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Chromosome Analysis Suite (ChAS)  

Chromosome Analysis Suite is a software offering intuitive analysis tailored for cytogenetics. Now ChAS 3.1 includes a database and automatic diploid-centering algorithm.

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Chromosome Analysis Suite (ChAS) provides an intuitive and flexible workflow for accurate analysis.

ChAS was developed with input from leading experts and is tailored for copy number and cytogenetics research analysis and reporting. ChAS enables you to view and summarize chromosomal aberrations across the genome. Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss/absence of heterozygosity (LOH/AOH).

Chromosome Analysis Suite 3.1 (ChAS 3.1)

With the release of the new ChAS 3.1, you will now be able to enhance your analysis by

  • Accessing a database for storing and querying segment data and annotations either locally (by a single user) or installed on a server/common workstation (multi-person use)
  • Displaying the entire (or relevant subset) database contents in a histogram track
Histogram track view
Histogram Track View
Segment intersections view
Segment intersections view
  • Comparing your current sample with segments in the database by using the segment intersections view
  • Expanding your reporting options with the ability to export to Microsoft® Word, create paragraph-style segment tables, generate automatic report filenames, and utilize a quick export button for all graphs and tables
  • Integrating your expression and copy number data with the Concurrent Molecular Analysis Profiling (CoMAP™) capability
  • Checking the duo/trio Mendelian consistency of your samples for both relatedness and identification of chromosomes with higher Mendelian errors rates
  • Automatically correcting the non-diploid status of your sample using normalization workflow for CytoScan® arrays
  • Using the new NetAffx® Genomic Annotation file NA33.1 (Hg19), which contains updated content from DGV, OMIM®, and RefSeq
Non-diploid normalization workflow
Non-diploid normalization workflow

For the full lists of new features, please download the latest release notes.

To install onto one or more analysis workstations or servers, download the ChAS zip file, extract the zip archive, and install by following the instructions in the Installation Instructions found in the ChAS 3.1 User Guide.

Download and install the CHAS 3.1.1 patch after installing ChAS 3.1

Hardware and Software Requirements, ChAS 3.1 (pdf, 121 KB)

Additional software files and sample datasets

GeneChip® Command Console® Software plug-ins
The Command Console® (AGCC) Software workstation requires a software plug-in to scan CytoScan® Cytogenetics Suite and OncoScan® FFPE Assay Kit arrays. Download the .zip file to the AGCC Software workstation, extract the archives, and install by following the instructions in the Installation Instructions file. AGCC library files are automatically installed when the .exe file is run.
Download the AGCC® CytoScan® HD Array Software plug-in (zip, 91.7 MB)
Download the AGCC® CytoScan® 750K Array Software plug-in (zip, 91.7 MB)
Download the AGCC® OncoScan® FFPE Assay Kit Software plug-in (zip, 97 MB)

Fluidics Scripts
A fluidics script necessary for the AGCC workstation must be downloaded and installed prior to the first run.
Download the Fluidics Scripts

Analysis files
Chas requires sets of analysis files to create and visualize copy number, LOH, and genotyping data files for CytoScan Cytogenetics Suite and OncoScan FFPE Assay Kit arrays:

Sample datasets
The sample data zip package for the different array types includes data files and a description key document:

CytoScan® HD Array
CytoScan® HD Array Sample Data Files (zip, 1.6 GB)
CytoScan® HD Array Sample Dataset Presentation (pdf, 3.13 MB)

CytoScan® 750K Array
CytoScan® 750K Array Sample Data Files (zip, 310 MB)
CytoScan® 750K Array Sample Dataset Presentation (pdf, 3.8 MB)

OncoScan® FFPE Assay Kit
OncoScan® FFPE Assay Sample Data (zip, 78 MB)
OncoScan® FFPE Assay Sample Data Presentation (pdf, 1.31 MB)

ChAS training videos
A collection of online training videos on the ChAS software provides step-by-step instructions for analyzing a sample.
Watch online ChAS general training videos


For Research Use Only. Not for use in diagnostic procedures.

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