CHAPTER10TheMappingAndAnalysisOfGenomesConceptsofGenomeandGenomicsGeonme:OnecompletecopyofthegeneticinformationGenome:Onecompletesetofchromosomes(monoploidorhaploid)ofanorganismGenomics:Thegeneticssubdisciplineofmapping,sequencing,andanalyzingthefunctionsofentiregenomesStructuregenomics:thestudyofthestructureofgenomesFunctionalgenomics:thestudyofthefunctionofthegenomes

HumanGeneProspectinginIcelandIcelandlocatedintheNorthAtlanticbetweenGreenlandandScandinaviaThe270000people,homogeneousdescendentsofVikingmorethan1100yrsagoThe15thcenturythepopulationplummetedfrom70000to25000becauseofplagueDuring1700s,thepopulationdroppedbelow50000becauseoffamineanddiseasebythevolcanoHeklaIceland’snationalhealthservicehaskeptfamilymedicalrecordssince1915In1977,KariStefansson(aHarvardgeneticist)returnedtohishomelandwiththegoalofidentifyinghumangenesThefirstsuccesswastheidentificationofthefamilyessentialtremorgenedeCODEGeneticsnegotiateda$200millioncontractwiththeSwissphamaceuticalgiantHoftmann-Laroche

TheHumanGenomeProject(HGP)

ThreeGreatProjectsinthe20thCentury

HumanGenomeProjectApril14,2003

ApolloProjectJuly20,1969

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

1.Geneticmap2.Physicalmap3.Transcriptionalmap4.Wholegenomesequencing

1990-2003BasicTaskTheHumanGenomeProject(HGP)

China’sContributionUSA,54%UK，34%Japan，6.8%France，2.8%Germany,2.2%China,1%WorkingDraft

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

TheHumanGenomeProject(HGP)

Cytogeneticmap

GbandingRbandingCbandingTheHumanKaryotype

FluorescentInSituHybridization(FISH)

1.Geneticmap

GeneticMap

Genelocationsrelativetoknowngenesbasedonrecombination,measuredincentimorgans.MethodUsemolecularmarkertocalculatetherecombinationfrequencybetweentwolinkedgenes,todeterminetherelativedistance.UnitCetimorgans(cM)SeparationfrequencyofgeneorfragmentduringchromosomalcrossoverRecombinationMapping

withaThree-PointTestcross

Linkagemapofmolecularmarkersonhumanchromosome4

STRmarkerShorttandemrepeat2.Physicalmap

PhysicalMap

Genedistancesmeasuredinnumberofbasepairs

BasedonanalysisofDNATools:restrictionendonucleaseUnit:Mb,kb,bpSequence-taggedsite,STS

RFLPRFLPMaps

RFLPmapofchromosome1inArabidopsis

RFLPmapSomatic-CellGenetics:AnAlternativeApproachtoGeneMappingCellfusion1960’sbyBarskiandEphrussi

Mappingthehumangenome

Radiationhybrid(RH)mapping

Ahigh-resolutionradiationhybridmapofhumanchromosome1

ARHmapCorrelatedGenetic,Cytological,AndPhysicalMapsOfChromosomes

3.SequencemapSequenceMap:SequencingallthebasesineachchromosomeMethod:Sangermethod,Shotgunmethod

4.TranscriptionalmapTranscriptionalmap:cDNAmapESTmap:ExpressedsequencetagsSequencingtheexpressedsequenceofgenome5.TheHumanGenomeProjectHumangenome:3x109bpHumangenomeProject:1990-2005Cost:$3billionGoal:(1)map70000-100000genes(2)constructadetailedphysicalmap(3)determinethenucleotidesequencesof24humanchromosomes

TheRacetoSequencetheHumanGenome

DNASequencing

AdvancesinDNAsequencing

BuildinganoverlappingsetofgenomicclonesBottom-up

approach

(1)OverlappingFragments

Whole-chromosomephysicalmap

PartialDigestion

PhysicalMapsandCloneBanks

Atop-down

approach

(2)Assigningchromosomalposition(3)Piecingtogetherawhole-chromosome

sequencemap

Differenttypesofmaps

(4)Shotgunsequencing

AfterHGPHapMap2002

Haplotypeisasetofsinglenucleotidepolymorphisms(SNPs)onasinglechromosomeofachromosomepairthatareassociatedstatistically.CanadaChinaJapanUSAGreatBritainAfterHGPTheRiceGenome

AfterHGPENCODE2003TheNationalHumanGenomeResearchInstitute(NHGRI)launchedapublicresearchconsortiumnamedENCODE,theEncyclopediaOfDNAElements,inSeptember2003,tocarryoutaprojecttoidentifyallfunctionalelementsinthehumangenomesequence.Theprojectstartedwithtwocomponents-apilotphaseandatechnologydevelopmentphase.USANHGRIGreatBritainEuropeEBIAfterHGPG1K2008The1000GenomesProjectisacollaborationamongresearchgroupsintheUS,UK,andChinaandGermanytoproduceanextensivecatalogofhumangeneticvariationthatwillsupportfuturemedicalresearchstudies.ItwillextendthedatafromtheInternationalHapMapProject,whichcreatedaresourcethathasbeenusedtofindmorethan100regionsofthegenomethatareassociatedwithcommonhumandiseasessuchascoronaryarterydiseaseanddiabetes.AfterHGPICGP2008TheInternationalCancerGenomeConsortium(ICGC)isavoluntaryscientificorganizationthatprovidesaforumforcollaborationamongtheworld'sleadingcancerandgenomicresearchers.TheICGCwaslaunchedin2008tocoordinatelarge-scalecancergenomestudiesintumoursfrom50cancertypesand/orsubtypesthatareofmainimportanceacrosstheglobe.(5)Positionalcloning:

fromphenotypetogene

Mappingadiseaselocus

Chromosomewalking

ChromosomeJumpsEachjump100kb

ChromosomeJumps6.RNAAndProteinAssaysOfGenomeFunction

Dotblothybridizations

Greenfluorescentprotein(GFP)

UseofGreenFluorescentProtein

asaReporterofProteinSynthesis

Genechip

UseofthegenechiptodetectmutationsBacterialGenomes

ModelOrganismsClassificationofthe4,288knownandputativegenesofE.coliaccordingtofunction

E.coliTheSaccharomycescerevisiaeGenome

Saccharomycescerevisiae

SelectedgenomesequencingprojectsOrganismSequenceInformationcompletedE.coli1997Genomesize4.64Mb,whichencodes4405genesB.subtilis1997Firstgram-positivebacterialgenometobesequencedS.cerevisiae1996Genomesize12Mb,6000genesC.elegans1998Genomesize100MbD.melanogaster2000Shotgunapproachused,14000genesin165MbAthiliana2000Genomesize117MbM.musculus20078.3millionSNPs,90%sequencesimilartohumanbeingsH.sapiens2003Genomesize3billion,30000genes

SomeinterestingfactsaboutourgenomeTheinformationwouldfilltwohundred500telephonedirectories.Betweenhumans,ourDNAdiffersbyonlyo.2%,or1in500bases(letters).Ifwerecitedthegenomeatoneletterpersecondfor24hrsadayitwouldtakeacenturytorecitethebookoflife.Iftwodifferentpeoplestartedtorecitingtheirindividualbooksatarateofoneletterpersecond,itwouldtakenearlyeightandahalfminutes(500sec)beforetheyreachedadifference.Atypisttypingat60wordspermin(around360le