alper-jccc molecular epidemiology symposiumapril14, 2007 jccc genotyping core: high throughput snp...
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Alper-JCCC Molecular Epidemiology SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
JCCC Genotyping Core:JCCC Genotyping Core: High Throughput SNP GenotypingHigh Throughput SNP Genotyping
www.genoseq.com
Alper-JCCC Molecular Epidemiology SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
Core EquipmentCore 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 SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
Genetic Assays at the GenoSeq CoreGenetic 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 at Storedroom temp frozen then
thawedLane 1 13 days -Lane 2 18 days -Lane 3 25 days -Lane 4 47 days -Lane 5 18 days -Lane 6 18 days -20 CLane 7 18 days -80 C
DNA Collection DNA Collection
1 2 3 4 5 6 7
GenoSeq WebpageGenoSeq Webpagewww.genoseq.com
Sample text for grant applications
Alper-JCCC Molecular Epidemiology SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
Genotyping Projects and CollaborationsGenotyping 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 SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
SNP PlatformsSNP PlatformsStudy SizeStudy 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 SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
The Genoseq Core is the The Genoseq Core is the Applied BiosystemsApplied Biosystems
SNPlexSNPlex Service Provider Service Provider
for the Western U.S.for the Western U.S.
SNPlex PanelsSNPlex Panels
Alper-JCCC Molecular Epidemiology SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
To Do a SNP Study at theTo Do a SNP Study at theGenoSeq CoreGenoSeq 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 SymposiumAlper-JCCC Molecular Epidemiology Symposium April14, 2007April14, 2007
GenoSeq Core Contact InfoGenoSeq Core Contact Infowww.genoseq.comwww.genoseq.com
The Sequencing and Genotyping Core is located at:
5309 Gonda Center695 Charles Young Drive SouthLos Angeles, CA 90095
For Information, contact:
Uma Dandekar, Assistant DirectorEmail: [email protected]: 310-267-2461
Dr. Jeanette Papp, Core DirectorEmail: [email protected]: 310-825-6204