Cancer Bioinformatics

279 Pages·2018·9.691 MB·English

by  coll.

Methods in
Molecular Biology 1878
Alexander Krasnitz Editor
Cancer
Bioinformatics
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Cancer Bioinformatics
Edited by
Alexander Krasnitz
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory,
Cold Spring Harbor, NY, USA
Editor
AlexanderKrasnitz
SimonsCenterforQuantitativeBiology
ColdSpringHarborLaboratory
ColdSpringHarbor,NY,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8866-2 ISBN978-1-4939-8868-6 (eBook)
https://doi.org/10.1007/978-1-4939-8868-6
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Preface
Moderncancerresearch,bothbasicandtranslational,routinelygeneratesmassiveamounts
ofdigitaldataandincreasinglyreliesoncomputingfortheirinterpretation.Thesedatacome
from a variety of sources, among them next-generation sequencing of tumor DNA and
RNA, epigenomics, imaging, and pathological evaluation. It is expected that in the near
future data-driven methods will become an integral part of clinical practice in oncology,
leading to earlier detection, more accurate diagnosis, and better-informed management of
thedisease.
With this development in mind, the present volume covers a wide variety of cancer-
relatedmethodsandtoolsfordataanalysisandinterpretation,reflectingthestateoftheart
in cancer informatics. The volume is designed to attract broad readership, ranging from
active researchers in computational biology and bioinformatics developers, to research and
clinical oncologists who require bioinformatics support, to anticancer drug developers
wishingtorationalizetheirsearchfor newcompounds.
ColdSpringHarbor,NY,USA AlexanderKrasnitz
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 APrimer forAccesstoRepositoriesofCancer-Related
GenomicBigData ...................................................... 1
JohnTorcivia-Rodriguez,HayleyDingerdissen,Ting-ChiaChang,
andRajaMazumder
2 BuildingPortableandReproducibleCancerInformaticsWorkflows:
AnRNASequencingCaseStudy.......................................... 39
GauravKaushikandBrandiDavis-Dusenbery
3 ComputationalAnalysisofStructuralVariationinCancerGenomes........... 65
MatthewHayes
4 CORE:ASoftwareToolforDelineatingRegionsofRecurrent
DNACopyNumberAlterationinCancer.................................. 85
GuoliSunandAlexanderKrasnitz
5 IdentificationofMutatedCancerDriverGenesinUnpaired
RNA-SeqSamples....................................................... 95
DavidMosen-Ansorena
6 AComputationalProtocolforDetectingSomaticMutations
byIntegratingDNAandRNASequencing................................. 109
MatthewD.Wilkerson
7 Allele-SpecificExpressionAnalysisinCancerUsingNext-Generation
SequencingData........................................................ 125
AlessandroRomanel
8 ComputationalAnalysisoflncRNAFunctioninCancer...................... 139
XuZhangandTsui-TingHo
9 ComputationalMethodsforIdentificationofTCellNeoepitopes
inTumors.............................................................. 157
VanessaIsabellJurtzandLarsRønnOlsen
10 ComputationalandStatisticalAnalysisofArray-BasedDNA
MethylationData....................................................... 173
JessicaNordlund,ChristoferBa€cklin,andAmandaRaine
11 ComputationalMethodsforSubtypingofTumorsandTheir
ApplicationsforDecipheringTumorHeterogeneity......................... 193
ShihuaZhang
12 StatisticallySupportedIdentificationofTumorSubtypes .................... 209
GuoliSunandAlexanderKrasnitz
vii
viii Contents
13 ComputationalMethodsforAnalysisofTumorClonality
andEvolutionaryHistory................................................ 217
GeraldGoh,NicholasMcGranahan,andGarethA.Wilson
14 PredictiveModelingofAnti-CancerDrugSensitivityfromGenetic
Characterizations ....................................................... 227
RaziurRahmanandRanadipPal
15 InSilicoOncologyDrugRepositioningandPolypharmacology .............. 243
FeixiongCheng
16 ModelingGrowthofTumorsandTheirSpreadingBehavior
UsingMathematicalFunctions ........................................... 263
BertinHoffmann,ThorstenFrenzel,Ru¨digerSchmitz,
UdoSchumacher,andGeroWedemann
Index ...................................................................... 279
Contributors
CHRISTOFERB€aCKLIN (cid:1) DepartmentofMedicalSciences,UppsalaUniversity,Uppsala,
Sweden
TING-CHIACHANG (cid:1) DepartmentofBiochemistryandMolecularMedicine,George
WashingtonUniversity,Washington,DC,USA
FEIXIONGCHENG (cid:1) Center forComplexNetworksResearch,NortheasternUniversity,Boston,
MA,USA
BRANDIDAVIS-DUSENBERY (cid:1) SevenBridgesGenomics,Cambridge,MA,USA
HAYLEYDINGERDISSEN (cid:1) DepartmentofBiochemistryandMolecularMedicine,George
WashingtonUniversity,Washington,DC,USA
THORSTENFRENZEL (cid:1) InstituteforAnatomyandExperimentalMorphology,University
CancerCenterHamburg-Eppendorf,Hamburg,Germany
GERALD GOH (cid:1) CancerResearchUKLungCancerCentreofExcellence,UniversityCollege
LondonCancerInstitute,London,UK;GenomeInstituteofSingapore,Singapore,
Singapore
MATTHEWHAYES (cid:1) ComputerScience,XavierUniversityofLouisiana,NewOrleans,LA,
USA
TSUI-TINGHO (cid:1) CancerInstitute,DepartmentofRadiationOncology,Universityof
MississippiMedicalCenter,Jackson,MS,USA
BERTINHOFFMANN (cid:1) CompetenceCenterBioinformatics,InstituteforAppliedComputer
Science,UniversityofAppliedSciencesStralsund,Stralsund,Germany
VANESSAISABELLJURTZ (cid:1) DepartmentofBioandHealthInformatics,TechnicalUniversity
ofDenmark,Lyngby,Denmark
GAURAVKAUSHIK (cid:1) FoundationMedicine,Cambridge,MA,USA
ALEXANDERKRASNITZ (cid:1) SimonsCenter forQuantitativeBiology,ColdSpringHarbor
Laboratory,ColdSpringHarbor,NY,USA
RAJAMAZUMDER (cid:1) DepartmentofBiochemistryandMolecularMedicine,GeorgeWashington
University,Washington,DC,USA
NICHOLASMCGRANAHAN (cid:1) CancerResearchUKLungCancerCentreofExcellence,
UniversityCollegeLondonCancerInstitute,London,UK
DAVIDMOSEN-ANSORENA (cid:1) DepartmentofBiostatistics,HarvardT.H.ChanSchoolofPublic
Health,Boston,MA,USA;DepartmentofBiostatisticsandComputationalBiology,Dana-
FarberCancerInstitute,Boston,MA,USA
JESSICANORDLUND (cid:1) DepartmentofMedicalSciencesandScienceforLifeLaboratory,
UppsalaUniversity,Uppsala,Sweden
LARSRØNNOLSEN (cid:1) DepartmentofBioandHealthInformatics,TechnicalUniversity
ofDenmark,Lyngby,Denmark
RANADIPPAL (cid:1) ElectricalandComputerEngineering,TexasTechUniversity,Lubbock,TX,
USA
RAZIURRAHMAN (cid:1) ElectricalandComputerEngineering,TexasTechUniversity,Lubbock,
TX,USA
AMANDARAINE (cid:1) DepartmentofMedicalSciencesandScienceforLifeLaboratory,Uppsala
University,Uppsala,Sweden
ix
x Contributors
ALESSANDROROMANEL (cid:1) CentreforIntegrativeBiology(CIBIO),UniversityofTrento,
Trento,Italy
RU¨DIGERSCHMITZ (cid:1) InstituteforAnatomyandExperimentalMorphology,UniversityCancer
CenterHamburg-Eppendorf,Hamburg,Germany
UDOSCHUMACHER (cid:1) InstituteforAnatomyandExperimentalMorphology,University
CancerCenterHamburg-Eppendorf,Hamburg,Germany
GUOLISUN (cid:1) IntuitInc.,MountainView,CA,USA
JOHNTORCIVIA-RODRIGUEZ (cid:1) DepartmentofBiochemistryandMolecularMedicine,George
WashingtonUniversity,Washington,DC,USA
GEROWEDEMANN (cid:1) CompetenceCenterBioinformatics, InstituteforAppliedComputer
Science,UniversityofAppliedSciencesStralsund,Stralsund,Germany
MATTHEWD.WILKERSON (cid:1) TheAmericanGenomeCenter,CollaborationHealthInitiative
ResearchProgram,DepartmentofAnatomy,PhysiologyandGenetics,UniformedServices
University,Bethesda,MD,USA
GARETHA.WILSON (cid:1) CancerResearchUKLungCancerCentreofExcellence,University
CollegeLondonCancerInstitute,London,UK;TranslationalCancerTherapeutics
Laboratory,TheFrancisCrickInstitute,London,UK
SHIHUAZHANG (cid:1) NationalCenterforMathematicsandInterdisciplinarySciences,Academy
ofMathematicsandSystemsScience,ChineseAcademyofSciences,Beijing,China
XUZHANG (cid:1) CenterofClinicalandTranslationalSciencesandDepartmentofInternal
Medicine,TheUniversityofTexasHealthScienceCenteratHouston,Houston,TX,USA
Chapter 1
A Primer for Access to Repositories of Cancer-Related
Genomic Big Data
John Torcivia-Rodriguez, Hayley Dingerdissen, Ting-Chia Chang,
and Raja Mazumder
Abstract
Theuseoflargedatasetshasbecomeubiquitousinbiomedicalsciences.Researchersinthefieldofcancer
genomicshave,inrecentyears,generatedlargevolumesofdatafromtheirexperiments.Thoseresponsible
forproductionofthisdataoftenanalyzeanarrowsubsetofthisdatabasedontheresearchquestiontheyare
trying toaddress: this is thecase whether or not they areacting independentlyor in conjunction with a
large-scalecancergenomicsproject.Therealityofthissituationcreatestheopportunityforotherresearch-
erstorepurposethisdatafordifferenthypothesesifthedataismadeeasilyandfreelyavailable.Newinsights
in biology resulting from more researchers having access to data they otherwise would be unable to
generate on their own are a boon for the field. The following chapter reviews several cancer genomics-
relateddatabasesandoutlinesthetypeofdatatheycontain,aswellasthemethodsrequiredtoaccesseach
database. While this list is not comprehensive, it should provide a basis for cancer researchers to begin
exploringsomeofthemanylargedatasetsthatareavailabletothem.
Keywords Cancerresources,Genomicsdatabases,Cancerontology,Cancergenomics
1 Introduction
Everydayarapidlyincreasingamountofbiologicalandbiomedical
dataisgeneratedduetohigh-throughputsequencing(HTS)meth-
ods being used to explore genomics and proteomics hypotheses.
Thesemethodologiesallowforthecaptureoflargeamountsofdata
relevant to a target or set of targets of interest for the researcher
thentofurtheranalyze.Thisdataandtherelatedanalysisareusually
thendepositedinadatabaseand/orpublishedinajournal.Because
ofthescaleandexpanseofthedatagenerated,thedatacanoftenbe
usedtoanswerquestionsfarbeyondtheoriginalresearchhypothe-
sismakinggeneralavailabilityofthisdataimportantfortheresearch
community.Severalconsortiumshavebeendevelopedtomoderate
access to such data due to potential privacy issues, allowing either
generalaccesstotheentiredatasetiftheseissuesarenotrelevantor
AlexanderKrasnitz(ed.),CancerBioinformatics,MethodsinMolecularBiology,vol.1878,
https://doi.org/10.1007/978-1-4939-8868-6_1,©SpringerScience+BusinessMedia,LLC,partofSpringerNature2019
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