May24,2018

IntroductiontoGenomics

Malvika Pillai

• WhatisGenomics?• GenomeSequencing• GenomicMedicine• Genotyping

OutlineforIntroductiontoGenomics

DefinitionofGenomics

Gen

omics Functional

Comparative

Structural

etc.

• Large-scalestudyofgroupsofgeneswithinoneorganismorbetweenmultipleorganisms

Collection ofinformation

Subsetofinformationtobeexpressed

Problem

GenomeSequencing

>NC_000017.11:c43125483-43044295 Homosapienschromosome17,GRCh38.p12PrimaryAssemblyGTACCTTGATTTCGTATTCTGAGAGGCTGCTGCTTAGCGGTAGCCCCTTGGTTTCCGTGGCAACGGAAAAGCGCGGGAATTACAGATAAATTAAAACTGCGACTGCGCGGCGTGAGCTCGCTGAGACTTCCTGGACGGGGGACAGGCTGTGGGGTTTCTCAGATAACTGGGCCCCTGCGCTCAGGAGGCCTTCACCCTCTGCTCTGGGTAAAGGTAGTAGAGTCCCGGGAAAGGGACAGGGGGCCCAAGTGATGCTCTGGGGTACTGGCGTGGGAGAGTGGATTTCCGAAGCTGACAGATGGGTATTCTTTGACGGGGGGTAGGGGCGGAACCTGAGAGGCGTAAGGCGTTGTGAACCCTGGGGAGGGGGGCAGTTTGTAGGTCGCGAGGGAAGCGCTGAGGATCAGGAAGGGGGCACTGAGTGTCCGTGGGGGAATCCTCGTGATAGGAACTGGAATATGCCTTGAGGGGGACACTATGTCTTTAAAAACGTCGGCTGGTCATGAGGTCAGGAGTTCCAGACCAGCCTGACCAACGTGGTGAAACTCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGCCGCTCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTAGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCATTGCACTCCAGCCTGGGCGACAGAGCGAGACTGTCTCAAAACAAAACAAAACAAAACAAAACAAAAAACACCGGCTGGTATGTATGAGAGGATGGGACCTTGTGGAAGAAGAGGTGCCAGGAATATGTCTGGGAAGGGGAGGAGACAGGATTTTGTGGGAGGGAGAACTTAAGAACTGGATCCATTTGCGCCATTGAGAAAGCGCAAGAGGGAAGTAGAGGAGCGTCAGTAGTAACAGATGCTGCCGGCAGGGATGTGCTTGAGGAGGATCCAGAGATGAGAGCAGGTCACTGGGAAAGGTTAGGGGCGGGGAGGCCTTGATTGGTGTTGGTTTGGTCGTTGTTGATTTTGGTTTTATGCAAGAAAAAGAAAACAACCAGAAACATTGGAGAAAGCTAAGGCTACCACCACCTACCCGGTCAGTCACTCCTCTGTAGCTTTCTCTTTCTT

Whatisagenome?

• Sangersequencing• NextGenerationSequencing(NGS)– IlluminaSequencingbySynthesis

Howdowesequenceagenome?

• AKAdideoxy chainterminationmethod• Dideoxynucleotides (ddNTPs)– Lack3’OHgroup– Chainterminator

SangerSequencing

ComparisonofGenomeSequencing&OpticalMappingTechnology

ComparisonsBetweenGenomeTechnologies

GenomicMedicine

Genotyping

• CRISPR-Cas9– ClusteredRegularlyInterspacedShortPalindromicRepeats

GeneEditing

Twinkletwinklebigstar Twinkletwinklebig star Twinkletwinklestar

CRISPR-Cas9

Twinkletwinklebigstar Twinkletwinklebiglittle star

Twinkletwinklebiglittlestar

Twinkletwinklebigstar Twinkletwinklebiglittle star

Twinkletwinklelittlestar

AnyQuestions?

IntroductiontoGenomics:Demo+Hands-OnExercise

NextClass

• MutatingRNAinMatlab– VisualizingRNAfolds– Comparingmutatedstrandstowildtypestrands

Demo

May31,2018

GenomicsFeatureExtraction

Malvika Pillai

• GenomicFeatures• GenomeVisualization• GenomeAnnotation

OutlineforFeatureExtraction

GenomicFeatures

DefinitionofaGenomicFeature

• Anygenomicregionwithsomeannotatedfunction

GeneCodingSequence(CDS)

mRNA

rRNA tRNA miRNA

siRNA DirectRepeat InvertedRepeat

OriginofReplication

GenomeVisualization

UCSCGenomeBrowser

GenomeAnnotation

AnnotationSources

Source:KimberlyRobasky

AnyQuestions?

GenomicFeatureExtraction:Hands-OnExploration

NextClass