JCCC Genotyping Core High Throughput SNP Genotyping www

JCCC Genotyping Core: High Throughput SNP Genotyping www. genoseq. com Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

Core Equipment • • • Two ABI 3730 capillary sequencers ABI Taqman 7900 Roche Light. Cycler 480 Real-Time PCR System Beckman CEQ 8000 sequencer PSQ 96 Pyrosequencer Two liquid handling robots Eight ABI 9700 thermalcylers 21 PCs 1 secure database server 1 secure webserver Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

Genetic Assays at the Geno. Seq Core • • • SNP Genotyping DNA Methylation Analysis Gene Expression LOH (loss of heterozygosity) si. RNA/RNAi, micro. RNA In/Del Analysis Microsatellite Genotyping Large Fragment Sizing Copy Number Analysis AFLP, RFLP • • Plate Preparation by Liquid Handling Robot Computer Lab / Analysis Software Database / Bioinformatics Services Statistical Analysis – Power calculations, Routine Linkage and Association testing • • • BAC Fingerprinting SAGE HLA Typing Conformation Analysis Allele Quantification Sequencing Resequencing Comparative Sequencing Mutation Detection Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

DNA Collection Time at room temp Lane 1 Lane 2 Lane 3 Lane 4 Lane 5 Lane 6 Lane 7 1 13 days 18 days 25 days 47 days 18 days 2 Alper-JCCC Molecular Epidemiology Symposium April 14, 2007 3 4 Stored frozen thawed -20 C -80 C 5 6 7

Geno. Seq Webpage www. genoseq. com Sample text for grant applications Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

Genotyping Projects and Collaborations Human Traits • Anemia • Asthma • Ataxia Telangiectasia • Bipolar Disorder • Breast Cancer • Colon Cancer • Corneal Disease • Endometriosis • Epilepsy • Fahr's Disease • Familial Combined Hyperlipidemia • Heart Disease • Hereditary Recurrent Vertigo • Horizontal Gaze Palsy • Hydrolethalus Syndrome • Hypertension • Inflammatory Bowel Disease • Leigh Syndrome Other Species • California Valley Oak • Monkey (Vervet) • Mouse • Low HDL-Cholesterol • Lung Cancer • Macular Degeneration • Meckel Syndrome • Migraine • Multiple Sclerosis • Obesity • Ophthalmoplegia • Oscillopsia • Osteoporosis • Parkinson's Disease • Prostate Cancer • Retinitis Pigmentosa • Rett Syndrome • Sick Sinus Syndrome • Tourette's Syndrome Center for Rapid Influenza Surveillance and Research Projects in Collaboration with the UCLA Conservation Genetics Resource Center • African Wild Dog • African Leaf Nosed Bat • Bird • Bobcat • Coyote • Dog • Fish • Fox • Gerbil • Golden Jackal • Grey Wolf • Hyena • Lizard • Yellowstone Wolf Genotyping Project Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

SNP Platforms Study Size • Affymetrix – many SNPs, many samples, ultra-high-throughput • SNPlex – moderate numbers of SNPs and samples, high-throughput • Taqman – fewer SNPs, fewer samples, moderate-throughput • Pyrosequencing – few SNPs, few samples, low-throughput Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

The Genoseq Core is the Applied Biosystems SNPlex Service Provider for the Western U. S. Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

SNPlex Panels Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

To Do a SNP Study at the Geno. Seq Core • Meet with the Geno. Seq Core personnel to plan and schedule your study. • You design and order your primer set (with help from ABI). • Give your primers and your DNA to the Core, we do the rest. • We manage and archive your data. • When the project is complete we deliver the data in the requested format. • The Core can do routine linkage or association analysis on your data, if requested. Alper-JCCC Molecular Epidemiology Symposium April 14, 2007

Geno. Seq Core Contact Info www. genoseq. com The Sequencing and Genotyping Core is located at: 5309 Gonda Center 695 Charles Young Drive South Los Angeles, CA 90095 For Information, contact: Uma Dandekar, Assistant Director Email: uma@ucla. edu Phone: 310 -267 -2461 Dr. Jeanette Papp, Core Director Email: jcpapp@ucla. edu Phone: 310 -825 -6204 Alper-JCCC Molecular Epidemiology Symposium April 14, 2007