Microarray Analysis Software for Postnatal Genetic Research

Reproducible results with powerful microarray analysis

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 research solutions for postnatal clinical research that are powered with robust workflows that make it easy to obtain 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 Software (ChAS) 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

There is no way to reset the password if it is forgotten. 
  • 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 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.

  • AI-driven data interpretation and reporting: Consistent, accurate results available in seconds so researchers can focus on discovery.
  • Improved evidence support: options for segment prioritization including the most up-to-date American College of Medical Genetics (ACMG) classifications, phenotype matching, literature searches and historic data.
  • Customized reporting: Inuitive and simple-to-use interface enables easy customization, reporting, evaluation, and sign-off.
  • Database management and expansion: Access to Franklin knowledge base enables users to link evidence with observations and assessments for internal database development and curation.
  • Actionable insights: Community driven cytogenetics research platform provides more than 350,000 shared classifications of variants and advanced metrics.

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 data 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 third-party software
  • View SMN testing results in table and graphical formats

Analysis files

ChAS 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.