ChAS was developed with input from leading experts and is customized 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).
The release of the new ChAS 4.0, enables you to enhance your analysis by:
- Updating ISCN 2016 nomenclature
- Improving your mosaic and LOH sample analysis with the B-Allele Frequency (BAF) track for CytoScan
- Integrating your NGS data with the VCF file visualization feature and the updated hg38 annotation option
- Incorporating updated databases, including Ensembl and a link to ClinVar
- 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
- 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 NA36 (Hg38), which contains updated content from DGV, OMIM™, Ensembl, ClinVar, and RefSeq
Additional software files and sample data sets
GeneChip™ Command Console Software plug-ins
The Command Console (AGCC) Software workstation requires a software plug-in to scan CytoScan Cytogenetics Suite, OncoScan CNV Plus Assay, and OncoScan CNV Assay 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.
A fluidics script necessary for the AGCC workstation must be downloaded and installed prior to the first run.
ChAS requires sets of analysis files to create and visualize copy number, LOH, and genotyping data files for CytoScan Cytogenetics Suite, OncoScan CNV Plus Assay, and OncoScan CNV Assay arrays.
To download these files into the appropriate ChAS library folder from within the software, use the Help>Update Library and Annotation Files functionality or download them from the Analysis Workflow using Utilities>Download Library Files.
Alternatively, to copy the files into your ChAS Library folder manually, download the Analysis Files.zip to the data analysis workstation, extract the zip archive, open the folder containing the files, copy all the files, and paste them into the ChAS Library, using the instructions in the ChAS 4.0 User Guide located in the ChAS software zip package.
Sample data sets
The sample data zip package for the different array types includes data files and a description key document:
CytoScan HD Array
CytoScan 750K Array
OncoScan CNV Plus Assay
For Research Use Only. Not for use in diagnostic procedures.