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Genomics & Proteomics Analysis Chapter 20

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Slide 2Overview of topics to be discussedcDNA can also be studiedwww.bio.davidson.edu/Courses/genomics/RTPCR/RT_PCR.html :SEQUENCING DNASlide 6Dideoxy key point!DNA PCR amplification is performed prior to sequence analysisSlide 9Slide 10AutoradiogramSlide 12Can you sequence without using radioactivity?Yes: Example of Labelled ProbesSlide 15Slide 16Slide 17Microarray AnalysisMicroarray ProtocolSlide 20Slide 21Example of: Microarrays from breast tumorsMicroarrays of 70 genesSlide 24Human Genome Project June, 2002Slide 26Mouse: Mus musculusGenomic Projects: provide us information about:Slide 29Slide 30VNTR’sPredicting Function fromComputational method predictionSlide 34Genomics & Proteomics AnalysisChapter 20Overview of topics to be discussedHow to sequence genomic DNA (we will have to touch briefly on polymerase chain reaction—a topic from the upcoming “PCR” lab).cDNAMicroarray AnalysisThe Human Genome ProjectHow to use information from any genome sequence:Single Nucleotide PolymorphismsPredicting Function from SequencecDNA can also be studiedwww.bio.davidson.edu/Courses/genomics/RTPCR/RT_PCR.html :cDNA:mRNAReverse transcriptaseSEQUENCING DNA Sanger-DideoxymethodSanger Method dideoxynucleotides: lack a 3’ OHBut have the 2’ and 3’ have hydrogenNO DNA EXTENSIONDideoxy key point!DNA PCR amplification is performed prior to sequence analysisAutoradiogramCan you sequence without using radioactivity?Radioactive!Yes: Example of Labelled ProbesddGTPddATPddTTPddCTPOrangeBlackRedBlueMicroarray AnalysisMicroarray ProtocolDNA or cDNA is added robotically to chipChips exposed to labeled cDNA Label monitored by laserExample of: Microarrays from breast tumorscDNA from breast tumors from 2 groups of patientsMetastatic Cancer Disease FreeMicroarrays of 70 genesMetastatic cancers(row is a patient’s tumor, a column a gene)Genomic DNATranscriptomeProteomeDATA BASEHuman Genome ProjectJune, 2002Dr. Craig VenterPresident ClintonDr. Francis CollinsThe initial draft of the Human Genome•3.4 billion base pairs•32,000 genes•Average gene 27,000 bases•Chromosome 17, 19, 22 high density •May encode 96,000 proteinsMouse: Mus musculus2.6 billion bp99% in common with human genomeGenomic Projects: provide us information about:Expressed-sequence tags (ESTs)Single-nucleotide polymorphisms (SNPs) & HaplotypesVariable Number Tandem Repeats (VNTRs)Need to understand cDNAHaplotype: A set of SNPs and other variants on the same chromosomeVariable number tandem repeats(VNTRs) in multiple lociShort stretches of DNA base pairs that are repeated at multiple loci in the chromosomes.GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGVNTR’sPredicting Function from Homology SearchComputational method predictionParalogOrthologParalogs: Homologous sequences in same speciesOrthologsHomologous Sequences in Different


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