Make confident decisions with trusted microarray solutions, from samples to insights
Thermo Fisher Scientific empowers cytogenetics researchers globally with data analysis software that is intuitive, simplified, and offers flexible workflow. Our software enables you to view and summarize chromosomal aberrations across the genome. Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss of heterozygosity (LOH).
Workflow
Thermo Fisher Scientific offers powerful microarray solutions for prenatal and postnatal clinical research that are powered with robust workflows that make it easy to enable consistent, reliable, and high-quality results.
Our complete microarray research platform, the CytoScan Cytogenetics Suite, includes hybrid-SNP arrays, automated and manual target preparation options, fully kitted reagents, the GeneChip System 3000 instrument for array processing, and Chromosome Analysis Suite (ChAS) software for data interpretation and reporting. These tools support laboratories to help maximize operational time.
Chromosome Analysis Suite Software (ChAS)
Developed with input from leading experts, Chromosome Analysis Suite (ChAS) software is designed specifically for copy number and cytogenetics research analysis and reporting. We work with our customers, listen to their valuable feedback, and continually empower them with enhanced features to make data analysis simpler and more intuitive.
ATTENTION: New process for changing the ChAS 4.5 DB administrator password
- Remember the new password after changing the ChAS DB administrator password
- Create another administrator user (as a backup to the admin user)
- Back up the ChAS database regularly, especially after modifying the database. If the password is forgotten, locate the last database backup, then:
- Uninstall ChAS 4.5
- Reinstall ChAS 4.5
- The ChAS DB administrator password will be restored to the default and then can be changed
- Restore the last database backup
Key features of ChAS are:
- Analyze copy number, mosaicism, and loss of heterozygosity (LOH) segment data at different levels of resolution
- Automatically prioritize segment data using scoring inspired by the American College of Medical Genetics and Genomics
- Customize and load your own annotations and regions for focused analysis
- Store, query, and display historic sample data and annotations for streamlined analysis
- Application programming interfaces (APIs) to push and pull segment coordinates in and out of ChAS software
- Automatic generation of a results file with zero manual setup required
Enhance your genetic data analysis with the new ChAS 4.5 software
- ChAS CEL Uploader installed in the workstation
- Option to change the default administrator password for increased security
- Left-right scroll button within the "Detail View" for easier scrolling
- New disorder-causing OMIM genes track for better navigating OMIM genes with aphenotype map key value of three
Updated mosaic segmentation algorithm with VCF visualization
- Improve mosaic segmentation in both detection as well as breakpoint accuracy
- Co-visualize NGS and microarray data together
Segment prioritization
- Access supporting evidence for segment prioritization. Add custom annotations prior to uploading into your personal ChAS database for reference in future sample investigation.
- Choose between two prioritization methods to suit your individual needs
Multi-Sample Viewer
- Load samples from ChAS software into the Multi-Sample Viewer (MSV) to visualize cohorts of samples simultaneously. Install the MSV as part of the Reproductive Health Analysis Software.
- Display database contents in a histogram track
- Expand 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
CytoScan Automated Interpretation and Reporting (AIR) Solution
Streamline genetic analysis to help increase productivity with consistent data interpretation and reporting.
Franklin by Genoox is an end to end research solution for the analysis of genetic data with advanced AI-driven interpretation. With CytoScan AIR, our customers can combine the power of both, ChAS and Franklin, to augment the visualizations of CNV gains, losses, and LOH with clinical research interpretation information.
Featured video
An overview of the ChAS features and updates.
ChAS training videos
Compare your current analysis pipeline and see what features you may be missing out on.
In addition to the support offered from our technical teams, we now offer these convenient on-demand training videos. They are easy to follow, cover a wide range of topics, and are each designed to be viewed in only 20-40 minutes. Whether you’re a seasoned expert looking for a refresher or a potential new user to ChAS, the videos offer helpful training when your schedule allows.
ChAS training modules:
1. ChAS Software Installation
2. Analysis Workflow Overview
3. Overview of the ChAS Browser
4. CNV and LOH Data Review
5. ChAS Database Overview
6. CytoRegions and Overlap Map: AED and BED Files
7. Sample case complete analysis workflow
8. ChAS version 4.2.1 features
Reproductive Health Analysis Software (RHAS)
RHAS for cytogenetic and variant analysis enables visualization and summarization of chromosomal aberrations, genotyping of specified variants.
RHAS provides tools to:
- Perform single sample copy number analysis of CEL files for CytoScan HT-CMA array plates.
- Perform genotyping of CEL files from CytoScan HTCMA
- Run QC, copy number, genotyping, variant calling, and SMN testing algorithms in selected workflows
- View sample QC cata in tables and graphs
- View variant data in cluster plots for all probe sets.
- View variant data in tables or as a batch summary
- Export your data in various formats for use in 3rd party software
- View SMN testing results in table and graphical formats
Analysis files
ChAS software requires sets of analysis files to create and visualize copy number, LOH, and genotyping data files for CytoScan Suite.
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.
Highlighted resources
There isn’t a way to reset it if you do not remember the password.
Best practices for ChAS database password change
- Remember the new password after changing the ChAS DB administrator password
- Create another administrator user (as a backup to the admin user)
- Back up the ChAS database regularly, especially after modifying the database. If the password is forgotten, locate the last database backup, then:
- Uninstall ChAS 4.5
- Reinstall ChAS 4.5
- The ChAS DB administrator password will be restored to the default and then can be changed
- Restore the last database backup
The sample data zip package for the different array types includes data files and a description key document.
CytoScan HD Accel Arrays
CytoScan HD arrays
For Research Use Only. Not for use in diagnostic procedures.