CytoScan™ 750K Training Kit (Available Outside US/Canada Only) - FAQs

It is critical to have correct size of the fragments for an optimal hybridization. The fragmentation reagent is very viscous, and it is easier to get a correct proportion of enzyme when a larger volume is used. Therefore, our recommendation is to always prepare a master mix for 24 samples, even if a smaller number of samples are processed.

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We can only guarantee the volume that is indicated on the label. Since our assurance guarantee is only provided for the label volume we advise not planning experiments or standard operating procedures based on potential overage volumes.

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After any stage in the assay (except digestion), samples can be stored at -20 degrees C if one is not proceeding directly to the next step. However, once a stage has been initiated, it must be completed before storage of the samples.

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CytoScan Reagent Kit (Cat. No. 901808) is validated for for 4 in-use freeze/thaw events but have to use the kit within a month (30 days) once opened even if they have not gone through 4 freeze-thaws.

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Both blood and cell line sample sources have been tested with the CytoScan assay.
Methods that include boiling or strong denaturants are not acceptable because the DNA would be rendered single-stranded. Genomic DNA extracted using the following methods have been tested at ThermoFisher Scientific:

QIAGEN - Gentra Puregene Kit
5 PRIME - PerfectPure DNA Blood Kit
The CytoScan assay requires genomic DNA concentration >50 ng/µL. Therefore, the elution volumes for each of the kits will need to be adjusted accordingly to achieve the desired concentration.

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DNA must be double-stranded genomic DNA.
DNA must be free of PCR inhibitors.
DNA must not be contaminated with other human genomic DNA sources or with genomic DNA from other organisms.
DNA must not be degraded.
DNA should have an A260/A280 between 1.7-2.1 (numeric rounding allowed).

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The CytoScan assay has been validated with blood and cell line samples.

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The use of the following magnetic racks is supported:
-DynaMag-2 Magnet (Cat. No. 123-21D)
-MagnaRack (Cat. No. CS15000)


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Pipetting viscous solutions using electronic pipettes may be very challenging and result in ineffective pipetting that could contribute to overall poor QC values. Therefore, the use of electronic pipettes is not recommended.

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For successful execution of the CytoScan assay, it is important that equipment be properly maintained and calibrated per the manufacturers specifications. Please be sure that the centrifuges, pipettes, thermal cyclers, and ThermoFisher Scientific equipment, including the 645 hybridization oven, fluidics station(s), and scanner, have had their recommended maintenance prior to running the assay. For lab equipment, it is typically a yearly calibration. For ThermoFisher Scientific equipment, there is typically a yearly preventative maintenance.

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CytoScan array CEL files are processed and analyzed in ChAS. This is a free download from the ThermoFisher Scientific web site. For processing and viewing the CEL files, a 64-bit computer with a minimum of 8 GB of RAM, is required. The recommended system specifications are included in the Chromosome Analysis Suite User Manual (Cat. No. 702943; http://assets.thermofisher.com/TFS-Assets/LSG/manuals/ChAS_Manual.pdf).

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Look at the serial number on the block. An “A” in the serial number indicates the block is aluminum; an “S” indicates it is silver. In addition, an aluminum block has a honeycomb appearance between the wells, whereas a silver block is smooth.

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Applied Biosystems GeneAmp PCR System 9700 (silver or gold-plated silver block only; do not use an aluminum block)
Applied Biosystems Veriti 96-Well Thermal Cycler
Bio-Rad DNA Engine PTC-200 Thermal Cycler
Eppendorf Mastercycler Pro S Thermal Cycler
Applied Biosystems 2720 (pre-PCR room only)

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The CytoScan assay requires either GeneChip Scanner 3000 7G System with Workstation and AutoLoader or GeneChip System 3000Dx v.2 and a GeneChip Hybridization Oven 645.

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CytoScan Cytogenetics Suite consists of CytoScan arrays and CytoScan Reagent Kit, GeneChip Command Console Software (AGCC), and Chromosome Analysis Suite (ChAS). It enables the performance of high-resolution, genome-wide DNA copy number analysis and also provides genotyping information for the detection of copy neutral loss/absence of heterozygosity (LOH/AOH), which can be used to detect uniparental isodisomy (UPD). The combination of high-resolution DNA copy number data and the ability to detect gains, losses, and UPDs on a single array makes CytoScan Cytogenetics Suite ideal for cytogenetics studies.

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Out of the six data files (ARR, AUDIT, DAT, CEL, CYCHP and CHPCAR), it is important to backup and archive the ARR, CEL, CYCHP and CHPCAR file at a minimum. This will allow you to maintain the ability to either reanalyze from the CEL file, or re-visualize the results using the CYCHP/CHPCAR files.

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A total of 6 files are produced that are key to the process:

ARR file - This file includes sample information
AUDIT file - This file is a log of the sample history
DAT file - This file is the raw data from the scanner
CEL file - This file is the gridded and processed data
CHPCAR file - This file stores user-annotated calls, interpretations, and modifications made to CHP file segment data
CYCHP file - This file is the output of ChAS and contains all of the analysis data

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Yes, genotypes can be generated in the Chromosome Analysis Suite (ChAS 3.3) Software. The software uses BRLMM for genotyping, which uses a Bayesian model based on prior clusters. This product is not intended for genome-wide association studies.

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Waviness SD failures can be caused by degraded DNA, an incompatible sample type, or a sample-specific effect. See the CytoScan Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf) and the Chromosome Analysis Suite User Manual (Cat. No. 702943) for more information.

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MAPD failures can be caused by assay drift due to variation in assay execution or over fragmentation. See the troubleshooting section of the CytoScan Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf) for more information.

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SNPQC failures can be caused by contamination of samples, equipment, or reagents. Other possible causes include over or under fragmentation of samples or a hybridization oven that is out of calibration. See the troubleshooting section of the CytoScan Assay User Manual (Cat. No. 703038) for more information (https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.