Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection 英文参考文献.docVIP

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Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection 英文参考文献.doc

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Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection 英文参考文献

DirectInferenceofSNPHeterozygosityRates andResolutionofLOHDetection Xiaohong Li1*,Steven G. Self1,Patricia C.Galipeau2,Thomas G. Paulson1,2,Brian J.Reid1,2,3,4 1DivisionofPublicHealthSciences,FredHutchinsonCancerResearchCenter,Seattle,Washington,UnitedStatesofAmerica,2DivisionofHumanBiology,FredHutchinson CancerResearchCenter,Seattle,Washington,UnitedStatesofAmerica,3DepartmentofMedicine,UniversityofWashington,Seattle,Washington,UnitedStatesofAmerica, 4DepartmentofGenomeSciences,UniversityofWashington,Seattle,Washington,UnitedStatesofAmerica Singlenucleotidepolymorphisms(SNPs)havebeenincreasinglyutilizedtoinvestigatesomaticgeneticabnormalities inpremalignancyandcancer.LOHisacommonalterationobservedduringcancerdevelopment,andSNPassayshave beenusedtoidentifyLOHatspecificchromosomalregions.Thedesignofsuchstudiesrequiresconsiderationofthe resolutionfordetectingLOHthroughoutthegenomeandidentificationofthenumberandlocationofSNPsrequiredto detect genetic alterations in specific genomic regions. Our study evaluated SNP distribution patterns and used probability models, Monte Carlo simulation, and real human subject genotype data to investigate the relationships between the number of SNPs, SNP HET rates, and the sensitivity (resolution) for detecting LOH. We report that variances of SNP heterozygosity rate in dbSNP are high for a large proportion of SNPs. Two statistical methods proposedfordirectlyinferringSNPheterozygosityratesrequiremuchsmallersamplesizes(intermediatesizes)andare feasibleforpracticaluseinSNPselectionorverification.UsingHapMapdata,weshowedthataregionofLOHgreater than200kbcanbereliablydetected,withlossessmallerthan50kbhavingasubstantiallylowerdetectionprobability when using all SNPs currently in the HapMap database. Higher densities of SNPs may exist in certain local chromosomalregionsthatprovidesomeopportunitiesforreliablydetectingLOHofsegmentsizessmallerthan50kb. Theseresultssuggestthattheinterpretationoftheresultsfromgenome-widescansforLOHusingcommerci