An Enhanced Single Base Extension Technique for the Analysis of Complex Viral Populations 英文参考文献.docVIP

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An Enhanced Single Base Extension Technique for the Analysis of Complex Viral Populations 英文参考文献.doc

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An Enhanced Single Base Extension Technique for the Analysis of Complex Viral Populations 英文参考文献

AnEnhancedSingleBaseExtensionTechniqueforthe AnalysisofComplexViralPopulations DaleR.Webster1,2.¤a,ArminG.Hekele3.¤b,AdamS.Lauring4,KaelF.Fischer2¤c,HaoLi2,RaulAndino3*, JosephL.DeRisi2,5 * 1BiologicalandMedicalInformaticsProgram,UniversityofCaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica,2DepartmentofBiochemistryand Biophysics, University of California San Francisco, San Francisco, California, United States of America, 3Department of Microbiology and Immunology, University of CaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica,4DepartmentofMedicine,UniversityofCaliforniaSanFrancisco,SanFrancisco,California, UnitedStatesofAmerica,5HowardHughesMedicalInstitute,UniversityofCaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica Abstract Manytechniquesforthestudyofcomplexpopulationsprovideeitherspecificinformationonasmallnumberofvariantsor general information on the entire population. Here we describe a powerful new technique for elucidating mutation frequenciesateachgenomicpositioninacomplexpopulation.Thissinglebaseextension(SBE)basedmicroarrayplatform was designed and optimized using poliovirus as the target genotype, but can be easily adapted to assay populations derivedfromanyorganism.Thesensitivityofthemethodwasdemonstratedbyaccurateandconsistentreadoutsfroma controlled population of mutant genotypes. We subsequently deployed the technique to investigate the effects of the nucleotideanalogribavirinonatypical polioviruspopulationthroughtworoundsofpassage.Ourresultsshowthatthis economical platform can be used to investigate dynamic changes occurring at frequencies below 1% within a complex nucleic acid population. Given that many key aspects of the study and treatment of disease are intimately linked to population-level genomicdiversity, our SBE-based technique provides ascalable andcost-effective complement toboth traditionalandnextgenerationsequencingmethodologies. Citation: Webster DR, Hekele AG, Lauring AS,