Alper-JCCC Molecular Epidemiology SymposiumApril14, 2007 JCCC Genotyping Core: High Throughput SNP Genotyping

Alper-JCCC Molecular Epidemiology SymposiumApril14, 2007 Core Equipment Two ABI 3730 capillary sequencers ABI Taqman 7900 Roche LightCycler 480 Real-Time PCR System Beckman CEQ 8000 sequencer PSQ96 Pyrosequencer Two liquid handling robots Eight ABI 9700 thermalcylers 21 PCs 1 secure database server 1 secure webserver

Alper-JCCC Molecular Epidemiology SymposiumApril14, 2007 Genetic Assays at the GenoSeq Core SNP Genotyping DNA Methylation Analysis Gene Expression LOH (loss of heterozygosity) siRNA/RNAi, microRNA 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

Time atStored room tempfrozen then thawed Lane 113 days- Lane 218 days- Lane 325 days- Lane 4 47 days- Lane 5 18 days- Lane 6 18 days -20 C Lane 7 18 days -80 C DNA Collection

GenoSeq Webpage Sample text for grant applications

Alper-JCCC Molecular Epidemiology SymposiumApril14, 2007 Genotyping Projects and Collaborations Projects in Collaboration with the UCLA Conservation Genetics Resource Center African Wild Dog African Leaf Nosed Bat Bird Bobcat Cat Coyote Dog Fish Fox Gerbil Golden Jackal Grey Wolf Hyena Lizard Yellowstone Wolf Genotyping Project 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 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 Other Species California Valley Oak Monkey (Vervet) Mouse Center for Rapid Influenza Surveillance and Research

Alper-JCCC Molecular Epidemiology SymposiumApril14, 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 SymposiumApril14, 2007 The Genoseq Core is the Applied Biosystems SNPlex Service Provider for the Western U.S.

SNPlex Panels

Alper-JCCC Molecular Epidemiology SymposiumApril14, 2007 To Do a SNP Study at the GenoSeq Core Meet with the GenoSeq 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 SymposiumApril14, 2007 GenoSeq Core Contact Info The Sequencing and Genotyping Core is located at: 5309 Gonda Center 695 Charles Young Drive South Los Angeles, CA For Information, contact: Uma Dandekar, Assistant Director Phone: Dr. Jeanette Papp, Core Director Phone: