Introduction to Genomics - University of North Carolina at ...€¦ · Introduction to Genomics:...
Transcript of Introduction to Genomics - University of North Carolina at ...€¦ · Introduction to Genomics:...
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May24,2018
IntroductiontoGenomics
Malvika Pillai
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• WhatisGenomics?• GenomeSequencing• GenomicMedicine• Genotyping
OutlineforIntroductiontoGenomics
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DefinitionofGenomics
Gen
omics Functional
Comparative
Structural
etc.
• Large-scalestudyofgroupsofgeneswithinoneorganismorbetweenmultipleorganisms
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Collection ofinformation
Subsetofinformationtobeexpressed
Problem
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GenomeSequencing
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>NC_000017.11:c43125483-43044295 Homosapienschromosome17,GRCh38.p12PrimaryAssemblyGTACCTTGATTTCGTATTCTGAGAGGCTGCTGCTTAGCGGTAGCCCCTTGGTTTCCGTGGCAACGGAAAAGCGCGGGAATTACAGATAAATTAAAACTGCGACTGCGCGGCGTGAGCTCGCTGAGACTTCCTGGACGGGGGACAGGCTGTGGGGTTTCTCAGATAACTGGGCCCCTGCGCTCAGGAGGCCTTCACCCTCTGCTCTGGGTAAAGGTAGTAGAGTCCCGGGAAAGGGACAGGGGGCCCAAGTGATGCTCTGGGGTACTGGCGTGGGAGAGTGGATTTCCGAAGCTGACAGATGGGTATTCTTTGACGGGGGGTAGGGGCGGAACCTGAGAGGCGTAAGGCGTTGTGAACCCTGGGGAGGGGGGCAGTTTGTAGGTCGCGAGGGAAGCGCTGAGGATCAGGAAGGGGGCACTGAGTGTCCGTGGGGGAATCCTCGTGATAGGAACTGGAATATGCCTTGAGGGGGACACTATGTCTTTAAAAACGTCGGCTGGTCATGAGGTCAGGAGTTCCAGACCAGCCTGACCAACGTGGTGAAACTCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGCCGCTCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTAGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCATTGCACTCCAGCCTGGGCGACAGAGCGAGACTGTCTCAAAACAAAACAAAACAAAACAAAACAAAAAACACCGGCTGGTATGTATGAGAGGATGGGACCTTGTGGAAGAAGAGGTGCCAGGAATATGTCTGGGAAGGGGAGGAGACAGGATTTTGTGGGAGGGAGAACTTAAGAACTGGATCCATTTGCGCCATTGAGAAAGCGCAAGAGGGAAGTAGAGGAGCGTCAGTAGTAACAGATGCTGCCGGCAGGGATGTGCTTGAGGAGGATCCAGAGATGAGAGCAGGTCACTGGGAAAGGTTAGGGGCGGGGAGGCCTTGATTGGTGTTGGTTTGGTCGTTGTTGATTTTGGTTTTATGCAAGAAAAAGAAAACAACCAGAAACATTGGAGAAAGCTAAGGCTACCACCACCTACCCGGTCAGTCACTCCTCTGTAGCTTTCTCTTTCTT
Whatisagenome?
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• Sangersequencing• NextGenerationSequencing(NGS)– IlluminaSequencingbySynthesis
Howdowesequenceagenome?
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• AKAdideoxy chainterminationmethod• Dideoxynucleotides (ddNTPs)– Lack3’OHgroup– Chainterminator
SangerSequencing
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ComparisonofGenomeSequencing&OpticalMappingTechnology
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ComparisonsBetweenGenomeTechnologies
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GenomicMedicine
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Genotyping
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• CRISPR-Cas9– ClusteredRegularlyInterspacedShortPalindromicRepeats
GeneEditing
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Twinkletwinklebigstar Twinkletwinklebig star Twinkletwinklestar
CRISPR-Cas9
Twinkletwinklebigstar Twinkletwinklebiglittle star
Twinkletwinklebiglittlestar
Twinkletwinklebigstar Twinkletwinklebiglittle star
Twinkletwinklelittlestar
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AnyQuestions?
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IntroductiontoGenomics:Demo+Hands-OnExercise
NextClass
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• MutatingRNAinMatlab– VisualizingRNAfolds– Comparingmutatedstrandstowildtypestrands
Demo
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May31,2018
GenomicsFeatureExtraction
Malvika Pillai
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• GenomicFeatures• GenomeVisualization• GenomeAnnotation
OutlineforFeatureExtraction
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GenomicFeatures
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DefinitionofaGenomicFeature
• Anygenomicregionwithsomeannotatedfunction
GeneCodingSequence(CDS)
mRNA
rRNA tRNA miRNA
siRNA DirectRepeat InvertedRepeat
OriginofReplication
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GenomeVisualization
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UCSCGenomeBrowser
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GenomeAnnotation
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AnnotationSources
Source:KimberlyRobasky
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AnyQuestions?
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GenomicFeatureExtraction:Hands-OnExploration
NextClass