Agilent CytoGenomics 1.5
For Detection of CNC, LOH and UPD
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Not approved for use in diagnostic
procedures
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 (uniparental 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.
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Not approved for use in diagnostic
procedures
Agilent CytoGenomics 1.5
System specs
• Client/server system with database.
• Possible configurations:
server
Client 1
Client and Server (Database) on same machine
Client 2
Client(s) and Server (Database)on separate machines
• multiple clients can access central database simultaneously.
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Not approved for use in diagnostic
procedures
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.
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Not approved for use in diagnostic
procedures
Agilent CytoGenomics 1.5
Workflow based system
• Preloaded default workflows available
• Customizing your workflow:
1. Configure analysis
method
2. Configure CytoReport
3. Configure Workflow
• Day to day usage:
– Technician (manual) / Auto-processing mode
1.
Upload TIFF images
2.
Map array to sample ID and other attributes
3.
Engage configured workflow to run FE and analysis
– Scientist
1.
Manual analysis / triage the sample and sign off
2.
Generate the CytoReport
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Not approved for use in diagnostic
procedures
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
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Not approved for use in diagnostic
procedures
Measuring SNPs using restriction enzymes
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•
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
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
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Not approved for use in diagnostic
procedures
Agilent CytoGenomics 1.5
Example: Consanguineous Sample
• SNP data detects blocks of cnLOH throughout the genome
AA AB
BB
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Not approved for use in diagnostic
procedures
Agilent CytoGenomics 1.5
Example: Sample with deletion on chr9 p-arm
• One copy deletion confirmed by SNP data
A
A
B
AA
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AB BB
Not approved for use in diagnostic
procedures
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
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Link out to and compare
aberrations in DGV and
UCSC genome browser
Preloaded tracks:
DGV-CNV
Not approved for use in diagnostic
procedures
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
Suppress aberrations
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Classify
aberrations
Edit
aberrations
Not approved for use in diagnostic
procedures
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
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Not approved for use in diagnostic
procedures
Agilent CytoGenomics 1.5
Multi Sample View
Sample A
Sample B
Sample C
Comparing 2 or more
samples side by side
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Not approved for use in diagnostic
procedures
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 trial @ https://earray.chem.agilent.com/earray/
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Not approved for use in diagnostic
procedures