Table Of Contentmore information - www.cambridge.org/9781107027527
ADVANCES IN STATISTICAL BIOINFORMATICS
Providing genome-informed personalized treatment is a goal of modern
medicine. Identifying new translational targets in nucleic acid characteriza-
tionsisanimportantsteptowardthatgoal.Theinformationtsunamiproduced
bysuchgenome-scaleinvestigationsisstimulatingparalleldevelopmentsinsta-
tisticalmethodologyandinference,analyticalframeworks,andcomputational
tools.
Withinthecontextofgenomicmedicineandwithastrongfocusoncancer
research,thisbookdescribestheintegrationofhigh-throughputbioinformatics
datafrommultipleplatformstoinformourunderstandingofthefunctionalcon-
sequencesofgenomicalterations.Thisincludesrigorousandscalablemethods
forsimultaneouslyhandlingdiversedatatypessuchasgeneexpressionarray,
miRNA,copynumber,methylation,andnext-generationsequencingdata.
Thismaterialiswrittenforstatisticianswhoareinterestedinmodelingand
analyzinghigh-throughputdata.Chaptersbyexpertsinthefieldofferathorough
introduction to the biological and technical principles behind multiplatform
high-throughputexperimentation.
Dr.Kim-AnhDoisProfessorandChairoftheDepartmentofBiostatisticsat
TheUniversityofTexasMDAndersonCancerCenter.
Dr. Zhaohui Steve Qin is an Associate Professor in the Department of Bio-
statistics and Bioinformatics at the Rollins School of Public Health, Emory
University.
Dr. Marina Vannucci is a Professor in the Department of Statistics at Rice
University,DirectoroftheInterinstitutionalGraduatePrograminBiostatistics
atRiceUniversity,andanadjunctfacultymemberofTheUniversityofTexas
MDAndersonCancerCenter.
ADVANCES IN STATISTICAL
BIOINFORMATICS
Models and Integrative Inference for
High-Throughput Data
Editedby
KIM-ANH DO
TheUniversityofTexasMDAndersonCancerCenter,Houston,TX
ZHAOHUI STEVE QIN
EmoryUniversity,Atlanta,GA
MARINA VANNUCCI
RiceUniversity,Houston,TX
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©CambridgeUniversityPress2013
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Firstpublished2013
PrintedintheUnitedStatesofAmerica
AcatalogrecordforthispublicationisavailablefromtheBritishLibrary.
LibraryofCongressCataloginginPublicationData
Advancesinstatisticalbioinformatics:modelsandintegrativeinference
forhigh-throughputdata/[editedby]Kim-AnhDo,UniversityofTexasMD
AndersonCancerCenter,ZhaohuiSteveQin,EmoryUniversity,AtlantaGA,
MarinaVannucci,RiceUniversity,Houston,TX.
pagescm
Includesbibliographicalreferencesandindex.
ISBN978-1-107-02752-7(hardback)
1.Bioinformatics–Statisticalmethods. 2.Biometry. 3.Genetics–Technique.
I.Do,Kim-Anh,1960– II.Qin,ZhaohuiSteve,1972– III.Vannucci,Marina,1966–
QH324.2.A395 2013
572.80285–dc23 2012049273
ISBN978-1-107-02752-7Hardback
CambridgeUniversityPresshasnoresponsibilityforthepersistenceoraccuracyofURLsfor
externalorthird-partyInternetWebsitesreferredtointhispublicationanddoesnotguarantee
thatanycontentonsuchWebsitesis,orwillremain,accurateorappropriate.
Contents
ListofContributors pagevii
Preface xi
1. AnIntroductiontoNext-GenerationBiologicalPlatforms
VirginiaMohlere,WentingWang,andGanirajuManyam 1
2. AnIntroductiontoTheCancerGenomeAtlas
BradleyM.BroomandRehanAkbani 31
3. DNAVariantCallinginTargetedSequencingData
WenyiWang,YuFan,andTerenceP.Speed 54
4. StatisticalAnalysisofMappedReadsfrommRNA-SeqData
ErnestTurroandAlexLewin 77
5. Model-BasedMethodsforTranscriptExpression-Level
QuantificationinRNA-Seq ZhaonanSun,HanWu,Zhaohui
Qin,andYuZhu 105
6. BayesianModel-BasedApproachesforSolexaSequencing
Data RitenMitra,PeterMueller,andYuanJi 126
7. StatisticalAspectsofChIP-SeqAnalysis JonathanCairns,
AndyG.Lynch,andSimonTavare´ 138
8. BayesianModelingofChIP-SeqDatafromTranscription
FactortoNucleosomePositioning RaphaelGottardoand
SangsoonWoo 170
9. MultivariateLinearModelsforGWAS ChiaraSabatti 188
10. BayesianModelAveragingforGeneticAssociationStudies
ChristinePeterson,MichaelSwartz,SanjayShete,and
MarinaVannucci 208
11. Whole-GenomeMulti-SNP-PhenotypeAssociationAnalysis
YongtaoGuanandKaiWang 224
v
vi Contents
12. MethodsfortheAnalysisofCopyNumberDatainCancer
Research BradleyM.Broom,Kim-AnhDo,MelissaBondy,
PatriciaThompson,andKevinCoombes 244
13. BayesianModelsforIntegrativeGenomics
FrancescoC.StingoandMarinaVannucci 272
14. BayesianGraphicalModelsforIntegratingMultiplatform
GenomicsData WentingWang,Veerabhadran
Baladandayuthapani,ChrisC.Holmes,andKim-AnhDo 292
15. GeneticalGenomicsData:SomeStatisticalProblemsand
Solutions HongzheLi 312
16. ABayesianFrameworkforIntegratingCopyNumberandGene
ExpressionData YuanJi,FilippoTrentini,andPeterMueller 331
17. ApplicationofBayesianSparseFactorAnalysisModelsin
Bioinformatics HaisuMaandHongyuZhao 350
18. PredictingCancerSubtypesUsingSurvival-SupervisedLatent
DirichletAllocationModels KeeganKorthauer,
JohnDawson,andChristinaKendziorski 366
19. RegularizationTechniquesforHighlyCorrelatedGene
ExpressionDatawithUnknownGroupStructure
BrentA.Johnson 382
20. OptimizedCross-StudyAnalysisofMicroarray-Based
Predictors XiaogangZhong,LuigiMarchionni,LeslieCope,
EdwinS.Iversen,ElizabethS.Garrett-Mayer,Edward
Gabrielson,andGiovanniParmigiani 398
21. FunctionalEnrichmentTesting:ASurveyofStatistical
Methods LailaM.PoissonandDebashisGhosh 423
22. DiscoverTrendandProgressionUnderlyingHigh-Dimensional
Data PengQiu 445
23. BayesianPhylogeneticsAdaptstoComprehensiveInfectious
DiseaseSequenceData JenniferA.Tom,JanetS.Sinsheimer,
andMarcA.Suchard 460
Index 477
Colorplatesfollowpage104.
List of Contributors
RehanAkbani
Department of Bioinformatics and Computational Biology, The University of
TexasMDAndersonCancerCenter
VeerabhadranBaladandayuthapani
Department of Biostatistics, The University of Texas MD Anderson Cancer
Center
MelissaBondy
DepartmentofPediatrics,BaylorCollegeofMedicine
BradleyM.Broom
Department of Bioinformatics and Computational Biology, The University of
TexasMDAndersonCancerCenter
JonathanCairns
DepartmentofOncology,UniversityofCambridge
KevinCoombes
Department of Bioinformatics and Computational Biology, The University of
TexasMDAndersonCancerCenter
LeslieCope
DepartmentsofOncologyandBiostatistics,JohnsHopkinsUniversity
JohnDawson
DepartmentofBiostatisticsandMedicalInformatics,UniversityofWisconsin–
Madison
Kim-AnhDo
Department of Biostatistics, The University of Texas MD Anderson Cancer
Center
YuFan
Department of Bioinformatics and Computational Biology, The University of
TexasMDAndersonCancerCenter
vii
viii ListofContributors
EdwardGabrielson
DepartmentsofOncologyandPathology,JohnsHopkinsUniversity
ElizabethS.Garrett-Mayer
DepartmentofBiostatistics,MedicalUniversityofSouthCarolina
DebashisGhosh
DepartmentofStatistics,PennStateUniversity
RaphaelGottardo
PublicHealthSciencesDivision,FredHutchinsonCancerResearchCenter
YongtaoGuan
DepartmentofMolecularandHumanGenetics,BaylorCollegeofMedicine
ChrisC.Holmes
DepartmentofStatistics,UniversityofOxford
EdwinS.Iversen
InstituteofStatisticsandDecisionSciences,DukeUniversity
YuanJi
CenterforClinicalandResearchInformatics,NorthShoreUniversityHealth-
System
BrentA.Johnson
DepartmentofBiostatisticsandBioinformatics,EmoryUniversity
ChristinaKendziorski
DepartmentofBiostatisticsandMedicalInformatics,UniversityofWisconsin–
Madison
KeeganKorthauer
DepartmentofBiostatisticsandMedicalInformatics,UniversityofWisconsin–
Madison
AlexLewin
DepartmentofEpidemiologyandBiostatistics,ImperialCollegeLondon
HongzheLi
DepartmentofBiostisticsandEpidemiology,UniversityofPennsylvania
AndyG.Lynch
DepartmentofOncology,UniversityofCambridge
HaisuMa
PrograminComputationalBiologyandBioinformatics,YaleUniversity
GanirajuManyam
Department of Bioinformatics and Computational Biology, The University of
TexasMDAndersonCancerCenter
LuigiMarchionni
DepartmentofOncology,JohnsHopkinsUniversity
RitenMitra
DepartmentofMathematics,UniversityofTexasatAustin
