几种基因芯片技术的比较

郭万峰1滕光菊2王升启1*(11008502302100039)基因芯片技术因其自身的优越性将成为基因组序列分析和基因表达研究的主要工具但是由于不同的实验室使用不同的技术平台,从25到80个碱基的寡核苷酸芯片和长度从数百到几千个碱基的cDNA阵列不同技术平台的存在,为芯片资料的利用和芯片领域的标准化分析带来了困难通过对不同技术平台的研究比较,短的和长的寡核苷酸芯片技术具有明显的优势,可望成为将来主要的技术方法基因芯片基因表达基因组:20040218*,:[e-mail],[1],,,,,,[2~3](genechip),DNA(microarray),DNA,,,cDNA,:;;cDNAcDNA111cDNA,cDNASchenacDNAcDNAcDNA[2,4]PCRcDNA,,,,121991,AffymetrixDNA[5],,,,,,,,,,(PM)(MM),MM,[6,7],25,,245CHINABIOTECHNOLOGY20045,,90%,25,,,13,,,,,,60mer[8,9],,100,,(,4),14,,cDNA,,,40~80,cDNA,,;cDNA,,cDNA,,,,,,,GC,,,[10],,219952004,PubMed5000,2003,cDNA,,,,NorthernRTPCR,,,(),[11,12]NatureMIAME(MinimumInformationaboutaMicroarrayExperimentGuidelines),,21cDNANCI,,Kuo[13]StanfordcDNAAffymetrix60(NCI60)56,2895mRNA,,cDNA,,,,,,,,,,22cDNAIncyteAffymetrix,Kothapalli[14]IncyteAffymetrix,,1624,,Affymetrix1030,cDNA38Northernblot,,,cDNA[15],AffymetrixIncytecDNA2184mRNA4218,RTPCR2189,cDNA,,cDNA,mRNA,,,cDNA[16,17]23,Kane[10]50mercDNA,50merPCR,,10mRNAHughes[8],cDNA20~60,,60mer,cDNAcDNA(r=097),,[9],331,,,,,,,32cDNAcDNA,cDNAPCR,,PCR,DNAPCR,,DNAs,,2~4PCR,33cDNA,,cDNAGC,cDNA,cDNA,100,cDNA,,cDNA,mRNAs[18,19],cDNA,cDNA,,175:4,2080PCR,PCR,,,,MIAME[11,12,20]:(1);(2);(3),;(4);(5);(6),,2530405060657080cDNA,SNP,,25cDNA,,,,,cDNA,,(serialanalysisofgeneexpression,SAGE)[21~23],,,[1]FoderSPA.DNAsequencing:Massivelyparallelgenomics.Science,1997,277:393~395[2]SchenaM,ShalonD,DavisRW,etal.QuantitativemonitoringofgeneexpressionpatternswithacomplementaryDNAmicroarray.Science,1995,270(5235):467~470[3]SchenaM,HellerRA,TheriaultTP,etal.Microarrays:biotechnologysdiscoveryplatformforfunctionalgenomics.TrendsBiotechnol,1998,16(7):301~306[4]SchenaM,ShalonD,HellerR,etal.Parallelhumangenomeanalysis:microarraybasedexpressionmonitoringof1000genes.ProcNatlAcadSciUSA,1996,93(20):10614~10619[5]FodorSP,ReadJL,PirrungMC,etal.Lightdirected,spatiallyaddressableparallelchemicalsynthesis.Science,1991,251(4995):767~773[6]LockhartDJ,DongH,ByrneMC,etal.Expressionmonitoringbyhybirdizationtohighdensityoligonucleotidearrays.NatBiotechnol,1996,14:1675~1680[7]LipshutzRJ,FodorSP,GingerasTR,etal.Highdensitysyntheticoligonucleotidearrays.NatGenet,1999,22(2):164~167[8]HughesTR,MaoM,JonesAR,etal.Expressionprofilingusingmicroarraysfabricatedbyaninkjetoligonucleotidesynthesizer.NatBiotechnol,2001,19(4):342~347[9]vantVeerLJ,DaiH,vandeVijverMJ,etal.Geneexpressionprofilingpredictsclinicaloutcomeofbreastcancer.Nature,2002,415(6871):530~536[10]KaneMD,JatkoeTA,StumpfCR,etal.Assessmentofthesensitivityandspecificityofoligonucleotide(50mer)microarrays.NucleicAcidsRes,2000,28(22):4552~4557[11]BrazmaA,HingampP,QuackenbushJ,etal.Minimuminformationaboutamicroarrayexperiment(MIAME)towardstandardsformicroarraydata.NatGenet,2001,29(4):365~371[12]StoeckertCJ,CaustonHC,BallCA.Microarraydatabases:standardsandontologies.NatGenet,2002,32,Suppl:469~473[13]KuoWP,JenssenTK,ButteAJ,etal.AnalysisofmatchedmRNAmeasurementsfromtwodifferentmicroarraytechnologies.Bioinformatics,2002,18(3):405~412[14]KothapalliR,YoderSJ,ManeS,etal.Microarrayresults:howaccuratearethey?BMCBioinformatics,2002,3(1):22[15]LiJ,PankratzM,JohnsonJA.DifferentialgeneexpressionpatternsrevealedbyoligonucleotideversuslongcDNAarrays.ToxicolSci,2002,69(2):383~390[16]YuenT,WurmbachE,PfefferRL,etal.AccuracyandcalibrationofcommercialoligonucleotideandcustomcDNAmicroarrays.NucleicAcidsRes,2002,30(10):e48[17]RhodesDR,BarretteTR,RubinMA,etal.Metaanalysisofmicroarrays:interstudyvalidationofgeneexpressionprofilesrevealspathwaydysregulationinprostatecancer.CancerRes,2002,62(15):4427~4433[18]ClarkTA,SugnetCW,AresM.GenomewideanalysisofmRNAprocessinginyeastusingsplicingspecificmicroarrays.Science,2002,296:907~910[19]ManiatisT,TasicB.AlternativepremRNAsplicingandproteomeexpansioninmetazoans.Nature,2002,418:236~243[20]BallCA,SherlockG,ParkinsonH,etal.Standardsformicroarraydata.Science,2002,298(5593):539[21]LiangP.SAGEGenie:asuitewithpanoramicviewofgeneexpression.ProcNatlAcadSciUSA,2002,99:11547~11548[22]EvansSJ,DatsonNA,KabbajM,etal.EvaluationofAffymetrixgenechipsensitivityinrathippocampaltissueSAGEanalysis.Eur1824JNeurosci,2002,16:409~413[23]SouletD,RivestS.Perspective:howtomakemicroarray,serialanalysisofgeneexpression,andproteomicrelevanttodaytodayendocrineproblemsandphysiologicalsystems.Endocrinology,2002,143:1995~2001ComparisonofGenechipPlatformsGUOWanfeng1TENGGuangju2WANGShengqi1(1BiochipKeyLaboratoryofthePLA,AcademyofMilitaryMedicalSciences,Beijing100850,China)(2DepartmentofInfectiousDisease,302HospitalofPLA,Beijing100039,China)AbstractGenechippromisestobearevolutionarytoolforlargescaleparallelanaylsisofgenomesequenceandgeneexpressionbecauseofitsadvantages.However,owingtothedifferentmicroarrayplatforms,whichcancontainoligonucleotidesof25to80basesinlengthandcDNAsofhundredsofbasestoseveralkilobasesinlength,therearemanydifficultiesinapplicationofmicroarraydatawidelyandstandardizationofmicroarrayfield.Comparionofseveralgenechipplatforms,shortandlongoligonucleotidetechnologiesofferadvantages,andcouldpossiblybecomethemajorcompetingplatformsinthenearf