the cytoscan hd array in. Microarray hybridization and analysis we performed microarray analysis of isolated genomic dna with three different commercially available microarray platforms. Autism spectrum disorder asd is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number. Get results quickly with a streamlined analysis workflow summarize chromosomal aberrations. The complete cytoscan hd cytogenetics solution includes cytoscan hd array, cytoscan reagent kit, easytouse chromosome analysis suite chas software, and the proven genechip instrument system. Affymetrix cytoscan hd array 1 affymetrix cytoscan hd array 2 cytoscan hd vs current array. View and summarize genomewide chromosomal aberration data from the cytoscan hd suite with just a few clicks using chas software. The cytoscan dx assay consists of five reagent modules, wash buffers ws, a microarray kit, and analysis software. Comprehensive performance comparison of highresolution array.
Chromosome analysis suite chas thermo fisher scientific us. Here we discuss the application of the cytoscan high density hd snparray for the detection of cnvs. Jul 20, 2015 for the love of physics walter lewin may 16, 2011 duration. Cel files are analyzed using the chromosome analysis suite chas software thermo fisher scientific, inc and converted to cychp files containing information on copy number, loss of heterozygosity loh, mosaicism, and genotype calls. Oct 31, 2016 microarray data is subject to noise and systematic variation that negatively affects the resolution of copy number analysis. Comprehensive performance comparison of highresolution. Patients with multiple primary cancers mpcs are suspected to have a hereditary cancer syndrome. Microarray data is subject to noise and systematic variation that negatively affects the resolution of copy number analysis. Epigendx dna methylation and pyrosequencing service.
Jan 31, 2017 patients with multiple primary cancers mpcs are suspected to have a hereditary cancer syndrome. Cytoscan hd cytogenetics solution the complete cytoscan hd cytogenetics solution includes cytoscan hd array, cytoscan reagent kit, easytouse chromosome analysis suite chas. High fidelity copy number analysis of formalinfixed and. Copy number variation and regions of homozygosity analysis. Improved copy number analysis with affymetrix arrays. Genotyping console software or chromosome analysis suite. Evaluation of the affymetrix cytoscan dx assay for. Cytoscan hd suite has greater than 99% sensitivity and can reliably detect 2550kb copy number changes across the genome at high specificity with singlenucleotide polymorphism snp. Apr 24, 2017 the platform specific software cnv call sets for the cytoscan hd array were obtained using the chas software affymetrix inc. Cytoscan hd microarray is a good method for copynumber analyses. May 25, 2018 autism spectrum disorder asd is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants cnv. Cytoscan dx microarrays and reagents were each randomly selected from 3 design validation lots and 12 replicates of the gdna samples were tested with cytoscan dx reagents and array at storage time 3 months. Cel files are analyzed using the chromosome analysis suite chas software thermo. Cel files are analyzed using the chromosome analysis suite chas software thermo fisher scientific, inc and converted to cychp files containing.
Copy number variant analysis was performed on all 19 patients and available family members if a cnv was identified with the. Here we discuss the application of the cytoscan high density. The platform specific software cnv call sets for the cytoscan hd array were obtained using the chas software affymetrix inc. The affymetrix chromosome analysis suite chas software is tailored to cytogenetic research analysis and reporting. Cytoscan hd suite includes cytoscan hd array, cytoscan reagent kit, the easytouse chromosome analysis suite chas, and the proven genechip instrument system. The cytoscan hd array in the diagnosis of neurodevelopmental. A variety of storage, freezethaw, in use and inversion conditions were tested. Exceptional performancecoverage without compromise. 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. Chromosome analysis suite chas thermo fisher scientific ng. For the love of physics walter lewin may 16, 2011 duration. The dependence of array analysis on fresh frozen tissues significantly limits its application in clinical setting.
This video walks through converting cel files to cychp or oschp files using the chas analysis workflow module. Rare copy number variants analysis identifies novel. The aim of the study was to identify new candidate genes for asd in the studied cohort of asddiagnosed patients. Cytoscan hd array, reagent kit, and the simple, userfriendly software. Cytoscan hd together, cytoscan hd array solution along with the command console and chromosome analysis suite software, enable you to perform highresolution genomewide dna copy number analysis.
Childrens mercy hospital experience with neoplastic samples validation of affymetrix cytoscan hd. The dependence of array analysis on fresh frozen tissues significantly limits its. The cytoscan dx assay has a similar probe content to the cytoscan hd array, which has been used previously by independent clinical laboratories and for research purposes. View and summarize genomewide chromosomal aberration data from the cytoscan hd suite with just a. It outlines various features within the analysis workflow. Highthroughput free fulltext the cytoscan hd array. Cytoscan 750k suite was designed to provide the most comprehensive coverage and.
The combined high resolution dna copy number data and the ability to detect gains, losses, and upds on a single array makes the cytoscan hd. Childrens mercy hospital experience with neoplastic samples cooley, linda d fiedler, stephanie d joyce, julie m mouron, barbara. The applied biosystems cytoscan hd suite, which comprises microarrays, reagents, and analysis software, is a comprehensive, highresolution whole. A comprehensive microarray workflow provides streamlined detection and analysis. Affy has told us that the control is unnecessary because their absolute values are accurate. Locate and download the zipped axiom analysis suite software package. Most of the clinical samples are in the form of formalinfixed and paraffinembedded tissue blocks. Cytoscan hd cytogenetics solution the complete cytoscan hd cytogenetics solution includes cytoscan hd array, cytoscan reagent kit, easytouse chromosome analysis suite chas software, and the proven genechip instrument system. Cytoscan hd suite was designed to provide the most comprehensive coverage and highest performance for detecting chromosomal aberrations in a broad range of sample.
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