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1、1Human Genomics2How much do you know about human Genome Project?3Human Genomic ProjectvAsaresultofhumangenomicproject,humansnowknowmoreaboutthemselves,atleastatthemolecularlevel,thantheyeverhavebefore.4History About Human Genome P0rojectsThecompletegeneticmaterialofanentireorganismisknownasitsgenome
2、.In1986,scientistsproposedaprojecttomakegeneticmapofhumanincluding:ChromosomallocationofallhumangenesCompleteDNAsequenceofthegenomeInFallof1989,theprojectwasstartedworkingbyfundingfromtheUSCongressJamesWatson,codiscovererofthedouble-helixDNAstructure,wasappointedasthefirstprojectdirector.The Belief
3、of WatsonHuman Genomic Project would tell us what it means to be human5Whose genome?vSeveraldonors:DNAfrombloodofwomenDNAfromspermofmenvCelera:twowhitemen(nowemerged)andthreewomenofAfrican-American,Chinese,andHispanicbackgroudvThepublicproject:twomalesandtwofemales6ThesequenceofDNAistheorderinwhicht
4、hefournucleotidebase(A,T,G,C)appearontheDNAmolecules.Thehumangenomecontainssome3.2billionbases.soitssequencinghaspresentednosmallchallengeRapidprogresswasmadepossiblebyshotguncloningapproach:entiregenomeisfirstfragmentedtheneachfragmentissequencedbyautomatedmachinesdifferentlaboratoriescanbesimultan
5、eouslyworkingondifferentpiecesofpuzzles!The First Goal: Determiningthe Human DNA Sequence7Basic Procedures of DNA Sequencing1.PrecursorApieceofsinglestrandedDNAtobesequencedisaddedtoatubewhichcontain:EnzymeforDNAsynthesisFournormalprecursorsFourabnormalprecursorsPrimer2. DNA synthesisWhenanormalblac
6、kprecursorisaddedtothetemplate,thechainkeepsgrowing.When,byrandomchance,anabnormalprecursorgetsaddedinstead,synthesisofthatchainstops.8Basic Procedures of DNA Sequencing3. ElectrophoresisThepiecescanthenbeseparatedbysizeusingelectrophoresis.4. Reading the sequenceDetectorreadseachbandofthegel,detect
7、ingthecolorofthedyelabelingthatband.9Basic Procedures of DNA SequencingDatafromsequencingcanbeanalyzedbycomputer.AutomatedDNAsequencinghasgreatlyincreasedthespeedatwhichgenomescanbesequencedandinformationcanbecollected10Basic Procedures of DNA SequencingAgene-sequencingfactoryhas300automatedDNAseque
8、ncers!11Another goal:mapping the human genomeItmeanstoidentify:ThechromosomallocationofeachgeneTheorderofthegenesrelativetooneanother.Note:JustdeterminingsequenceofapieceofDNAdoesnottellyouitslocationinthegenome.12vNature 405, 311-319 (18 May 2000) | doi:10.1038/35012518; Received 17 April 2000; Acc
9、epted 3 May 2000vThe DNA sequence of human chromosome 21vM.Hattori1,A.Fujiyama1,T.D.Taylor 1,H.Watanabe1,T.Yada 1,H.-S.Park1,A.Toyoda1,K.Ishii1,Y.Totoki 1,D.-K.Choi1,E.Soeda2,M.Ohki3,T.Takagi 4,Y.Sakaki1,4,S.Taudien8,K.Blechschmidt8,A.Polley8,U.Menzel8,J.Delabar6,K.Kumpf8,R.Lehmann8,D.Patterson7,K.R
10、eichwald14,A.Rump14,M.Schillhabel14,A.Schudy14,W.Zimmermann14,A.Rosenthal14,J.Kudoh8,K.Shibuya8,K.Kawasaki8,S.Asakawa8,A.Shintani8,T.Sasaki8,K.Nagamine8,S.Mitsuyama8,S.E.Antonarakis9,S.Minoshima8,N.Shimizu8,G.Nordsiek10,K.Hornischer10,P.Brandt10,M.Scharfe10,O.Schn10,A.Desario11,J.Reichelt10,G.Kauer1
11、0,H.Blcker10,J.Ramser12,A.Beck12,S.Klages12,S.Hennig12,L.Riesselmann12,E.Dagand12,T.Haaf12,S.Wehrmeyer12,K.Borzym12,K.Gardiner7,D.Nizetic13,F.Francis12,H.Lehrach12,R.Reinhardt12&M.-L.Yaspo12vConsortiuminstitutions:vRIKEN,GenomicSciencesCenter,Sagamihara228-8555,JapanvInstitutfrMolekulareBiotechnolog
12、ie,Genomanalyse,D-07745Jena,GermanyvDepartmentofMolecularBiology,KeioUniversitySchoolofMedicine,Tokyo160-8582,JapanvGBF(GermanResearchCentreforBiotechnology),GenomeAnalysis,D-38124Braunschweig,GermanyvMax-Planck-InstitutfrMolekulareGenetik,D-14195Berlin-Dahlem,GermanyvCollaboratinginstitutions:vRIKE
13、N,LifeScienceTsukubaResearchCenter,Tsukuba305-0074,JapanvCancerGenomicsDivision,NationalCancerCenterResearchInstitute,Tokyo104-0045,JapanvHumanGenomeCenter,InstituteofMedicalScience,UniversityofTokyo,Tokyo108-8639,JapanvUMR8602CNRS,UFRNeckerEnfants-Malades,Paris75730,FrancevEleanorRooseveltInstitute
14、,Denver,Colorado80206,USAvMedicalGeneticsDivision,UniversityofGenevaMedicalSchool,Geneva1211,SwitzerlandvCNRSUPR1142,InstitutdeBiologie,Montpellier,34060,FrancevSchoolofPharmacy,UniversityofLondon,LondonWC1N1AX,UKvCorrespondenceto:Y.Sakaki1,4CorrespondenceandrequestsformaterialsshouldbeaddressedtoY.
15、S.(e-mail:Email:sakakigsc.riken.go.jp),A.R.(e-mail:Email:),N.S.(e-mail:Email:shimizudmb.med.keio.ac.jp),H.B.(e-mail:Email:bloeckergbf.de)orM.L.Y.(e-mail:Email:yaspomolgen.mpg.de).Genomicclonescanberequestedfromanyofthefivegroups.Detailedcloneinformation,maps,FISHdata,annotatedgenecatalogue,genenamea
16、liasandsupportingdatasetsareavailablefromtheRIKENandMPIMGwebsites(seeMethods).Interactivechromosome21databases(HSA21DB)aremaintainedatMPIMGandRIKEN.AllsequencedatacanbeobtainedfromGenbank,EMBLandDDBJ.Theyarealsoavailablefromtheindividualwebpages.13The basic approachvCutthesamelongpiecewithtwodiffere
17、ntrestrictionenzymesvDerivethesequencesofeachofthepiecesvUsethecomputerstodiscoverhowthetwosetsofpiecesoverlap14Mapping of DNA sequencesInthisexample,aDNAsequenceof150basesiscutwithtwodifferentrestrictionenzymes,producingthefollowingfragmentseachofwhichhasbeensequenced.Trytopiecethefragmentarysequen
18、cetogetherbeforegoingtonextslide.123456ABCDEFGH2-4-1-5-6-3H-C-A-B-G-D-F-E15Mapping of DNA sequencesWhenthetwosetsoffragmentsarelinedupinthisway,theorderofbasesinthefirstrowisthesameastheorderofbasesinthesecondrow.Geneticsusuallyworkwithhundredsoffragmentsatonce,eachofthemlongerthantheaboveentiresequ
19、ence,sothetaskofplacingthemtogetherismuchmoredifficult!16Mapping of DNA sequencesThe same approach was successfully used on mapping of genomes of the 599 viruses, 31 eubacteria, and 7 archaebacteria between 1995 and 2002.When working with human genomes, there are obstacles:oneobstacleisthesize.Human
20、genomeisabout25timeslargerthananypreviouslysequencedgenome.anotherobstacleisthenon-codingDNA,muchofthenon-codingDNAinthehumangenomeiscomposedofrepeatedsequencesofnucleotides.Specieswhosegenomeshadpreviouslybeensequenceddonotcontaintheserepeats.These enormously complicate the jobs of putting pieces i
21、nto unambiguous order!17The International Human Genome Sequencing ConsortiuminvolvinglaboratoriesfromUS,British,Japan,France,Germany,andChina.publishedtheirresultsinNature(Volume409,p860)Celera GenomicsabiotechnologycompanypublishedtheirresultsinScience(Volume409,P.1304)InFebruary2001,twogroupssimul
22、taneouslyannouncedcompletionofadraftofthesequenceofhumangenome.Thedraftcoversabout94%oftheestimated3billionbasesinthecompletedgenome.Ofthose3billionbases:1billionhavebeensequencedtocompletionother2billionbasescontainsgapsandareaswheredifferenteffortsatsequencinghaveresultedindifferentanswers.Complet
23、ion of Human Genomic Draft SequenceChina: Chromosome 3, 30Mb, 1% genome in 199919991999年年9 9月月9 9日日9 9时时9 9分分9 9秒，华大基因秒，华大基因在北京空港工业区在北京空港工业区B B区区6 6号楼号楼3 3层开启层开启了了“1%1%计划计划”的准备工作。的准备工作。9 9月月9 9日亦定为华大基因的庆典日。日亦定为华大基因的庆典日。 18ContributionvUS: 54%vUK: 33%vJapan: 7%vFrance: 2.8%vGermany: 2.2%vChina: 1% (1
24、.13%)1920Celera Genomics vsHuman Genomic Sequencing Consortium21Two years after, it was fully sequencedInApril2003,onlytwoyearsafterpublicationofdraftsequence,thefirstfullsequencingofthehumangenomewascompleted.ItspublicationinjournalNaturewastimedtocoincidewiththefiftiethanniversaryofWatsonsarticled
25、escribingtheDNAdoublehelixstructure.Key results from human genomic sequencingsupportsomepreviouslyestablishedhypotheses,butalsoproducedsomesurprises,hasspawnedmanypracticaladvancesinbiotechnologyandgeneticengineering.22Nature 440, 346-351 (16 March 2006) | doi:10.1038/nature04569; Received 17 Decemb
26、er 2005; ; Accepted 31 December 2005The finished DNA sequence of human chromosome 12StevenE.Scherer1,DonnaM.Muzny1,ChristianJ.Buhay1,RuiChen1,AndrewCree1,YanDing1,ShannonDugan-Rocha1,RachelGill1,PreethiGunaratne1,R.AlanHarris1,AliciaC.Hawes1,JudithHernandez1,AnneV.Hodgson1,JenniferHume1,AndrewJackso
27、n1,ZiadMohidKhan1,ChristieKovar-Smith1,LoraR.Lewis1,RyanJ.Lozado1,MichaelL.Metzker1,AleksandarMilosavljevic1,GeorgeR.Miner1,KateT.Montgomery2,MargaretB.Morgan1,LynneV.Nazareth1,GrahamScott1,EricaSodergren1,Xing-ZhiSong1,DavidSteffen1,RuthC.Lovering3,DavidA.Wheeler1,KimC.Worley1,YiYuan1,ZhengdongZhan
28、g1,CharlesQ.Adams1,M.AliAnsari-Lari1,MuluAyele1,MaryJ.Brown1,GuanChen1,ZhijianChen1,KerstinP.Clerc-Blankenburg1,ClayDavis1,OliverDelgado1,HuyenH.Dinh1,HeatherDraper1,ManuelL.Gonzalez-Garay1,PaulHavlak1,LarondaR.Jackson1,LeniS.Jacob1,SusanH.Kelly1,LiLi2,ZhangwanLi1,JingLiu1,WenLiu1,JingLu1,ManjulaMah
29、eshwari1,Bao-VietNguyen1,GeoffreyO.Okwuonu1,ShiranPasternak1,LesetteM.Perez1,FarahJ.H.Plopper1,JirehSantibanez1,HuaShen1,PaulE.Tabor1,DanielVerduzco1,LeneeWaldron1,QiaoyanWang1,GabrielleA.Williams1,JingKunZhang1,JianlingZhou1BaylorCollegeofMedicineHumanGenomeSequencingCenterSequenceProductionTeam*,D
30、avidNelson1,RajuKucherlapati2,GeorgeWeinstock1andRichardA.Gibbs12324vLaunchedinJanuary2008vTosupportthediscoveryandunderstandingofgeneticvariantsthatinfluencehumandiseasevConsortium:UK,China(BGI),andUSvSamples:volunteerdonors(2500global-er)The 1000 Genomes Project25Changes in the number and order of
31、 genes (A-D) create genetic diversity within and between populations26Nature. 2010 October 28; 467(7319): 10611073vA map of human genome variation from population scale sequencingThe 1000 Genomes Project Consortium1.SNPswith1%orhigherfrequency2.0.1-0.5%infunctionalgeneregions3.Structuralvariants-cop
32、ynumbervariants-otherinsertionsanddeletions-inversions27MoreProjectsv千种动植物基因计划v万种微生物计划.美洲华大.欧洲华大.日本华大.香港华大28Sequence and expression analysis of gaps in human chromosome 20.MinocherhomjiS,SeemannS,MangY,El-SchichZ,BakM,HansenC,PapadopoulosN,JosefsenK,NielsenH,GorodkinJ,TommerupN,SilahtarogluA.Nucleic
33、AcidsRes.2012Apr17.EpubaheadofprintAddress: 3unfinishedgapsonitsq-arm;Gene-denseregionsand/oroverlapdisease-associatedloci,includingtheDLGAP4locus29Key Result (1)Humangenomehas3.2billionbases,whichismuchlargerthanmicroorganisms.Muchofitsexcesssizeisduetothosenon-coding,repeatedsequences.About 95% of
34、 the human genome represents non-coding DNA, a large portion ofwhich is composed of repetitive sequences. Less than 5%of the human genome iscomposed of genes that code for RNA and proteins.“Complexity of an organisms does not directly correlate with the size of its genome.30Key Result (2)The actual
35、number of genes is smaller than previously estimated.Thehumangenomehasanunexpectedlysmallnumberofgenes(30,000,previousestimatesbetween50,000and100,000genes),halfofwhichfunctionisunknownThehumangenomeisnearlythesameinallpeople(99.9%)Surprisingly, humans have a small coding genome.only a third larger
36、than a nematode worm!31Key Result (3)The protein products of many genes remain unknown.Ithasbeenfoundthatmanyoftheknowngenescanbetranslatedindifferentwaystoproducealternativeproteinvariantsfromthesamegene.Thus,althoughwehaveonlytwiceasmanygenesasfruitflies,wemayhavefivetimesasmanydifferentproteins.3
37、2Key Result (4)A very high percentage of our genes are not unique to humansbut are closely similar to comparable genes from other species.Infact,only1%ofhumangeneshavenosequencesimilaritytoanyotherorganismsOurgenesaresimilarto46%ofgenesinyeastMorethan200humangenesandtheirproteinproductshavebeenfound
38、tohavesignificantsimilaritytothoseinbacteriaAmongmammalsthedifferencesareevenfewer.Humanshaveonly300genesthathavenocounterpartinthemousegenome.What we learned from the sequence of human genome ishow very like other organisms we are Itseemstransferofgenefromonespeciestoanother,notonlybyartificialmean
39、sofgeneticengineering,butalsooccursinnature.33Guess：In a mouse these unique genes are linked to - and -. smell and reproduction More than 90 percent of genes associated with disease are identical in humans and mice the tremendous value of the mouse in laboratory experiments. 34Key Result (5)Within e
40、ach single gene, there is an average of 15 sites at which different individuals carry a different nucleotide.Thesevariations,calledsinglenucleotidepolymorphisms(SNPs),aregreatlyexpandinghowmanyalleleswethinkarepossiblefordifferentgenesMostofthesepolymorphismsareassociatedsmallchangesinproteinfunctio
41、norregulationThischallengesourconceptsoftermssuchasheterozygous,dominantandrecessiveItmakesusclearthatthereisnosuchthingasthehumangenomesequence.Thegenomesequencewithineachindividualisunique.Itisestimatedthatonepersondiffersfromanotherinabout0.01%ofthe3billionbasepairsinhumangenome.35vVirtually, the
42、re is no human genome.vThe only people who share every letter of the genetic code are identical twins, and every one of us is otherwise unique.vStill importantly, what human genome sequence provides is a reference.36How finished is the genome?vLessthan1%oftheprotein-codingregionsstillmissingalongwithhigherproportionsofnon-codingjunkDNAvCentromeresatthemiddleofchromosomesvTelomeresattheendsofchromosomes-DuetosomuchrepetitiveDNAthatstandardtechnologyhasstrugglestoreadthem.37Questions:1.Genome concept2.Human Genome Program (HGP, Two Goals)3.Key results of HGP4.Basic procedure of DNA sequencing
