HLA imputation.doc

HLAimputationTheopen-(Ashkenazi)andthereference(European).Furthermore,alargenumberofSNPs(~4500),alimitednumberofSNPs(~1000)wasavailableinallthreedatasets(GENEMSA,2,andIMSGC),,-AHLA-BHLA-CHLA-DRB1HLA-DQB1Europeans(allSNPs)(limitedSNPs)(allSNPs)(limitedSNPs),,,wesetadifferentthresholdforthequalitymetricforeachallele,--Agene,uracyofimputation(y-axis)versusthecallrate(x-axis)fordifferentthresholdoftheconfidencemetric(colorscale).-A,%accuracyand100%%accuracy,wewouldsacrifice50%callrate,-Bgene,wechoseathresholdofconfidencemetricthatyielded94%accuracyat95%-C,therewasasteepdrop-%accuracywhileachievingover95%-DRB1,wewereabletoachieve90%accuracywithacallrateof80%.Asshownintheplotbelow,uracy,say95%,couldnotbeachievedwithoutasignificancesacrificeofcallratetobelow60%.ForHLA-DQB