Benefits to validating GWAS studies with custom genotyping

Transcription

1 Benefits to validating GWAS studies with custom genotyping Daniel Peiffer, PhD Sr. Product Manager Genotyping Applications 2010 Illumina, Inc. All rights reserved. Illumina, illuminadx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iselect, CSPro, GenomeStudio, Genetic Energy, HiSeq, and HiScan are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.

2 Overview Cycle of discovery and validation Custom genotyping applications Application in study design Overview of Illumina technologies 2

3 Targeted resequencing RNA-sequencing Next-Gen Sequencing Identifying Variants GWAS Arrays Confirming Variants Custom Validation Arrays Re-Confirming Variants Low Density Panels Barcoding & QCing Samples Low Density Arrays Deploying Variants 3

4 Custom Genotyping Applications Sample quality control Sample barcoding (identification) / fingerprinting Candidate gene region studies Deeper follow-up of meta analysis hit list Fine mapping of GWAS hit regions Detection of lower frequency variants 4

5 Common Considerations When Designing a Custom GT Project Complexity of disease / focus of study Breadth of information currently known on disease / focus Sample size targeted for adequate power of study Availability (value) of samples Consistency of sample preparation and identification Availability of funding Timelines driving project 5

6 Illumina s Custom Genotyping Solutions iselect HD 3K - 200K-plex Infinium HD Assay Guaranteed >80% beadtype success rate Multi-sample BeadChip formats GoldenGate 96-3K-plex GoldenGate Assay 32-sample BeadChip format Scalable integration with LIMS and automation GoldenGate Indexing plex GoldenGate Assay Highest throughput (up to1,536 samples per run) Fully integrated LIMS + automation VeraCode plex GoldenGate Assay ASPE Assay Cost effective solution for QC and screening Eco Real- Time PCR System 48 samples up to 4-plex Open platform, supports all chemistries and real-time PCR applications, including HRM, GEX, SNP genotyping, viral load and SBS library validation +/- 0.1 o C temperature uniformity, 1 copy sensitivity 12 x12 x13, 30 lbs 6

7 Infinium iselect HD Custom Genotyping 3,000 60, ,000 24x1 12x1 7

8 Custom Genotyping Applications: Replication / Validation / Candidate Gene Region Researchers incorporate some or all of the following into their study design: Key hits from initial GWAS SNPs with compelling ρ trends from previous studies (if done) SNPs from GWAS arrays in LD blocks around hit regions SNPs in regions of interest (e.g., HLA, MHC, suspected gene regions) Wild card SNPs of interest Loci for copy number variation information 8

9 Custom Genotyping Applications: Sample QC / Sample Barcoding Gender ID Mendelian Inconsistencies Ensure Project and Data Quality Sample Quality Genotyping Barcode Core Service labs like CIDR* have begun implementing barcoding as a standard process prior to running GWAS or large custom genotyping projects Findings: Avg. savings on a 3,000-sample GWA study was $40,000 (excluding labor) Maximum savings to date was over $300,000 *ASHG 2009 Poster: Impact of sample pretesting in a high through-put genotyping facility. B. Marosy, C. Boehm, B. Craig, J.Romm, C. Oncago, M. Zilka, M. Adams-Carr, Y. Osimokun, K. Hetrick, H. Ling, E. W. Pugh, K. F. Doheny CIDR/GRCF-IGM, JHU-SOM, Baltimore, MD. 9

10 Custom Genotyping Applications: Implementing LIMS in High Throughput Processing Tracking QC LIMS Workflow Management Reporting Track samples and reagents through the entire process Reduce sample to sample variability Reduce sample handling and processing errors Dramatically increase throughput 10

11 Custom Genotyping on the Infinium Assay The right content lets you capture more biology Dog Pine Corn Mouse Applications Chicken Soy Bean Atlantic Salmon Grape Vine Citrus Barley Tomato Sweet Sorghum Zebra Finch Genome-wide selection Genetic Prediction SNP discovery Cotton Rapeseed Spruce Human P. falciparum Zebra Fish Commercial Agriculture screening panels Targeted follow-up studies after GWAS Targeted disease panels Atlantic Cod Cat Lettuce Rat False Brome Citrus Cacao Cattle Swine Horse Sheep Targeted rare variant panels Sample QC and tracking panels Consumer Genomics Poplar Peach Turkey Rhesus Rice Forensics Wheat Honey Bee Rye grass Canola Armadillo 11

12 Example of Focused Genotyping Panels - Ag BovineSNP50/BovineHD Developed in collaboration with USDA Beltsville, University of Missouri, and University of Alberta CanineSNP20/CanineHD Developed in collaboration with the LUPA consortium ~170K validated SNP probes derived from the CamFam2.0 assembly EquineSNP50 Developed in collaboration with: International Equine Genome Mapping Workshop and the Morris Animal Foundation's Equine Genome Consortium PorcineSNP60 Developed in collaboration with Int l Porcine SNP Consortium (Martien Groenen: Wageningen Univ) OvineSNP50 Developed in collaboration with the International Sheep Genomics Consortium (ISGC) MaizeHD Developed in collaboration with Pioneer, Syngenta, USDA, and Trait Genetics 12

13 Examples of Focused Genotyping Panels - Human HumanCVD Developed in collaboration with the Institute of Translational Medicine and Therapeutics at the Univ. of Pennsylvania, the Broad Institute, and the NHLBI Candidate diseases include myocardial infarction, heart failure, stroke, insulin resistance, metabolic disorders, dyslipidemia and inflammation Human Cardio-Metabo Developed in collaboration with Broad, University of Michigan, Sanger Interrogates loci of interest for researchers studying the genetics of the Cardiovascular and Metabolic disease in humans 13

14 The Right Technology Enables Truly Novel Discovery Targeted Re- Sequencing Array Genotyping Multi-plex PCR Mass Spec Content Density High Structural Variations, SNP Discovery Fine mapping hit regions SNPs in LD, wild card Top Hits Low Months Weeks Time from Content Design to Analyzed Results 14

15 Thank You and Questions 2010 Illumina, Inc. All rights reserved. Illumina, illuminadx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iselect, CSPro, GenomeStudio, Genetic Energy, HiSeq, and HiScan are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.

16 Choosing a product Speed Results Factors for Consideration Complexity of disease / focus of study Breadth of information currently known Sample size targeted for adequate power of study Availability (value) of samples Consistency of sample preparation and identification Timelines driving project Availability of funding 16