Addressing the growing demand for CNV and UPD detection Dr. Ruth Burton — Product Manager
Today’s agenda
Today’s agenda <ul><li>Introduction </li></ul><ul><li>CytoSure™ arrays and analysis software </li></ul><ul><li>Latest upda...
The OGT aCGH design process aCGH arrays All possible human genome probes Oligome TM  database Further selection based on O...
CytoSure cytogenetics range    high quality data    meaningful results    standardisation <ul><ul><li>Arrays </li></...
Today’s agenda <ul><li>Introduction </li></ul><ul><li>CytoSure™ arrays and analysis software </li></ul><ul><li>Latest upda...
The new CytoSure ISCA UPD array <ul><li>Fast and easy data generation and interpretation of cytogenetic results  </li></ul...
Normal Inheritance What is UPD? father mother
Uniparental disomy (UPD) Heterodisomy Isodisomy
407,787 human SNPs Select most informative SNPs (minor allele frequency of 0.4-0.6) 87,133 SNPs Elect candidate SNPs using...
Step 1: Selecting the SNPs What are the challenges? Validation of UPD detection against clinical samples Validation on fur...
Allele 1 Allele 2 Step 2: Final design <ul><li>One probe is designed to target each allele. </li></ul><ul><li>The differen...
CytoSure Interpret  Software <ul><li>Provided with arrays for aCGH data analysis </li></ul><ul><li>Enables automatic aberr...
CytoSure Interpret and UPD — Visualisation Gain Loss
CytoSure Interpret and UPD — Visualisation Gain Loss Genotype Assignment Homozygosity above user-definable threshold Perce...
CytoSure Interpret and UPD — Visualisation Gain Loss Whole Genome Chromosome 6
<ul><li>For each SNP: </li></ul><ul><ul><li>Compare signal  intensities of the 2 alleles </li></ul></ul><ul><ul><li>Apply ...
CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul>
CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul><ul><...
CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul><ul><...
CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul><ul><...
CytoSure Interpret and UPD — Validation Segmental UPD
CytoSure Interpret and UPD — Validation Segmental UPD
CytoSure Interpret and UPD — Validation Segmental UPD
Today’s agenda <ul><li>Introduction </li></ul><ul><li>CytoSure™ Arrays and data analysis with Interpret </li></ul><ul><li>...
CytoSure — excellence from sample to result <ul><li>Optimized, double-validated array content — regularly updated to ISCA ...
Acknowledgements OGT Collaborators and Customers
Thank you www.ogt.co.uk
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Addressing the growing demand for CNV and UPD detection

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  • ISCA developed with the ISCA steering committee. Optimised by OGT. Several groups have appreciated the cleaner calls and better coverage and have switched to the CytoSure platform. OGT is the exclusive distributor of the SciGene range of automated products for aCGH. Initially when labs move into using arrays they start using a manual approach. Our experience has shown that many labs quickly ramp up their sample numbers so automation becomes an important consideration. Having automation can also standardise results. Interestingly, OGT uses some of the Scigene products in its HT service facility. For example the Little Dipper for array washing and drying – also useful in FISH and GBanding. We have a Little Dipper on the booth this week if youd like to come and have a look.
  • Results Figure 1: Figure showing the SNP selection and probe design validation process used to identify probes capable of discriminating between SNP alleles
  • Results Figure 1: Figure showing the SNP selection and probe design validation process used to identify probes capable of discriminating between SNP alleles
  • General outsourced services: CRUK, ICR Custom aCGH services: UVA,, Leuven, Wessex, Sanger, UCSD, CSHL Custom aCGH products: Karolinska, Emory, Greenwood Custom Methylation Services: Greenwood
  • Addressing the growing demand for CNV and UPD detection

    1. 1. Addressing the growing demand for CNV and UPD detection Dr. Ruth Burton — Product Manager
    2. 2. Today’s agenda
    3. 3. Today’s agenda <ul><li>Introduction </li></ul><ul><li>CytoSure™ arrays and analysis software </li></ul><ul><li>Latest updates — UPD and CNV detection on a single array </li></ul><ul><li>Probe design </li></ul><ul><li>Analysis </li></ul><ul><li>Summary </li></ul>
    4. 4. The OGT aCGH design process aCGH arrays All possible human genome probes Oligome TM database Further selection based on OGT probe rating and desired coverage and content Selection based on specificity, T m , GC, etc. Optimised array design for catalogue and custom products Design & hyb two different aCGH arrays Optimised aCGH design Selection of best performing probes based on experimental results
    5. 5. CytoSure cytogenetics range  high quality data  meaningful results  standardisation <ul><ul><li>Arrays </li></ul></ul><ul><ul><ul><li>ISCA and Syndrome Plus </li></ul></ul></ul><ul><ul><ul><li>Chromosome X </li></ul></ul></ul><ul><ul><ul><li>Aneuploidy </li></ul></ul></ul><ul><ul><ul><li>DMD* </li></ul></ul></ul><ul><ul><ul><li>New! Emory Panel Arrays </li></ul></ul></ul><ul><ul><ul><li>New! ISCA UPD </li></ul></ul></ul><ul><ul><li>Labelling kit </li></ul></ul><ul><ul><li>Software </li></ul></ul><ul><ul><li>Oligome custom arrays </li></ul></ul><ul><ul><ul><li>Cancer designs </li></ul></ul></ul><ul><ul><li>Hyb buffers, backing plates </li></ul></ul><ul><ul><li>Full automation options </li></ul></ul>
    6. 6. Today’s agenda <ul><li>Introduction </li></ul><ul><li>CytoSure™ arrays and analysis software </li></ul><ul><li>Latest updates — UPD and CNV detection on a single array </li></ul><ul><li>Probe design </li></ul><ul><li>Analysis </li></ul><ul><li>Summary </li></ul>
    7. 7. The new CytoSure ISCA UPD array <ul><li>Fast and easy data generation and interpretation of cytogenetic results </li></ul><ul><ul><li>Regions of LOH and UPD are easily identified using CytoSure Interpret Software </li></ul></ul><ul><li>Confident detection of CNV and UPD on a single array </li></ul><ul><ul><li>Amplifications and deletions are shown alongside SNP data </li></ul></ul><ul><li>Superior aberration detection sensitivity and specificity with complete coverage of the ISCA* regions </li></ul><ul><ul><li>Content focussed on disease causing and syndromic regions </li></ul></ul><ul><li>Reliable detection of UPD and LOH using established methodology </li></ul><ul><ul><li>No need to change your reference sample or your optimised aCGH protocol </li></ul></ul>* International Standards for Cytogenomic Arrays (ISCA)
    8. 8. Normal Inheritance What is UPD? father mother
    9. 9. Uniparental disomy (UPD) Heterodisomy Isodisomy
    10. 10. 407,787 human 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 Step 1: Selecting the SNPs What are the challenges? Microarray Design Analyse to determine functional probe designs
    11. 11. Step 1: Selecting the SNPs What are the challenges? Validation of UPD detection against clinical 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
    12. 12. Allele 1 Allele 2 Step 2: Final design <ul><li>One probe is designed to target each allele. </li></ul><ul><li>The difference between the intensities of these two probes indicates the genotype of the sample. </li></ul><ul><li>This difference in intensity is not always consistent between SNPs and probe designs. </li></ul>
    13. 13. CytoSure Interpret Software <ul><li>Provided with arrays for aCGH data analysis </li></ul><ul><li>Enables automatic aberration detection (sample vs reference) </li></ul><ul><li>New functionality required for SNP data analysis! </li></ul><ul><ul><li>Isodisomy </li></ul></ul><ul><ul><li>Heterodisomy </li></ul></ul>Developing the Software
    14. 14. CytoSure Interpret and UPD — Visualisation Gain Loss
    15. 15. CytoSure Interpret and UPD — Visualisation Gain Loss Genotype Assignment Homozygosity above user-definable threshold Percentage Homozygosity
    16. 16. CytoSure Interpret and UPD — Visualisation Gain Loss Whole Genome Chromosome 6
    17. 17. <ul><li>For each SNP: </li></ul><ul><ul><li>Compare signal intensities of the 2 alleles </li></ul></ul><ul><ul><li>Apply weighting factors </li></ul></ul><ul><ul><li>Assign genotype based on user-definable threshold </li></ul></ul><ul><li>“ Normal” chromosome: ~50% Homozygosity </li></ul>CytoSure Interpret and UPD — Analysis
    18. 18. CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul>
    19. 19. CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul><ul><ul><li>Chr 15 Isodisomy </li></ul></ul> 
    20. 20. CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul><ul><ul><li>Chr 15 Isodisomy </li></ul></ul><ul><li>Wessex Regional Genetics Laboratory </li></ul><ul><ul><li>Chr 6 Isodisomy </li></ul></ul>  
    21. 21. CytoSure Interpret and UPD — Validation <ul><li>Coriell Samples </li></ul><ul><ul><li>Chr 8 Isodisomy </li></ul></ul><ul><ul><li>Chr 15 Isodisomy </li></ul></ul><ul><li>Wessex Regional Genetics Laboratory </li></ul><ul><ul><li>Chr 6 Isodisomy </li></ul></ul><ul><ul><li>Chr 7 ? </li></ul></ul>  
    22. 22. CytoSure Interpret and UPD — Validation Segmental UPD
    23. 23. CytoSure Interpret and UPD — Validation Segmental UPD
    24. 24. CytoSure Interpret and UPD — Validation Segmental UPD
    25. 25. Today’s agenda <ul><li>Introduction </li></ul><ul><li>CytoSure™ Arrays and data analysis with Interpret </li></ul><ul><li>Latest Updates — UPD and CNV detection on a single array </li></ul><ul><li>Probe design </li></ul><ul><li>Analysis </li></ul><ul><li>Summary </li></ul>
    26. 26. CytoSure — excellence from sample to result <ul><li>Optimized, double-validated array content — regularly updated to ISCA specifications </li></ul><ul><li>Reliable detection of CNV and LOH on a single array — CytoSure ISCA UPD array </li></ul><ul><li>Effortless data analysis — easy-to-use, class-leading software </li></ul><ul><li>Expert, high-throughput cytogenetics aCGH service — CytoSure Services </li></ul>The complete solution for cytogenetics — arrays (product or custom), software, labelling, reagents, automation, services
    27. 27. Acknowledgements OGT Collaborators and Customers
    28. 28. Thank you www.ogt.co.uk

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