分子生物学第2章和基因组多态性

Chapter2.Geneand第二 Section1.Section2.GenomeandGenomicsSection3.GenomicPolymorphismChapter2.Geneand Section3.Genomic Section4.ApplicationsofGenomic

WhattypesofDNApolymorphismSNP:SingleNucleotide(单核苷酸多态性Indel(InsertionorDeletion,插入或缺失VNTR:Variablenumberoftandemrepeats（串联重复序列数态性 lite( 串联重复序列数量多态性STR:Shorttandemrepeats（短片段串联重复– lites( 串联重复序列数量多态性)多态性的种G

Short“Indels”AVariableNumberofTandemShortTandemRepeats

Structual（SV，结构变异SegmentStructualvariation(SV)inour“Reference“ReferenceCopynumbervariantSegmentalduplicationEstimateisthat

peoplearefor30-50deletionslargerthan5kb(affectingtheexpressionofhundredsofgenes)Conradetal.,NatureGenetics38,75-81SingleNucleotidePolymorphism单核苷酸多SingleNucleotidePolymorphism 码单个碱基的变化，主要表现 组苷酸水平上的变异引起的DNA序列多态 StructuralVariationin>1kb（大于1kb 组变异-ThoughttobeCommon12%ofthegenome(Redonetal.2006)-Likelyinvolvedin

variationand-Untilrecentlymostmethodsfordetectionwerelowresolution(>50kb)SizeDistributionofCNVinaHumanGenome WhydowecareaboutGenomic多态性为何如此重要Whystudygenomicpolymorphismandgeneticvariationinmedicine? Commonin“normal”humangenomes-Commonincertaindiseases,particularlyNowshowingupinraredisease;autism,influencingHIVinfectionandAIDSdevelopmentCCR5indel和HIVHIV-1Env-mediatedfusionand requirescellularreceptors:CXCR4andTheCCR5receptormacrophageinflammatoryprotein1a(MIP-1a),macrophageinflammatoryprotein1b(MIP-1b),CCR5isexpressedon:macrophages,monocytes,memoryTcells,dendriticcells,andmicroglialcellsFrom:CourtneyPetersonGeorgetown32-bpdeletionresultsinprematuretruncationofthe 32-bp32-bpislocatedMutantCCR5receptorhasnofunctionalasmutantproteinisunstableintheDEL32(CCR5)andHIVDEL32(CCR5)andHIVHomozygotes(1%ofcaucasians)resistHIVinfectionPHASESOFAIDSArepeoplewithdel32(CCR5)areIndividualshomozygousforthemutantallelearehealthyandhavenoapparentgenotypicfrequenciesdonotdiffersignificantlyfromthosepredictedbyHardy-WeinbergsuggestingnoeffectonOtherhomologouschemokinereceptorsbindanoverlap setofchemokines.Theycancompensateforadeficiencyinasinglechemokinereceptor.DNACopyNumberChangesinTumorCells NormalTumor

HomologousrepeatsSegmentalduplicationsDuplicativetranspositions

AmylasecopynumberCMTand病。CMT可根据是否有伴随神经传导阻滞（CMTI）的雪旺17p11.2–p12间1.5Mb 引起，剂量敏感型外周 Section4.Applicationsof (Susceptibilityof

GeneticChromosomeSegmentalduplications,CopynumberTransposableShortdeletionsandTandemNucleotideInsertionsandDeletionsSingleNucleotidePolymorphisms(SNPs)

SizeDistributionofCNVinaHumanGenome 学数量性状是许多微 的联合效应造成的,它们的效应相等可加，所以微 又称加 (Additive effect 由于微效的效应微小，多（Polygenes）并不能予以个别辨认，只能按性状的表现在一起研究，对所涉及的对子数做粗Polymorphismsincancer-relatedInmouseitworksforsure20-50folddifferenceinlungtumorsusceptibilitybetweenthesensistiveA/JmousestrainandtheresistantC57Bl6isduetoapolymorphisminthesecondintronofK-InHumanP53polymorhismsincreasedsusceptibilityincreasedsusceptibilitytoHPV-inducedinhomozygousp53Argindividuals.(7timesmorethan ARG/ARGp53codon72 Prop53Argandp53Provariantsdifferintheirabilitiestobindtranscriptionalmachinerycomponents,Inactivationof ininducinginrepressingthetransformationofprimaryp53Argp53Argissignificantlymoresusceptiblethanp53ProtothedegradationinducedbyHPVE6protein.Pro/Pro=23%,Pro/Arg=49%,Arg/Arg=28%inChinaInCaucasiansfrequenciesarealmostthesame;ThePro/ProgenotypewasThePro/Progenotypewasassociatedamarkedlylowerriskofprostatecancer(OR=TP53Pro/ProisprotectiveTP53Arg/Argiscancer-pronep53p53Arg/Arggenotypeisincreasedinlungcancercomparedtonormalcontrols(50%vs24.2%,Arg72-containingalleleispreferentiallyandretainedinvarioushumantumors,includinglunge.g.TheProallelewaslostin11cases(78.6%),whiletheArgallelewaslostinthree(21.4%).Gene-EnvironmentInteractionsandGeneenvironmentNeedstronginitialhypothesisaboutthee.g.,ChronicObstructivePulmonaryDisease(COPD)andsmoking(DeMeoetal.,AJHG2006,SERPINE2gene)Environmentalexposurescanbedifficulttocharacterize(e.g.,pollution)GenexEnvironmentReducedEnvironmentalModificationofexposure-inducedModificationofexposure-inducedCanwegeneralizeaboutriskassociatedwithspecificModulationModulationofResponsetoGeneticGeneticGeneticModulationofGeneticModulationofBiologicalResponseGeneticVariationMetabolism,ordistribution,affectsdosetotheDetectionandrepairofDifferencesingrowthandrecoveryfromGeneticModulationofExposure

RiskLevel

4-Fold +PAH-Benzo[a]pyrene(苯并(a)芘 +

PAH-

BladderCancerRiskAssociatedwithSmokingandGSTM1Null1(+)

11-50>50

Exposure ExposureGeneticGeneticBelletal,JNCIalizedMedicineandalizedAllpatientswithsameTreatwithDesignnew

drugorTreatwithdrugornotpredisposed

BetterAvoidoresideEvans,Johnson.AnnuRevGenomicsHumGenetDifferentSideEffectsareLikelyCausedbyGeneticDifferencesinNormalCellsofIndividualsAllele:DNAoccupyingagivenlocus(position)onachromosomeWildtype:themostcommonphenotypeinthenaturalpopulation(W)Variant:DNAcompositionisdifferentthanwildtypeHomozygous:TwoidenticalallelesatoneHeterozygous:TwodifferentallelesatoneAllelefrequency:ameasureoftherelativefrequencyofanalleleonExamplesofApplyingPharmacogeneticstoS6-Mercaptopurine(Purinethol®)巯嘌Childhoodacutelymphoblasticleukemia(ALL)andimmunosuppressantDLT=急性白血病是小儿最高的，在我国儿童中是急性淋巴细胞白血病（acutelymphoblasticleukemia，ALL）的无病生存率明显提，有望成最先攻克恶性肿瘤，但化疗药物的副作用以及其与白血病复发率的关系，患儿的生命及正常生长发育。属于该领域疑难问题之。急性白血病儿童 间对绝大多数化疗物的治疗果及正常组的 异。常规疗失败分原因能为用药剂量不当所致。而，治疗失往往直接导致 ，的 响A体间化疗药物不同反应的了解在儿童血病领域得尤为重要 是儿童白血 6-MPandThiopurineMethyltransferase6-MPachievescytotoxiceffectincorporationintoDNAorRNA•Inactivatedby•移酶ThiopurineMethyltransferase巯嘌呤甲基转TPMTactivitycanbemeasuredintheredbloodInCaucasian~90%individualshavehighTPMTactivity10%haveintermediateTPMTactivity0.3%havelowornoLackofTPMTactivityresultsinhighriskofseverehematologicPharmacogenomics.ColdSpringHarborLab.TPMT*2,*3Aand*3CallelecarriershavelowerTPMTAllelefrequenciesaredifferentamongvarious*3Aisthemostcommonvariantin*3CisthemostcommonvariantineastandwestAfricanpopulations(Ghanaian),AfricanAmericansandinAsianVariantcarriershavelowerTPMTactivity,higherriskoftoxicityPharmacokinetics&Pharmacodynamics:PrinciplesofTherapeuticDrugMonitoring4thVariantCarriersHaveLowerTPMTActivity,HigherRiskofToxicityRellingetal,JNatlCancerInst1999;91:2001-ProposalonHowthe6-MPLabelCouldBeDosageandDr.Lesko.FDAFDAResponse(October23,…mandatorytestingforTPMTintheabsenceofclear ysis,istooearly…”“…(testsforTPMT)increasesawarenessthatthereisproblemandthatsomethingcanDr.Lesko.FDATPMTgenoty isnowavailableasamoleculardiagnosticfromreferencelabRevisedCamptosarLabel(EffectiveJune7th,KeyDifferentsideeffectsarelikelycausedbygeneticdifferencesinnormalcellsofPharmacogeneticswhichut