Application of Genome-Wide Single Nucleotide Polymorphism Typing Simple Association and Beyond 英文参考文献.docVIP

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Application of Genome-Wide Single Nucleotide Polymorphism Typing Simple Association and Beyond 英文参考文献.doc

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Application of Genome-Wide Single Nucleotide Polymorphism Typing Simple Association and Beyond 英文参考文献

Review ApplicationofGenome-WideSingle NucleotidePolymorphismTyping: SimpleAssociationandBeyond J.Raphael Gibbs, Andrew Singleton* ABSTRACT technologies,muchofthisarticlefocusesontheoutputand metricsproducedusingtheIlluminaIn?niumassays,because ourprimaryin-houseworkhascenteredonthisplatform. However,manyoftheconceptsandapplicationsdiscussed hereareapplicabletodataderivedfromotherplatforms. T heInternationalHapMapProjectandthearrivalof technologiesthattypemorethan100,000SNPsina singleexperimenthavemadegenome-widesingle nucleotidepolymorphism(GW-SNP)assayarealistic endeavor.Thishassparkedconsiderabledebateregardingthe promiseofGW-SNPtypingtoidentifygeneticassociationin disease.Ashasalreadybeenshown,thisapproachhasthe potentialtolocalizecommongeneticvariationunderlying diseaserisk.Thedataprovidedfromthistechnologyalso lendsitselftoseveralotherlinesofinvestigation;autozygosity mappinginconsanguineousfamiliesandoutbred populations,directdetectionofstructuralvariation, admixtureanalysis,andotherpopulationgeneticapproaches. Inthisreviewwewilldiscussthepotentialusesandpractical applicationofGW-SNPtypingincludingthoseaboveand beyondsimpleassociationtesting. Genome-WideAssociation GW-SNPassayshavebeenanticipatedasatoolforthe dissectionofdiseaseriskfactorsformanyyears[4].Muchof thediscussionsurroundingtheapplicationofGW-SNPassays hascenteredontheutilityofthismethodinidentifying commongeneticvariabilitythatunderliesdisease[5,6].This discussionhasfocusedontherelativepowerofthesetypesof studyandthepotentialproblemsandpitfallsassociatedwith thisapproach,resultinginnumerousreviewandopinion pieces.Forthesakeofbrevitywewillnotdiscussthese considerationsindetail.Brie?y,however,theprimary concernbeforeundertakingagenome-wideassociation experimentisoneofstatisticalpowertoobserveaneffectofa speci?csize.Todatethisissuehaslargelybeenaddressedby prospectivepowercalculationsusingsimulation.These analysesgenerallyrelyonparameterssuchasthemodelof diseaserisk(dominant,recessive,additive)andes