Molecular Photofitting: Predicting Ancestry and Phenotype Using DNA PDF
Preview Molecular Photofitting: Predicting Ancestry and Phenotype Using DNA
MOLECULAR PHOTOFITTING This page intentionally left blank MOLECULAR PHOTOFITTING P R E D I C T I N G A N C E S T R Y A N D P H E N O T Y P E U S I N G D N A Tony N. Frudakis With a Chapter 1 Introduction by Mark D. Shriver AMSTERDAM • BOSTON (cid:127) HEIDELBERG (cid:127) LONDON NEW YORK (cid:127) OXFORD (cid:127) PARIS (cid:127) SAN DIEGO SAN FRANCISCO (cid:127) SINGAPORE (cid:127) SYDNEY (cid:127) TOKYO Academic Press is an imprint of Elsevier AcquisitionsEditor:JenniferSoucy Assoc.DevelopmentalEditor:KellyWeaver ProjectManager:ChristieJozwiak PublishingServicesManager:SarahHajduk CoverDesigner:AlisaAndreola Composition:SPi Printer:ChinaTranslation&PrintingServices,Ltd. AcademicPressisanimprintofElsevier 30CorporateDrive,Suite400,Burlington,MA01803,USA 525BStreet,Suite1900,SanDiego,California92101-4495,USA 84Theobald’sRoad,LondonWC1X8RR,UK Thisbookisprintedonacid-freepaper. Copyright(cid:1)2008,ElsevierInc.Allrightsreserved. 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ISBN:978-0-12-088492-6 ForinformationonallAcademicPresspublications visitourWebsiteatwww.books.elsevier.com PrintedinChina 07 08 09 10 9 8 7 6 5 4 3 2 1 T A B L E O F C O N T E N T S Foreword xi Preface xiii Acknowledgments xv Chapter1 ForensicDNAAnalysis:FromModestBeginningstoMolecularPhotofitting,Genics, Genetics,Genomics,andthePertinentPopulationGeneticsPrinciples 1 PartI:MarkD.Shriver Introduction:BriefHistoryofDNAinForensicSciences 1 TheStatisticsofForensicDNAAnalysis 6 TheNatureofHumanGeneticVariation 10 PopulationGeneticsandPopulationGenomics 11 ThePromiseofMolecularPhotofittingasaToolinForensicScience 16 PartII: TheBasicPrinciples 19 LackofHumanDiversityRelativetoOtherSpecies 32 Chapter2 AncestryandAdmixture 35 WhatAreAncestryandAdmixture? 35 TheNeedforMolecularTestsforAncestry 37 AncestryInformativeMarkers 43 BiogeographicalAncestryAdmixtureasaToolforForensicsandPhysicalProfiling 54 Chapter3 BiogeographicalAncestryAdmixtureEstimation—TheoreticalConsiderations 57 EstimatingbyAnthropometricTraitValue 57 AdmixtureandGeneFlowEstimatedfromSingleLoci 59 AdmixtureinIndividualSamples 68 UsingtheHanisMethodonPopulationModelsk>2 71 ParameterUncertainty 75 BayesianMethodsforAccommodatingParameterUncertainty 84 SamplingError 88 AssumptionsaboutMarkerLinkageandIntensityofAdmixtureinParents 90 Pritchard’sStructureProgram 92 InDefenseofaSimpleAdmixtureModel 94 PracticalConsiderationsforBuildinganAncestryAdmixtureTest 95 vi TABLE OF CONTENTS SelectingAIMsfromtheGenome—HowManyAreNeeded? 103 ComparingthePowerofSpecificLociforSpecificResolutions 110 GenomicCoverageofAIMs 114 MoreElaborateMethodsofSelectingMarkersforInformationContent 115 ShannonInformation 116 FischerianInformationContent 118 InformativenessforAssignment 119 TypeofPolymorphisms 123 InterpretationofAncestryEstimates 125 ObjectiveInterpretation 132 GeneticMappingandAdmixture 133 Appendix(AncestryFrequencyTable) 137 Chapter4 BiogeographicalAncestryAdmixtureEstimation—PracticalityandApplication 145 TheDistributionofHumanGeneticVariabilityandChoiceofPopulationModel 146 MarkerSelection 163 SampleCollection 164 PresentingIndividualBiogeographicalAncestry(BGAA)Results 179 ConceptualIssues 190 Chapter5 CharacterizingAdmixturePanels 203 ParentalSamplePlots 203 ModelChoicesandDimensionality 205 SizeofConfidenceContours 210 Repeatability 213 Sensitivity 220 AnalysisofResultsforGenealogists 222 AnalysisofResultsforNongenealogists 230 BlindChallengeofConcordancewithSelf-AssessedRace 232 ConfidenceIntervalWarping 235 SampledPedigrees 237 SimulatedPedigrees 240 ComparingDifferentAlgorithmswiththeSameAIMPanel 241 AnalysisUsingSubsetsofMarkers 243 ResolvingSampleMixtures 245 SampleQuantity 250 NonhumanDNA 251 PerformancewithAlteredParentalAlleleFrequencies 253 CorrelationwithAnthropometricPhenotypes 257 Simulations 260 CreatingSimulatedSamples 262 TABLE OF CONTENTS vii SourceofErrorMeasuredwithSimulations 263 RelationshipbetweenErrorinPopulationsandwithinIndividuals 265 Precisionofthe71AIMPanelfromSimulations 268 TrendsinBiasfromthe71AIMPanel 270 95%ConfidenceThresholdfor71AIMPanel 273 Precisionofthe171AIMPanelfromSimulations 275 MLEThresholdsforAssumptionofBonaFideAffiliation 277 Comparisonof71and171AIMPanels 277 ObservedandExpectedBias 277 WhatDotheSimulationsTeachUsaboutInterpretingBGA AdmixtureResults? 279 BiasSymmetry 280 ImpactofMLEAlgorithmDimensionality 282 SimulationsofAdmixedIndividuals 284 MLEPrecisionfromtheTrianglePlots 285 ConfidenceofNonzeroAffiliation 286 StandardDeviationfromConfidenceIntervals 286 TestingtheRelationbetweenConfidenceMeasuresinIndividuals andPopulations 288 SpaceoutsidetheTrianglePlot 289 CombinedSourcesSuggestanAverageError 294 Chapter6 ApportionmentofAutosomalDiversityWithContinentalMarkers 297 TheNeedforPopulationDatabases—WordsMeanLessThanData 297 TrendsonanEthnicLevel:AutosomalVersusSexChromosome Pattern 299 WhatDoContinentalAncestryAIMsSayaboutEthnicity? 303 TheSignificanceofFractionalAffiliationResultsonaPopulation Level 305 ReconstructingHumanHistoriesfromAutosomalAdmixtureResults 310 SharedRecentAncestryVersusAdmixture:WhatDoesFractional ContinentalAffiliationforanEthnicGroupMean? 311 ReturningBrieflytotheNamingProblem—Relevancefor InterpretingtheApportionmentofAutosomalDiversity 313 ASamplingofEthnicitiesUsingthe171AIMPanel 316 InterpretationofAncestryProfilesforEthnicPopulations 322 EastAsianAdmixtureintheMiddleEastandSouthAsia 337 ResolutionwithinContinentsBasedontheFour-PopulationModel 351 InterpretationofContinentalBGAResultsinLightofWhatWe HaveLearnedfromApplicationtoEthnicPopulations 352 viii TABLE OF CONTENTS AppropriatenessofaFour-PopulationModel 355 DoAlleleFrequencyEstimationErrorsAccountfortheSecondaryAffiliations inEthnicSubpopulations? 357 IndicationsofCrypticPopulationStructure 359 Chapter7 ApportionmentofAutosomalDiversitywithSubcontinentalMarkers 361 SubpopulationAIMsandEthnicStratification 361 WithintheEuropeanBGAGroup—ABriefHistoryofEuropeans 363 HowDoWeSubdivideEuropeansforForensicsUse? 366 DevelopmentofaWithin-EuropeanAIMPanel 367 TheEuro1.0AIMPanelforaFour-PopulationSubcontinentalModel 369 EstablishingtheOptimalParentalRepresentatives 370 BlindChallengewithEthnicallyAdmixedEuropean-AmericanSamples 378 PopulationIsolatesandTransplants 380 CorrelationswithAnthropometricTraits 384 TestError 387 HierarchicalNatureofEuro1.0—PriorInformationRequired 397 Euro1.0PedigreesasanAidtoInterpretingResults 403 Euro1.0—InterpretationofVariationwithinGroups 407 AnHistoricalPerspective 410 MoreDetailedSubpopulationStratifications—k¼7 412 WhatDotheGroupsNOR1,NOR2 ... Mean? 414 EvaluatingtheResultsfromthek¼7EuropeanModel 416 ComparisonwithPreviousStudiesBasedonGeneMarkers 417 ComparisonwithResultsfromOtherStudies 419 BlindChallengeofthek¼7ModelResultswithEthnicSamples 420 CorrelationwithAnthropometricTraits 423 Pedigrees 425 SubstantialVariationinAdmixturewithinEthnicGroups 425 AlternativeStylesforEstimatingEthnicAdmixture 427 Chapter8 IndirectMethodsforPhenotypeInference 429 EstimatesofGenomicAncestryAllowsforInferenceofCertainPhenotypes 429 PhenotypeVariationasaFunctionofHumanPopulationHistoryandIndividualAncestry 430 SourcesofPhenotypicVariation 432 EmpiricalObservationofAdmixture-BasedCorrelationEnablesGeneralization 438 EmpiricismasaToolfortheIndirectMethodofMolecularPhotofitting 440 ReverseFacialRecognitionUsingGenomicAncestryEstimates 450 EstimatingPhenotypefrom2DDigitalPhotographs 454 EstimatingPhenotypefrom3DDigitalPhotographs 456 ExamplesofDatabaseQueries—GlobalCharacteristicsfromDigitalPhotographs 458 TABLE OF CONTENTS ix ExamplesofDatabaseQueries—EthnicDescriptorsandGeopoliticalAffiliations 461 VariationandParameterizationofDatabaseObservations 464 CanSocialConstructSuchasRaceBeInferredfromDNA? 468 IndirectApproachUsingFinerPopulationModels 472 IndirectInferenceofSkinPigmentation 477 SourcesoftheAncestry-SkinPigmentationCorrelation 485 CanWeInferMKnowingGenomicAncestry? 488 InferencesofCompositeCharacteristics 490 WhyNotUsetheDirectMethodInstead? 490 IndirectInferenceofIrisPigmentation 491 Chapter9 DirectMethodofPhenotypeInference 497 Pigmentation 500 HistoryofPigmentationResearch 503 TheGeneticsofHumanPigmentation—AComplexPuzzle 504 BiochemicalMethodsofQuantifyingPigment 507 IrisColor 513 IrisColorPhenotyping:TheNeedforaThoughtfulApproach 514 MakingIrisColorMeasurements 517 PopulationSurveysofIrisMelaninIndex(IMI)Values 523 RelationofIMItoSelf-DescribedIrisColor 524 HistoryofGeneticResearchonIrisColor 527 RecentHistoryofAssociationMappingResults 530 OCA2—ThePrimaryIrisColorGene 534 AnEmpiricalOCA2-BasedClassifierfortheInferenceofIrisColor 543 TheEmpiricalMethodofDirectPhenotypeInference 553 CaseReports 558 HairColor 562 SkinPigmentation 583 FinalConsiderationsfortheDirectInferenceofSkinPigmentation 596 Chapter10 TheFirstCaseStudiesofMolecularPhotofitting 599 CaseReports 599 LouisianaSerialKillerMultiagencyHomicideTaskForceInvestigation 599 OperationMinstead 603 TheBoulder,ColoradoChaseCase 607 OtherCases 607 Chapter11 ThePoliticsandEthicsofGeneticAncestryTesting 609 Resistance 610 Articles—InsightintoPublicReaction 613
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