1. Agilent CytoGenomics 1.5 For Detection of CNC, LOH and UPD
Not approved for use in diagnostic procedures
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2. Agilent CytoGenomics 1.5 Value Proposition
Streamlining the Cytogenetic data analysis workflow for CNC (copy number changes) and/or cnLOH (copy neutral Loss of Heterozygosity) / UPD (uni-parental disomy) detection of samples processed on Agilent SurePrint G3 CGH and CGH+SNP Microarrays.
Value Proposition:
To enable the Cytogenetic Researcher to analyze a normal constitutional CGH (or CGH+SNP) sample in less than 5 minutes, including report generation.
Not approved for use in diagnostic procedures
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3. Agilent CytoGenomics 1.5 System specs
Client/server system with database.
Possible configurations:
multiple clients can access central database simultaneously.
server
Client(s) and Server (Database)on separate machines
Client 1
Client 2
Client and Server (Database) on same machine
Not approved for use in diagnostic procedures
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4. Agilent CytoGenomics 1.5 System specs
Supported OS for the PC: XP, Windows 7.
Supported OS for the Mac: OS X Leopard, OS X Snow Leopard.
Supported on both 32 and 64 bit machines.
Minimum of 4GB of memory needed for 32 bit (8GB for 64 bit).
FE (Feature extraction) is integrated component of CytoGenomics software.
Not approved for use in diagnostic procedures
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5. 1. Configure analysis method
Agilent CytoGenomics 1.5 Workflow based system
Preloaded default workflows available
Customizing your workflow:
Day to day usage:
Technician (manual) / Auto-processing mode
Upload TIFF images
Map array to sample ID and other attributes
Engage configured workflow to run FE and analysis
Scientist
Manual analysis / triage the sample and sign off
Generate the CytoReport
1. Configure analysis method
2. Configure CytoReport
3. Configure Workflow
Not approved for use in diagnostic procedures
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6. Agilent CytoGenomics 1.5 Streamlined data analysis and reporting for Cytogenetic research labs
Fast 5-minute data analysis and report generation for a normal constitutional sample.
Convenient input and output support allowing for integration with LIMS.
Cyto
report
Manual analysis & sign off
Run data
analysis
Sample info
Laboratory LIMS
Not approved for use in diagnostic procedures
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7. Measuring SNPs using restriction enzymes
Genotype SNPs using restriction digestion (Alu/Rsa)
We measure the copy number of one allele at each SNP site relative to a known reference
Regions of LOH are located by finding genomic regions with a statistically significant scarcity of heterozygous calls
~5-10 Mb LOH/UPD resolution across the entire genome
Not approved for use in diagnostic procedures
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8. Agilent CytoGenomics 1.5 Powerful algorithms for calling CNC, LOH and UPD
Log2 ratio of
intensities to call CNCs
No. of uncut alleles
to call LOH/UPD
Feature
Extraction AA AB BB
ADM-1
ADM-2
SNP CN & LOH
GC correction
Not approved for use in diagnostic procedures
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9. Agilent CytoGenomics 1.5 Example: Consanguineous Sample
SNP data detects blocks of cnLOH throughout the genome AA AB BB
Not approved for use in diagnostic procedures
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10. Agilent CytoGenomics 1.5 Example: Sample with deletion on chr9 p-arm
One copy deletion confirmed by SNP data A A B AA AB BB
Not approved for use in diagnostic procedures
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11. Agilent CytoGenomics 1.5 Sample Triage – Access to external databases
Upload custom tracks
Not approved for use in diagnostic procedures
Link out from genes associated with aberrations to external Databases: DGV, OMIM, Entrez
Link out to and compare aberrations in DGV and UCSC genome browser
Preloaded tracks: DGV-CNV
Not approved for use in diagnostic procedures
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12. Agilent CytoGenomics 1.5 Sample Triage – Sample and Aberration annotation
Add notes to sample
Add notes to aberrations
Not approved for use in diagnostic procedures
Classify aberrations
Edit aberrations
Suppress aberrations
Not approved for use in diagnostic procedures
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13. Agilent CytoGenomics 1.5 Sample Triage – Using the CytoGenomics in house Database
Auto updated tracks based on aberration classification in CytoGenomics Database
Showing number of samples with overlapping aberrations in database
Not approved for use in diagnostic procedures
Right click on Classification allows query for overlapping aberrations in database: results will be shown as new track along the gene view
Not approved for use in diagnostic procedures
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14. Agilent CytoGenomics 1.5 Multi Sample View
Sample A
Sample B
Sample C
Comparing 2 or more samples side by side
Not approved for use in diagnostic procedures
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15. Agilent CytoGenomics 1.5 Key feature summary
Easy 5 minute data analysis for constitutional normal sample, including report generation.
Powerful algorithms for detecting CNC, cnLOH and UPD.
Interval classification and database queries for similar aberrations.
Workflow Automation Mode for automatic processing of TIFF images and report generation.
Linking out to external databases such as OMIM, DGV and Entrez.
Data upload to ISCA DB via Cartagenia bench.
Help videos available inside the software explaining key functionality.
Download CytoGenomics free
Not approved for use in diagnostic procedures
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