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Addressing the growing demand for CNV and UPD detection
- 1. Addressing the growing demand for CNV and UPD detection Dr. Ruth Burton — Product Manager
- 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
- 8. Normal Inheritance What is UPD? father mother
- 9. Uniparental disomy (UPD) Heterodisomy Isodisomy
- 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. 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
- 14. CytoSure Interpret and UPD — Visualisation Gain Loss
- 15. CytoSure Interpret and UPD — Visualisation Gain Loss Genotype Assignment Homozygosity above user-definable threshold Percentage Homozygosity
- 16. CytoSure Interpret and UPD — Visualisation Gain Loss Whole Genome Chromosome 6
- 22. CytoSure Interpret and UPD — Validation Segmental UPD
- 23. CytoSure Interpret and UPD — Validation Segmental UPD
- 24. CytoSure Interpret and UPD — Validation Segmental UPD
- 27. Acknowledgements OGT Collaborators and Customers
Hinweis der Redaktion
- 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