Genetic Variation in an Individual Human Exome 英文参考文献.docVIP

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Genetic Variation in an Individual Human Exome 英文参考文献.doc

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Genetic Variation in an Individual Human Exome 英文参考文献

GeneticVariationinanIndividualHumanExome PaulineC.Ng*,SamuelLevy,JiaqiHuang,TimothyB.Stockwell,BrianP.Walenz,KelvinLi,Nelson Axelrod,DanaA.Busam,RobertL.Strausberg,J.CraigVenter J.CraigVenterInstitute,Rockville,Maryland,UnitedStatesofAmerica Abstract Thereismuchinterestincharacterizingthevariationinahumanindividual,becausethismayelucidatewhatcontributes significantlytoaperson’sphenotype,therebyenablingpersonalizedgenomics.Wefocushereonthevariantsinaperson’s ‘exome,’whichisthesetofexonsinagenome,becausetheexomeisbelievedtoharbormuchofthefunctionalvariation. We provide an analysis of the ,12,500 variants that affect the protein coding portion of an individual’s genome. We identified ,10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which ,15–20% are rareinthehumanpopulation.Wepredict,1,500nsSNPsaffectproteinfunctionandthesetendbeheterozygous,rare,or novel. Of the ,700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions ofamino acids in thecorresponding protein, rather than introducing frameshifts. Codingindels also occurfrequentlyattheterminiofgenes,soevenifanindelcausesaframeshift,analternativestartorstopsiteinthegene canstillbeusedtomakeafunctionalprotein.Insummary,wereducedthesetof,12,500nonsilentcodingvariantsby,8- foldtoasetofvariantsthataremostlikelytohavemajoreffectsontheirproteins’functions.Thisisourfirstglimpseofan individual’sexomeandasnapshotofthecurrentstateofpersonalizedgenomics.Themajorityofcodingvariantsinthis individualarecommonandappeartobefunctionallyneutral.Ourresultsalsoindicatethatsomevariantscanbeusedto improvethecurrentNCBIhumanreferencegenome.Asmoregenomesaresequenced,manyrarevariantsandnon-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformaticmethodstohoneinonpossiblefunctionalvariation. Citation:NgPC,LevyS,HuangJ,StockwellTB,WalenzBP,etal.(2008)GeneticVariationi