Addressing the growing demand for CNV and UPD detection
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Transcript of Addressing the growing demand for CNV and UPD detection
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Addressing the growing demand for CNV and UPD detection
Dr. Ruth Burton — Product Manager
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Today’s agenda
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Today’s agenda
Introduction
CytoSure™ arrays and analysis software
Latest updates — UPD and CNV detection on a single array
• Probe design• Analysis
Summary
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The OGT aCGH design process
aCGH arrays
All possible human genome probes
OligomeTM database
Further selection based on OGT probe rating and desired coverage and content
Selection based on specificity, Tm, GC, etc.
Design & hyb two different aCGH arrays
Optimised aCGH design
Selection of best performing probes based on experimental results
Optimised array design for catalogue and custom products
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CytoSure cytogenetics range
high quality data
meaningful results
standardisation
• Arrays• ISCA and Syndrome Plus• Chromosome X• Aneuploidy• DMD*• New! Emory Panel Arrays• New! ISCA UPD
• Labelling kit
• Software
• Oligome custom arrays• Cancer designs
• Hyb buffers, backing plates
• Full automation options
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Today’s agenda
Introduction
CytoSure™ arrays and analysis software
Latest updates — UPD and CNV detection on a single array
• Probe design• Analysis
Summary
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The new CytoSure ISCA UPD array
• Fast and easy data generation and interpretation of cytogenetic results • Regions of LOH and UPD are easily identified using CytoSure Interpret
Software
• Confident detection of CNV and UPD on a single array• Amplifications and deletions are shown alongside SNP data
• Superior aberration detection sensitivity and specificity with complete coverage of the ISCA* regions
• Content focussed on disease causing and syndromic regions
• Reliable detection of UPD and LOH using established methodology
•No need to change your reference sample or your optimised aCGH protocol
* International Standards for Cytogenomic Arrays (ISCA)
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Normal Inheritance
father mother
What is UPD?
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Uniparental disomy (UPD)
Heterodisomy Isodisomy
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407,787 human SNPs407,787 human SNPs
Select most informative SNPs (minor allele frequency of 0.4-0.6)
87,133 SNPs
Select most informative SNPs (minor allele frequency of 0.4-0.6)
87,133 SNPs
Elect candidate SNPs using OGT probe selection algorithms
19,489 SNPs
Elect candidate SNPs using OGT probe selection algorithms
19,489 SNPs
Microarray DesignMicroarray Design
Analyse to determine functional probe designs
Analyse to determine functional probe designs
Step 1:Selecting the SNPs
What are the challenges?
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Step 1:Selecting the SNPs
What are the challenges?
Validation of UPD detection against clinical samples
Validation of UPD detection against clinical samples
Validation on further set of known genotype samples
Validation on further set of known genotype samples
6,186 SNPs, each targeted by 2 optimised probes in triplicate, incorporated into 4x180k
ISCA aCGH design of 137,100 copy number probes
6,186 SNPs, each targeted by 2 optimised probes in triplicate, incorporated into 4x180k
ISCA aCGH design of 137,100 copy number probes
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Allele 1 Allele 2
Step 2: Final design
• One probe is designed to
target each allele.
• The difference between the
intensities of these two probes
indicates the genotype of the
sample.
• This difference in intensity is
not always consistent between
SNPs and probe designs.
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CytoSure Interpret Software
• Provided with arrays for aCGH data analysis
• Enables automatic aberration detection (sample vs reference)
• New functionality required for SNP data analysis!
• Isodisomy• Heterodisomy
Developing the Software
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Gain
Loss
CytoSure Interpret and UPD — Visualisation
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Gain
Loss
CytoSure Interpret and UPD — Visualisation
Genotype Assignment
Homozygosity above user-
definable threshold
Percentage Homozygosity
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Gain
Loss
CytoSure Interpret and UPD — Visualisation
Whole Genome
Chromosome 6
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• For each SNP:
• Compare signal intensities of the 2 alleles
• Apply weighting factors
• Assign genotype basedon user-definablethreshold
• “Normal” chromosome: ~50% Homozygosity
CytoSure Interpret and UPD — Analysis
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CytoSure Interpret and UPD — Validation
• Coriell Samples
• Chr 8 Isodisomy
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CytoSure Interpret and UPD — Validation
• Coriell Samples
• Chr 8 Isodisomy
• Chr 15 Isodisomy
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CytoSure Interpret and UPD — Validation
• Coriell Samples
• Chr 8 Isodisomy
• Chr 15 Isodisomy
• Wessex Regional Genetics Laboratory
• Chr 6 Isodisomy
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CytoSure Interpret and UPD — Validation
• Coriell Samples
• Chr 8 Isodisomy
• Chr 15 Isodisomy
• Wessex Regional Genetics Laboratory
• Chr 6 Isodisomy
• Chr 7 ?
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CytoSure Interpret and UPD — Validation
Segmental UPD
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CytoSure Interpret and UPD — Validation
Segmental UPD
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CytoSure Interpret and UPD — Validation
Segmental UPD
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Today’s agenda
Introduction
CytoSure™ Arrays and data analysis with Interpret
Latest Updates — UPD and CNV detection on a single array
• Probe design• Analysis
Summary
![Page 26: Addressing the growing demand for CNV and UPD detection](https://reader035.fdocuments.us/reader035/viewer/2022081603/5578fc1fd8b42a675b8b4ba2/html5/thumbnails/26.jpg)
CytoSure — excellence from sample to result
• Optimized, double-validated array content — regularly updated to ISCA specifications
• Reliable detection of CNV and LOH on a single array — CytoSure ISCA UPD array
• Effortless data analysis — easy-to-use, class-leading software
• Expert, high-throughput cytogenetics aCGH service — CytoSure Services
The complete solution for cytogenetics — arrays (product or custom), software, labelling, reagents, automation, services
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AcknowledgementsOGT Collaborators and Customers
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Thank youwww.ogt.co.uk