Chromosome Analysis Suite software offers an intuitive and flexible workflow for genetic analysis and is specially tailored for cytogenetic use

Chromosome Analysis Suite (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). Recent updates to the software include features to aid in exon level copy number analysis. ChAS is comprised of three software applications: Reproductive Health Research Analysis Software (RHAS) for analysis worklfow setup and customization, Multi-Sample Viewer (MSV) for QC and copy number and variant analysis of your sample set, and ChAS for in depth analysis of individual samples.

Chromosome Analysis Suite 4.1 (ChAS 4.1)

The release of ChAS 4.1 enables you to enhance your analysis by:

  • Improving your mosaic and LOH sample analysis with the B-Allele Frequency (BAF) track for CytoScan 
  • Integrating your NGS data for visualization with your copy number data
  • Incorporating updated annotations, including RefSeq, Ensembl, and OMIM
  • 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 database contents in a histogram track 
  • Expanding your reporting options with the ability to export to Microsoft Word files, create paragraph-style segment tables, generate automatic report file names, and use a quick export button for all graphs and tables
  • Checking the duo/trio Mendelian consistency of your samples for both relatedness and identification of chromosomes with higher Mendelian error rates 
  • Automatically correcting the non-diploid status of your sample using the normalization workflow for CytoScan arrays or manually recenter samples when needed

Additional software files and sample data sets

Analysis files

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. Within RHAS you can download them from Preferences>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 of the files, and paste them into the ChAS Library, using the instructions in the ChAS 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

Required products