Mitra Lecture - 1 Next Generation Sequencing Technologies...

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Unformatted text preview: 1 Next Generation Sequencing Technologies Rob Mitra 11/15/10 Forward Genetics Genotype Phenotype Hypothesis Test Hypothesis By Genetic Manipulation Forward Genetics Genotype Two groups: 1. Develop Colorectal cancer Mutation in APC Gene Phenotype Hypothesis Test Hypothesis By Genetic Manipulation At Young Age 2. Do not APC is a Tumor Supressor Gene Delete APC in Mouse Control: Isogenic APC+ The Cycle of Forward Genetics Genotype Observation ?Sequencing? Thinking In 2005 $9 million/genome Not feasible Phenotype Hypothesis Test Hypothesis By Genetic Manipulation Gene Deletion/Replacement Recombinant Technology End Runs • Linkage Studies (Humans, Model Organisms) • Association Studies (GWAS) BUT, these end runs have a cost! 1. Requires a large family (many crosses in model organisms); very difficult to analyze multi-factorial traits 2. Common variants But, these end runs will not be needed in 5-10 years. Why? The Problem with Forward Genetics Genotype Observation Sequencing Thinking Currently $40,000* /genome Cost is rapidly dropping Phenotype Hypothesis Test Hypothesis By Genetic Manipulation Gene Deletion/Replacement Recombinant Technology 2 Bp/US dollar: increases exponentially with time Adapted from Shendure et al 2004 Two questions: • How was this dramatic acceleration achieved? • What will it mean? How was this achieved? • Integration (Think about sequencing pipeline) • Parallelization • Miniaturization Same concepts the revolutionarized integrated circuits Plus one additional insight Read Length is Not As Important For Resequencing 0% 10% 20% 30% 40% 50% 8 10 12 14 16 18 20 Length of K-mer Reads (bp)...
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