Biobanking: Methods and Protocols

443 Pages·2019·8.975 MB·English

by  William H. Yong

Methods in
Molecular Biology 1897
William H. Yong Editor
Biobanking
Methods and Protocols
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
Biobanking
Methods and Protocols
Edited by
William H. Yong
Division of Neuropathology, Department of Pathology and Laboratory Medicine,
Brain Tumor Translational Resource, Jonsson Comprehensive Cancer Center,
David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
Editor
WilliamH.Yong
DivisionofNeuropathology
DepartmentofPathologyandLaboratoryMedicine
BrainTumorTranslationalResource
JonssonComprehensiveCancerCenter
DavidGeffenSchoolofMedicineatUCLA
LosAngeles,CA,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8933-1 ISBN978-1-4939-8935-5 (eBook)
https://doi.org/10.1007/978-1-4939-8935-5
LibraryofCongressControlNumber:2018962741
©SpringerScience+BusinessMedia,LLC,partofSpringerNature2019
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis
concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction
onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation,
computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply,
evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations
andthereforefreeforgeneraluse.
Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto
betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty,
expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade.
Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations.
This Humana Press imprint is published by the registered company Springer Science+Business Media, LLC, part of
SpringerNature.
Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A.
Dedication
InmemoryandhonorofDr.HenryYong,Dr.CarlChan,andBrighamOlson
WithheartfeltthankstoPatricia,Marjorie,andMax
v
Preface
Biospecimens are the fuel that feeds the engine of modern biomedical research, and
biobanks are critical to harvesting, storing, and providing that fuel. This book covers
numerous practical topics in biomedical banking. It was crafted and written with the hope
andbeliefthatitwouldbeofvaluefornovicebiobankers,forpracticingbiobankers,andfor
end-user researchers. Besides many common biobanking topics, the book spans areas not
often touched including an overview of what is needed to start a biobank, training of new
biobanking personnel, and ethnic representation in biospecimen collection. Fascinating
chapters pertaining to aspects of flora and fauna biobanking provide different insights into
ourfieldandexpandthehorizonsofthoseofusinbiomedicalbiobanking.Inparticular,itis
my hope that this book is an incremental contribution toward sending cancer and other
diseasesintothedustyconfinesofancienthistory.Thisbookwouldnothavebeenpossible
without the many wonderful patients, families, and colleagues who have supported our
biobankingworkthroughtheArtoftheBrainFoundationatUCLA.Ithankalsothemany
laboratorymembersespeciallySergeyMareninovwhothroughtheyearshavedonethehard
workatthebench.Lastly,IwouldliketoacknowledgeDr.AfreenJasim,Dr.HannahLee,
Krishil Gandhi, and Madeline Olson for their generous assistance with logistical aspects of
thebook.
LosAngeles,CA,USA WilliamH.Yong
vii
Contents
Preface ..................................................................... vii
Contributors................................................................. xiii
1 SustainabilityinBiobanking.............................................. 1
MaramAbdaljaleel,ElyseJ.Singer,andWilliamH.Yong
2 AnIntroductiontoStartingaBiobank .................................... 7
MitraD.Harati,RyanR.Williams,MasoudMovassaghi,
AminHojat,GregoryM.Lucey,andWilliamH.Yong
3 AnIntroductiontoHardware,Software,andOtherInformation
TechnologyNeedsofBiomedicalBiobanks ................................ 17
KyuseokIm,DorinaGui,andWilliamH.Yong
4 DisasterPreventionandRecovery......................................... 31
ChonBoonEngandWeiLingTan
5 MinorityParticipationinBiobanks:AnEssentialKeytoProgress............. 43
PaulaKimandErinL.Milliken
6 OrientationandTrainingofNewBiobankPersonnel........................ 51
RyanR.Williams,DiviyaGupta,andWilliamH.Yong
7 ProcurementandStorageofSurgicalBiospecimens ......................... 65
AminHojat,BowenWei,MadelineG.Olson,QinwenMao,
andWilliamH.Yong
8 AutopsyBiobanking:BiospecimenProcurement,Integrity,Storage,
andUtilization ......................................................... 77
RandyS.Tashjian,RyanR.Williams,HarryV.Vinters,
andWilliamH.Yong
9 Procurement,Storage,andUseofBloodinBiobanks ....................... 89
JaclynN.Perry,AfreenJasim,AminHojat,andWilliamH.Yong
10 Procurement,Transportation,andStorageofSaliva,BuccalSwab,
andOralWashSpecimens................................................ 99
JenniferS.WooandDavidY.Lu
11 BiobankingofCerebrospinalFluid........................................ 107
RandyS.Tashjian,HarryV.Vinters,andWilliamH.Yong
12 BiobankingofUrineSamples............................................. 115
NedaA.Moatamed
13 ProcurementandStorageofPleuralandPeritonealFluids
forBiobanking ......................................................... 125
AlbertoM.Marchevsky,ShikhaBose,andBeatriceKnudsen
14 FluidPreservationofZoologicalSpecimens................................ 135
ThomasP.V.Hartman
15 PhotographingFluid-PreservedSpecimens................................. 149
DavidGlynneFoxandThomasP.V.Hartman
ix
x Contents
16 CastsofFluidPreservedSpecimens ....................................... 155
SarahBurhouseandThomasP.V.Hartman
17 CollectionandPreservationofTerrestrialArthropods....................... 163
Jeffrey D.Whitman,DouglasYanega,ColeB.G.Watson,
andVincentW.Strode
18 ProcurementandPreservationofPlants ................................... 191
AllisonD.RudalevigeandJeffreyD.Whitman
19 BiosafetyandBiohazards:UnderstandingBiosafetyLevels
andMeetingSafetyRequirementsofaBiobank............................. 213
LisaTa,LauraGosa,andDavidA.Nathanson
20 DecontaminationofBiobankFacilities .................................... 227
XinhaiZhang,SaiedMirshahidi,andChien-ShingChen
21 LaboratorySafety:ChemicalandPhysicalHazards.......................... 243
SaeedAsiryandLee-CynAng
22 MakingFormalin-Fixed,ParaffinEmbeddedBlocks......................... 253
AlirezaSadeghipourandPegahBabaheidarian
23 Microtomy:CuttingFormalin-Fixed,Paraffin-EmbeddedSections............ 269
JoanneSyandLee-CynAng
24 PerformingandCuttingFrozenSections .................................. 279
RamirS.Arcega,JenniferS.Woo,andHaodongXu
25 AnIntroductiontothePerformanceofImmunohistochemistry .............. 289
ShinoMagaki,SeyedA.Hojat,BowenWei,AlexandraSo,
andWilliamH.Yong
26 AnIntroductiontoPerformingImmunofluorescenceStaining ............... 299
KyuseokIm,SergeyMareninov,M.FernandoPalmaDiaz,
andWilliamH.Yong
27 MakingaTissueMicroarray.............................................. 313
MatthewKoo,JillM.Squires,DaphneYing,andJiaotiHuang
28 NucleicAcidIsolationandQualityControl................................ 325
LingDong,JaniceYoshizawa,andXinminLi
29 FundamentalsofRNAAnalysisonBiobankedSpecimens.................... 345
SamuelP.Strom
30 NucleicAcidExtractionfromHumanBiologicalSamples.................... 359
SureniV.Mullegama,MichaelO.Alberti,CoraAu,YanLi,
TraciToy,VaninaTomasian,andRenaR.Xian
31 AnOverviewofDNAAnalyticalMethods ................................. 385
ValerieA.ArboledaandRenaR.Xian
32 ShotgunProteomicProfilingofBloodborneNanoscale
ExtracellularVesicles .................................................... 403
PeteHeinzelman,DavidN.Powers,JamesA.Wohlschlegel,
andVargheseJohn
33 SamplePreparationforTransmissionElectronMicroscopy................... 417
ParastouTizro,CeciliaChoi,andNegarKhanlou
Contents xi
34 ProcessingofPrimaryPatientTumorsandSubsequentGeneration
ofPrimaryCellLines.................................................... 425
LauraGosa,LisaTa,andDavidA.Nathanson
35 DomesticandInternationalShippingofBiospecimens ...................... 433
DominiqueGordy,RandyS.Tashjian,HannahLee,
MasoudMovassaghi,andWilliamH.Yong
Index ...................................................................... 445
Contributors
MARAMABDALJALEEL (cid:1) DivisionofNeuropathology,DepartmentofPathologyandLaboratory
Medicine,DavidGeffenSchoolofMedicineatUCLA,LosAngeles,CA,USA
MICHAELO.ALBERTI (cid:1) DepartmentofPathologyandLaboratoryMedicine,DavidGeffen
SchoolofMedicineatUCLA,LosAngeles,CA,USA
LEE-CYNANG (cid:1) DepartmentofPathology(Neuropathology)andLaboratoryMedicine,
UniversityHospital–LondonHealthSciencesCenter,London,ON,Canada;Department
ofPathologyandLaboratoryMedicine,WesternUniversity,London,ON,Canada
VALERIE A.ARBOLEDA (cid:1) DepartmentofPathologyandLaboratoryMedicine,DavidGeffen
SchoolofMedicineatUCLA,LosAngeles,CA,USA
RAMIRS.ARCEGA (cid:1) DepartmentofPathologyandLaboratoryMedicine,DavidGeffenSchool
ofMedicineatUCLA,LosAngeles,CA,USA
SAEEDASIRY (cid:1) DepartmentofPathology,LenoxHillHospital–NorthwellHealth,NewYork,
NY,USA
CORAAU (cid:1) DepartmentofPathologyandLaboratoryMedicine,DavidGeffenSchoolof
MedicineatUCLA,LosAngeles,CA,USA
PEGAHBABAHEIDARIAN (cid:1) DepartmentofPathology,IranUniversityofMedicalSciences,
Tehran,TehranProvince,Iran
SHIKHA BOSE (cid:1) DepartmentofPathologyandLaboratoryMedicine,CedarsSinaiMedical
Center,LosAngeles,CA,USA
SARAH BURHOUSE (cid:1) NaturalHistoryMuseumatWollatonHall,Nottingham,UK
CHIEN-SHING CHEN (cid:1) BiospecimenLaboratory,LomaLindaUniversityCancerCenter,
LomaLinda,CA,USA;DivisionofHematologyandMedicalOncologyandBiospecimen
Laboratory,DepartmentofInternalMedicine,LomaLindaUniversitySchoolofMedicine,
LomaLinda,CA,USA
CECILIACHOI (cid:1) DivisionofNeuropathology,DepartmentofPathologyandLaboratory
Medicine,DavidGeffenSchoolofMedicineatUCLA,LosAngeles,CA,USA
M.FERNANDOPALMA DIAZ (cid:1) DepartmentofPathologyandLaboratoryMedicine,David
GeffenSchoolofMedicineatUCLA,LosAngeles,CA,USA
LING DONG (cid:1) TechnologyCenter forGenomicsandBioinformatics (TCGB),Departmentof
PathologyandLaboratoryMedicine,UniversityofCalifornia,LosAngeles,LosAngeles,
CA,USA
CHONBOONENG (cid:1) TissueRepository,NationalUniversityHospital,NationalUniversity
HealthSystem,Singapore,Singapore
DAVIDGLYNNEFOX (cid:1) SchoolofLifeSciences,UniversityofNottingham,Nottingham,UK
DOMINIQUEGORDY (cid:1) DivisionofNeuropathology,DepartmentofPathologyandLaboratory
Medicine,DavidGeffenSchoolofMedicineatUCLA,LosAngeles,CA,USA
LAURAGOSA (cid:1) DepartmentofMolecularandMedicalPharmacology,DavidGeffenSchoolof
MedicineatUCLA,LosAngeles,CA,USA;AhmansonTranslationalImagingDivision,
DavidGeffenSchoolofMedicineatUCLA,LosAngeles,CA,USA
DORINA GUI (cid:1) DepartmentofPathologyandLaboratoryMedicine,UCDavisSchoolof
Medicine,Sacramento,CA,USA
DIVIYAGUPTA (cid:1) DivisionofNeuropathology,DepartmentofPathologyandLaboratory
Medicine,DavidGeffenSchoolofMedicineatUCLA,LosAngeles,CA,USA
xiii