Affymetixs competitors in the dna microarray business include illumina, ge healthcare, applied biosystems, beckman coulter, eppendorf biochip systems, and agilent. Analyze cel intensity data to generate sequence data view the chp analysis results create reports export data in formats that can be used by other software applications to start gseq. Application areas include plant and animal genomics and transcriptomics, including basic research, technologies for breeding, population diversity and conservation, trait analysis, cancer research. Genechipcompatible software providers thermo fisher. Comparison of identical single nucleotide polymorphisms. Genechip sequence analysis software gseq enables scientists to perform comparative sequencing by providing highquality sequence information and automatic detection of snp sites in a single analysis package. Genechip targeted genotyping analysis software gtgs. For the first snp arrays, affymetrix designed software modules mpam, dm to genotype individual snps, one array at a time. Affymetrix microarray analysis software are freely available for the. The genechip scanner 3000 7g is an extension of the genechip scanner 3000 gcs 3000 series that allows you to scan nextgeneration higherdensity arrays, including snp arrays with up to 900,000 snps, tiling arrays for transcription and allexon arrays for wholegenome analysis. Axiom genomewide array plates human and nonhuman axiom mydesign array plates. Genotyping analysis software gtype support materials.
The genechip fluidics station 450 is used for the wash and stain operation of genechip arrays. The cgf offers several affymetrix snp genotyping microarray assays for fresh and ffpet samples. A quartet consists of match and mismatch probes for the two alleles. Arraystar is a desktop gene expression analysis software package designed to work with normalized affymetrix genechip expression data files. The arrays were scanned individually using the genechip scanner 3000 7g under the genechip operating software gcos. Genechip sequence analysis software gseq thermo fisher. Affymetrix genechip genotyping analysis software gtype.
Application areas include plant and animal genomics and transcriptomics, including basic research, technologies for breeding, population diversity and conservation, trait analysis, cancer research, and clinical validation and cytogenetics. Aug 15, 2008 the probe arrays were scanned after the staining and washing protocols were completed. Affymetrix genechip genotyping analysis software gtype is part of the genechip mapping array system, specifically designed to give highly accurate, automated snp allele calls for the genechip mapping arrays. There are only four molecules, or bases, in every dna chain. Thermofisher scientific affymetrix affymetrix genechip products, tools, and resources help advance the work of researchers via microarray analysis. In addition, the affymetrix custommade genechip targeted genotyping tg.
Gtgs is specifically designed to give highly accurate, automated snp allele calls for the targeted genotyping mip assay, available for both. In addition, gcos contains an embedded database that manages both experiment information and data. Read microarray data from affymetrix genechip file matlab. Snp genotyping of saliva dna using affymetrix genechip. Stratagene array assist lite, affymetrix genechip sequence analysis software gseq, affymetrix genechip genotyping analysis software. Snp genotyping of saliva dna using affymetrix genechip targeted genotyping system a comparison of the performance of paired blood and saliva dna samples in the affymetrix genechip targeted genotyping assay trena a. Microarray analysis software thermo fisher scientific us. The company also manufactured machinery for high speed analysis of biological samples, and its genechip operating software as a system for managing affymetrix microarray data. Logratios and allelespecific measurements can be easily imported into infoquant software from cychp or cnchp files generated using affymetrix chromosome analysis suite or genotyping console respectively. The company also manufactured machinery for high speed analysis of biological samples, and its genechip operating software as a system. In addition, gtype was developed to enable workflows for a variety of snp mapping applications. Affymetrix provides a suite of products designed for researchers exploring the role of copy number in human disease. Raw data were acquired from the scanner using the gcos software.
Xp support and validation for affymetrix software and instrumentation pdf, 122 kb. A call rate of greater than or equal to 93 percent at a dm confi dence threshold of 0. Affymetrix is a brand of dna microarray products sold by thermo fisher scientific that. Free affymetrix analysis software transcriptome analysis console tac. Fasttrack genotyping services group for analyzing infinium genotyping data with the illumina genomestudio genotyping module to optimize call rates. Affymetrix genechip genotyping analysis software gtype 4. Automated genotype calls in software the genechip human mapping 500k array set is used in conjunction with genechip genotyping analysis software gtype, which uses an automated, modelbased genotypecalling algorithm that provides a confidence score for each individual genotype. High throughput genotyping and gene expression microarrays. The affymetrix genotyping console software enables rapid primary analysis and quality checking of genotyping data generated by the affymetrix genechip and genetitan platforms. Perform snp genotyping analysis on data generated from. Affymetrix support by product for genechip genotyping. With multiple genomic targets potentially contributing to disease, analysis requires flexibility and accuracy. Affymetrix genechip targeted genotyping analysis software.
Genotyping analysis software gtype pdf, 236 kb manuals. The dynamic model algorithm dm, 2 generates a qc call rate for each array. Affymetrix genechip snp oneclickgch, cgh fusion and cntrack are fully affymetrixcompatible solutions. With illumina human genotyping arrays, you can choose expertly designed content, use consortiumdeveloped markers, or customize array content according to your research objectives. Gtgs is specifically designed to give highly accurate, automated snp allele calls for the targeted genotyping mip assay, available for both applicationspecific fixed assays and custom snp assays. The nucleotide sequence is assessed for the presence of drugassociated resistance mutations by comparison to an hiv1 pol gene reference library defined as wild type by the manufacturer and derived from the analysis of 200 drugnaive.
Gseq provides an integrated analysis workflow to enable highcontent, highthroughput, and accurate sequencing applications. Genechip arrays are the result of the combination of a number of technologies, design criteria, and quality control processes. Genechip command console software thermo fisher scientific fr. All protocols included in this manual have been used successfully by scientists at affymetrix, or have. Compatible with all the commercially available genechip analysis. Following its release of new snp arrays called genechips. Different statistical principles and ideas have been applied to the construction of genotyping algorithms for example, likelihood versus bayesian modelling, and whether to genotype one or all arrays at a time. Oct 07, 2008 lgcs kasp genotyping chemistry explained.
Genotyping analysis software gtype pdf, 447 kb additional support. Genechip sequence analysis software gseq genechip targeted genotyping analysis software gtgs cytoscan optima suite genechip fluidics station scripts genechip instrument control ic software genechip scanner 3000 highresolution scanning patch genechip operating software gcos service pack 2 software update tiling array tools. Reproducibility of genotypes as measured by the affymetrix. Snp genotyping data analysis genomestudio software enables efficient snp genotype calling, data normalization, loss of heterozygosity loh calculation, cnv analysis, and more. Our microarray solutions provide trusted performance and support highthroughput, multiplex processing for largescale population studies, clinical research, and. The data was processed using the affymetrix genotyping analysis software gtype with the brlmm calling algorithm. Affymetrix is dedicated to developing stateoftheart technology for acquiring, analyzing, and managing complex genetic information for use in biomedical research. The instrument includes design advancements to provide improved ease of use and true walkaway freedom dramatically improving efficiency in your genetic analysis. Genotyping analysis software gtype support materials for more information, please see the product page. Microarray data analysis is the final step in reading and processing data produced by a microarray chip. How affymetrix genotyping microarrays work all genechip microarrays use the natural chemical attraction between dna molecules.
Some platforms permit users to pick custom snps but the highest throughputs are available only in fixed contents. It can read affymetrix chp files associated with affymetrix genechip arrays for expression assays only. If a custom cluster file is required, clustering should be done. This software integrates single nucleotide polymorphism snp, copy number polymorphism cnp and loss of heterozygosity loh analyses into one application. Affymetrix support by product for genechip genotyping analysis. User guide, affymetrix genechip sequence analysis software. The affyread function can read affymetrix exp, dat, cel, clf, bgp, cdf, and gin files associated with affymetrix genechip arrays for expression, genotyping snp, or resequencing assays. These applications provide analysis solutions for affymetrix genotyping arrays, which are used for genomewide linkage or association studies. Genechip sequence analysis software gseq is used to analyze data from the resequencing arrays gseq allows you to. Many different genotyping approaches are available low to high throughput 2. Genechipcompatible software providers thermo fisher scientific.
Genechip command console software provides an intuitive set of tools for instrument. The command console software provides an intuitive set of tools for. The dm software was introduced with the release of the 100 k genechip and is based on statistical modelling of quartets. The data was processed using the affymetrix genotyping analysis software. Genechip targeted genotyping analysis software gtgs is part of the genechip targeted genotyping system. The easytouse software provides users with stateoftheart visualization and statistical analysis tools that are useful in monitoring expressionlevel changes throughout your experiments and in. Multiple formats will be required to carry out most projects targeting. This manual is a technical guide for using genechip expression analysis probe arrays. Export the data to other software applications for further study introduction affymetrix genechip sequence analysis software gse q 4. Affymetrix genechip products, tools, and resources help advance the work of researchers via microarray analysis. Data acquisition and basic analyses genechip command console agcc.
Genechip genotyping analysis software gtype, which uses an automated, modelbased genotype calling algorithm that provides a confidence score for each individual genotype. Snp genotyping and copy number variation cnv data analysis tools can analyze results for millions of markers and probes and detect sample outliers, providing insight into the functional consequences of genetic variation. Snp genotyping of saliva dna using affymetrix genechip targeted genotyping system. Analysis begins with preliminary sample quality evaluation to determine which samples may require reprocessing or removal. The data from the scanned array are analyzed by using the genechip software, version 3. Samples undergo various processes including purification and scanning using the microchip, which then produces a large amount of data that requires processing via computer software. High throughput microarrays school of biological sciences. Visit cytogenetic analysis with microarrays for information about genechip array solutions for. The dynamic model algorithm dm, 2 generates a qc call rate. The companys first product, an hiv genotyping genechip, was introduced in 1994 and the. Thermofisher scientific affymetrix research instruments. The genechip operating software gcos is an operating system software that controls our instruments, acquires data, and executes gene expression analysis. Human genotyping microarrays for population and disease studies.