_Dr. Wu's lecture_3_02_04_lecture_web

_Dr. Wu's lecture_3_02_04_lecture_web - PMI 285 Cellular...

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PMI 285 “Cellular basis of disease” Winter 2004 Bioinformatics and Genechip for disease research (I) The principle and application of DNA Microarray Yin Chen Yin Chen University of California at Davis University of California at Davis
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DNA Microarray: reshaping molecular biology one gene in one experiment whole picture
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Potential application domains ± Identification of complex genetic diseases Identification of complex genetic diseases ± Drug discovery and toxicology studies Drug discovery and toxicology studies ± Mutation/polymorphism detection (SNP Mutation/polymorphism detection (SNP ’s) s) ± Pathogen analysis Pathogen analysis ± Differing expression of genes over time, between tissues, Differing expression of genes over time, between tissues, and disease states and disease states ± Preventive medicine Preventive medicine ± Ability to subtype disease and design drugs that treat Ability to subtype disease and design drugs that treat disease causes, rather than symptoms disease causes, rather than symptoms ± Specific genotype (population) targeted drugs Specific genotype (population) targeted drugs ± More targeted drug treatments More targeted drug treatments – AIDS AIDS ± Genetic testing and privacy Genetic testing and privacy
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Formats for DNA Microarray Format I : probe cDNA (hundred or kilo- bases long) spotted on glass slides or nylon membrane. Format II : an array of oligonucleotide (20~80-mer oligos). This method, "historically" called DNA chips, was developed at Affymetrix, Inc. , which sells its photolithographically fabricated products under the GeneChip® trademark.
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GENERAL STEPS OF MICROARRAY
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It's goal is to compare gene transcription in two or more different kinds of cells. There is four main steps in making an array experiment : Array fabrication Sample preparation and hybridization Scanning the array Exploring the results
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Making the chip Designing the chip : choosing genes of interest for the experiment Selection of chip probes that represent the investigated genes. Finding sequences, usually in the EST database. Problems : sequencing errors, alternative splicing, chimeric sequences, contamination…
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Microspotting and ink-jetting
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Arrayer
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Photolithography (Affymetrix method)
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The Surfaces of DNA Microarrays cDNA Array (Duggan et al ., Nature Genetics 21: 10-14, 1999) OligoGenechip (Southern et al ., Nature Review Genetics 21(Suppl): 5-9, 2001)
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_Dr. Wu's lecture_3_02_04_lecture_web - PMI 285 Cellular...

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