Not approved for use in diagnostic procedures

Agilent CytoGenomics 1.5For Detection of CNC, LOH and UPD

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• 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

Agilent CytoGenomics 1.5 Value Proposition

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• Client/server system with database.

• Possible configurations:

• multiple clients can access central database simultaneously.

Not approved for use in diagnostic procedures

Agilent CytoGenomics 1.5 System specs

Client and Server (Database) on same machine Client(s) and Server (Database)on separate machines

Client 1 Client 2

server

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• 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

Agilent CytoGenomics 1.5 System specs

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• Preloaded default workflows available

• Customizing your 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

1. Configure analysis method

2. Configure CytoReport 3. Configure Workflow

Agilent CytoGenomics 1.5 Workflow based system

Not approved for use in diagnostic proceduresSlide 5 out of 15

• Fast 5-minute data analysis and report generation for a normal constitutional sample.

• Convenient input and output support allowing for integration with LIMS.

Not approved for use in diagnostic procedures

Sample info

Laboratory LIMS

Cytoreport

Manual analysis & sign off

Run dataanalysis

Agilent CytoGenomics 1.5Streamlined data analysis and reporting for Cytogenetic research labs

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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 proceduresSlide 7 out of 15

Not approved for use in diagnostic procedures

FeatureExtraction

ADM-1ADM-2SNP CN & LOH

Log2 ratio ofintensities to call CNCs

No. of uncut alleles to call LOH/UPD

Agilent CytoGenomics 1.5Powerful algorithms for calling CNC, LOH and UPD

GC correction

AA

AB

BB

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• SNP data detects blocks of cnLOH throughout the genome

Not approved for use in diagnostic procedures

Agilent CytoGenomics 1.5Example: Consanguineous Sample

AA ABBB

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• One copy deletion confirmed by SNP data

Not approved for use in diagnostic procedures

Agilent CytoGenomics 1.5Example: Sample with deletion on chr9 p-arm

AAAB BB

A

A

B

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Not approved for use in diagnostic procedures

Preloaded tracks: DGV-CNV

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

Agilent CytoGenomics 1.5Sample Triage – Access to external databases

Upload custom tracks

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Not approved for use in diagnostic procedures

Add notes to sample

Add notes to aberrations

Classify aberrations

Agilent CytoGenomics 1.5Sample Triage – Sample and Aberration annotation

Suppress aberrations

Not approved for use in diagnostic procedures

Edit aberrations

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Not approved for use in diagnostic procedures

Auto updated tracks based on aberration classification in CytoGenomics Database

Showing number of samples with overlapping aberrations in database

Agilent CytoGenomics 1.5Sample Triage – Using the CytoGenomics in house Database

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 1.5Multi Sample View

Comparing 2 or more samples side by side

Sample A Sample B Sample C

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• 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.

Not approved for use in diagnostic procedures

Agilent CytoGenomics 1.5 Key feature summary

Download CytoGenomics free trial @ https://earray.chem.agilent.com/earray/

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