Addressing the growing demand for CNV and UPD detection

Dr. Ruth Burton — Product Manager

Today’s agenda

Today’s agenda

Introduction

CytoSure™ arrays and analysis software

Latest updates — UPD and CNV detection on a single array

• Probe design• Analysis

Summary

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

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

Today’s agenda

Introduction

CytoSure™ arrays and analysis software

Latest updates — UPD and CNV detection on a single array

• Probe design• Analysis

Summary

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)

Normal Inheritance

father mother

What is UPD?

Uniparental disomy (UPD)

Heterodisomy Isodisomy

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?

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

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.

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

Gain

Loss

CytoSure Interpret and UPD — Visualisation

Gain

Loss

CytoSure Interpret and UPD — Visualisation

Genotype Assignment

Homozygosity above user-

definable threshold

Percentage Homozygosity

Gain

Loss

CytoSure Interpret and UPD — Visualisation

Whole Genome

Chromosome 6

• 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

CytoSure Interpret and UPD — Validation

• Coriell Samples

• Chr 8 Isodisomy

CytoSure Interpret and UPD — Validation

• Coriell Samples

• Chr 8 Isodisomy

• Chr 15 Isodisomy

CytoSure Interpret and UPD — Validation

• Coriell Samples

• Chr 8 Isodisomy

• Chr 15 Isodisomy

• Wessex Regional Genetics Laboratory

• Chr 6 Isodisomy

CytoSure Interpret and UPD — Validation

• Coriell Samples

• Chr 8 Isodisomy

• Chr 15 Isodisomy

• Wessex Regional Genetics Laboratory

• Chr 6 Isodisomy

• Chr 7 ?

CytoSure Interpret and UPD — Validation

Segmental UPD

CytoSure Interpret and UPD — Validation

Segmental UPD

CytoSure Interpret and UPD — Validation

Segmental UPD

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

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

AcknowledgementsOGT Collaborators and Customers

Thank youwww.ogt.co.uk