3/11/2015

WhatssospecialaboutNextGenerationsequencing?OxbridgeBiotechRoundtable

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OxbridgeBiotechRoundtable>RoundtableReview>PolicyPulse>WhatssospecialaboutNextGeneration
sequencing?

WhatssospecialaboutNextGenerationsequencing?
Sunday,19thAugust2012
PolicyPulse

NextGenerationDNAsequencingtechnologyisprogressingrapidly,producingconsiderableadvancementsin
diversefieldsrangingfromretracingthestepsofa5,000yearoldIcemantodevelopingbreastcancertherapies.A
searchforNextGenerationSequencinginthePubMeddatabaserevealsover1,000paperspublishedinthelastyear
alone,withmanygeneticsstudiesreachingmainstreamnewssitessuchastheBBC,GuardianScienceandthe
Telegraph.Withthesenewtechnologiesawiderangeofscienceisnowfeasiblethatwaspreviouslyunimaginable.
Wholegenomesequencingofthe5,000yearoldIcemantzi,foundintheFrenchAlpsin1991,revealedagenetic
predispositiontoheartdiseaseandvaluablehistoricalinformationabouttzisorigin,bloodtypeandcluestohis
appearance(1,2).TheHumanMicrobiomeProjectaimstosequenceallthebacteriaandmicrobesinthehumanbody
(3)improvingdiagnosis,treatmentandunderstandingofanarrayofdiseases.Sequencingofcancergenomesis
revealingawidegeneticvariationwithinasingletumour,withimplicationsfordrugresistanceandtreatmentofthe
disease(46).TheCancerGenomicsHubwasannouncedinCaliforniainMaythisyearacollectionofallthedata
fromthethreebigsequencingcentresintheUSA,holding5petabytesofinformationoncancergenomics(7,8).
Whiletheseandotherprojectsadvancerapidly,theyaredependentonthetechnologyandhowgovernments,doctors
andscientistsarechoosingtouseit.Earlierthisyear,theannouncementbyOxfordNanoporeTechnologies(9)ofa
USBsizedmachineinwhichsequencingcanbecarriedoutinaslittleas15minuteswithanexpectedretailofaround
$900willhaveimportantimplicationsinbothacademicandmedicallabs.Pavingtheway,Norwayannouncedthis
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yearthatNextGenerationSequencingwillbeincludedinitshealthserviceforthetreatmentofcancer(10),while
manyothercountriesareusingNextGenerationTechnologiesinresearchhospitals.Whiletheseadvancementssound
spectacular,theyhavecomeafterthehardworkofgreatscientistsofanearlierera,andmuchworkremainsto
overcomethelingeringhurdlesofthescienceandalsotheregulationofNextGenerationsequencing.
Lettherebelight
WhileNextGenerationSequencingtechnologiesallowforthesequencingofawholegenomeinjustafewdays,
originalsequencingtechnologiesofteninvolveddangerousradiationandtedioustimeconsumingsteps.
Thefirstbigbreakthroughsinsequencingtechnologieshappenedinthemid1970s,withaseriesofmethodsbased
onpolyacrylamidegelelectrophoresis,whichallowsDNAfragmentstobedistinguishedbytheirsize.Frederick
Sangersinitialplusandminussequencingmethod,publishedin1975,wasthefirstofthese.Itwasdependenton
comparingthelengthsofnucleotidesextendedinthepresence(plus)orabsence(minus)ofaparticularnucleicacid
(A,C,T,orG).Whilethiswasquiteanadvance,thismethodhadlimitations:itcouldonlydetermine50basesper
reaction,notallbasesinthemiddleoftheruncouldbedetermined,anditwasdifficulttodeterminethelengthofthe
sequencingruns(11).
Twomethodspublishedin1977tookthisconceptevenfurther.ThefirstofthesewasMaxamGilbertsequencing,or
ChemicalSequencing,developedbyAllanMaxamandWalterGilbert,andwasthefirstwidelyusedsequencing
method.TheprocessusedradioactivelabelingofdoublestrandedDNAfragments.TheDNAwasthencleavedby
basespecificchemicalreactionsandthefragmentsseparatedbyelectrophoresis(Fig.1a).Thesecondmethodwas
FrederickSangersimprovementonhisplusandminusmethodwiththedideoxyorchainterminationmethod.The
processisstillwidelyusedtoday.InsteadofchemicalcleavageoftheDNA,theprocessdependson32Plabelled
chainterminatingdideoxynucleotides,whichpreventfurtherextensionofthesequenceuponincorporation[Fig.1b].
Eachreactionthusgeneratesfragmentsofincreasingsize,endingatthebasespecifiedbythereactioni.e.eachA,T,
CorG.Thismethodoriginallyallowedreadingofsequencesupto100basepairslong(11).SangerandGilbert
receivedtheNobelPrizeforchemistryin1980fortheircontributiontoDNAsequencingtechnologies,sharedwith
PaulBergforhisworkonthechemistryofDNAandrecombinantDNA(12).Improvementsinthegeltechnology
andbettergelresolution,duetoradioactivelabellingwith35Sorfluorescenttagsratherthan32P,allowedsequencing
ofupto30,000basesofDNAinoneday,withuptoapproximately400basessequencedperreactionbytheearly
1980s(11).

Figure1TheOriginalSequencingTechnologies
A)MaxamGilbert(Chemicalsequencing)andB)SangerDideoxyChaintermination
sequencing.Part3showsDNAfragmentsresolvedonapolyacrylamidegelandasequencing
tracefromamodernautomatedsequencingmachine.FiguresbySarahEtheridge
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Withproductionofsuchlargequantitiesofsequencingdata,thedataprocessingsoonbecamearesearchtopicinitself
andthebirthofbioinformaticswasinevitable.Thenin1986,encouragingtheriseofthisnewfield,LeroyHoodat
Caltec
h,incollaborationwithAppliedBiosystems(ABI),publishedthefirstreportofsequencingdatabeingcollected
directlytoacomputer.Thetechnology,basedonSangersdideoxymethod,usessequencingprimersfluorescently
endlabelledwithfourdifferentcolourstorepresenteachbase.Reactionsarethenrunsimultaneouslythrougha
polyacrylamidetubegel,withtheDNArecognisedbyitsfluorescenceasitpassesadetector.Aseriesofnewand
improvedABImachineswerereleasedinthefollowingyearswithdedicatedsequencingfacilitiessetupwiththe
eventualaimofsequencingthehumangenome(11).
Sequencingjustgotbetter
DiscussionsabouttheHumanGenomeProjectofficiallybeganatameetingin1985,witha5yearplanpublishedto
theDOEandNIHin1990.AlthoughbeginningintheUS,theprojectbecameaninternationalcollaborationbetween
centresintheUS,EuropeandJapanwitheachcentrefocusingonparticularregionsofthegenome.In1992,Craig
VenterandcolleaguesattheNIHsetuponeofthefirstdedicatedsequencingfacilitiesTheInstituteforGenomic
ResearchTIGR.

Figure2WholeGenomeShotgunsequencing(WGS)
Adaptedfrom:
http://www.bio.davidson.edu/courses/genomics/method/shotgun.html
andhttp://www.biomedcentral.com/1471
2164/11/438/figure/F1?highres=y
In1995,hisgroupandcollaboratorsreportedthecompletegenomesequencesofthebacteriaHaemophilusinfluenzae
andMycoplasmagenitalium,thelargestgenomicsequencespublishedatthattime.Venterandhisteamintroduced
criticalimprovementstoamethodknownastheWholeGenomeShotgun(WGS)approach,whichlaterformedthe
basisofNextGenerationSequencing.InWGS,wholegenomicDNAisrandomlyfragmentedandclonedintoE.Coli
[Fig.2].Theclonesaresequencedatrandomandassembledwithspecialisedsoftware.TheTIGRassemblerwasone
ofthefirstpiecesofsoftwarethatallowedtheanalysisofthousandsofsequencereadsmakinginterpretationofthe
datapossible.
ThedevelopmentoftheABI3700Capillarysequencerinthelate1990swasanotherkeyprogressionduringthistime,
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allowingsimultaneoussequencingofupto96samplesthroughseparatecapillariesfilledwithnoncrosslinked
polymermatrix.CraigVenterandcolleaguesadoptedtheABI3700withtheircompanyCelera,whichworkedin
directcompetitiontothepublicHumanGenomeproject.Theresultsofeachprojectwerepublishedinthesame
week,withthefirstdraftsequencesoftheHumanGenomeProjectpublishedinNatureandSciencein2001.
WhiletheWGSapproachledtothedevelopmentoftheNextGenerationSequencingmethods,whichreadhundreds
orthousandsofsequencesinparallel,thehighthroughputtechnologycancompromisetheaccuracyandlengthofthe
sequencessuchthatfollowupwithdideoxySangersequencingisoftennecessary.ExomeSequencing,alsoknown
asTargetedExomeCapture,isavariationofNextGenerationSequencingthatonlysequencesDNAregionsthat
encodeproteins,knownasexons.Exonsonlyaccountforaround1%ofthegenome,sothismethodallowsthe
exclusionofthelargeintronicsequencesfoundwithinandbetweengenes,thussavingtimeandreducingcost.This
methoddoesriskexcludingmutationsinnoncodingregionsofthegenome,however,andseveraldiseaseshave
recentlybeenlinkedtomutationsintheseareas.
SomeofthefirstcommerciallyavailableNextGenerationtechnologiesweredevelopedby454LifeSciencesand
Solexatechnology,laterpurchasedbyIllumina.BothmethodsinvolverandomshearingofgenomicDNA,followed
bylinkingtobeadsoraspecialisedslide.The454LifeSciencessystem[Fig.3A]isbasedonthepyrosequencing
method,whichallowsshotgunsequencingwithoutcloninganyoftheDNA.PyrosequencinginvolvesaDNA
synthesisreaction,witheachofthefourdNTPbasesappliedoneafteranother.DuringaDNAsynthesisreaction,a
Phosphategroupisreleasedwhentwonucleotidesarebound.Pyrosequencingmeasurestheamountofphosphate
releasedaseachdNTPisaddedtothereactionandincorporatedintothesequence(13).Drawbacksincludetheriskof
basesbeingfalselyinsertedorremoved/deletedfromthesequenceduetomisjudgmentsinthelengthofthe
sequencingrun.TheseerrorsareknownasIndels.Themethodcanproduceonemillionbasesofsequencewith
99.5%accuracy,witheachreadmorethan250baseslong(13).Solexatechnology[Fig.3B]alsousesDNAsynthesis
reactionsbutmeasuringfluorescenceratherthanpyrophosphatereselase.Fluorescentlylabeledchainterminating
nucleotidesareincorporatedintothesequenceandmeasuredbyadetector.However,theincorporationofthechain
terminatingnucleotideisreversible,allowingthesynthesistocontinueuntilanotherchainterminatingnucleotideis
incorporated,sothebasesineachsequencearemeasuredoneatatime.Aseachbaseofthesequenceisreadinan
individualstep,thenumberofindelsisreducedcomparedtothe454technology.Reversibledyeterminator
nucleotidesarenotincorporatedefficiently,meaningasmallerreadlengthcomparedtothe454andmorebase
substitutionerrors.Themethodcanproduce1billionbasesof3040basesequencesinasinglerun(14).

Figure3NextGenerationSequencingMethodsA)454Methodadaptedfrom
(13)http://www.wellcome.ac.uk/Educationresources/Teachingand
education/Animations/DNA/WTX056046.htm
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B)SolexaTechnology,adaptedfrom
(14)http://wellcome.ac.uk/Educationresources/Teachingand
education/Animations/DNA/WTX056051.htm
Asdescribedabove,theannouncementofthereleaseoftheNanoporeSequencingtechnologyisanexciting
development,withthepotentialtorevolutionisethesequencingworldandgenomicmedicine.Thetechnologyis
remarkablysmart:DNAnucleotidesareguidedthroughnanoporesbyanenzyme,interruptingtheflowofions
throughtheporewhentheypassthrough.Eachnucleotidecanthusbedetectedasadistinctelectricalsignaldueto
differencesintheinterruptionofionflow.LongstrandsofDNAcanbereadnucleotidebynucleotideinthismanner
[Fig.4].Furtherdetailsofthetechnologyanditscompetitioncanbefoundhere.Nanoporetechnologyrepresentsa
rapidstepforwardbecausenomodificationoramplificationoftheDNAisneededbeforesequencingtakesplace,
savingtimeandreducingerrorssosequencingcanbecarriedoutinaslittleas15minutes.TheportableMinION
devicewouldallowdoctorstosequencedirectlyfromapatientsbloodintheclinic,whilethelargerGridION
devicecansequenceanentiregenomeinaday.Thelowoperatingandretailcostsalsomeanthatthegoalofthe
longawaited$1,000dollargenomehasnowbeenreached,makinggenomicmedicinearealistictreatmentoptionfor
manypatientsinthenearfuture(1517).

Figure4NanoporeSequencingTechnologyProteinnanoporesaresetinanelectrically
resistantmembranebilayer.Anioniccurrentispassedthroughthenanopores,andifan
analytepassesthroughtheporeornearitsaperture,acharacteristicdisruptionofcurrentis
created.Bymeasuringthatcurrent,itispossibletoidentifythemoleculeinquestion.
Duringsequencing,forexample,aDNAstrandisfedthroughthenanoporebyanenzyme
andeachofthefourstandardDNAbasesG,A,TandCcanbeidentified.From(16)
http://www.nanoporetech.com/technology/introductiontonanoporesensing/introduction
tonanoporesensing
Anethicalnomansland
Withtherapidlydecreasingcostandtimeofgenomesequencingcomeseverallegalandethicalissues.Ownershipof
thesequencingdata,storage,accessandprivacyaresignificantconcernsoncethepatientssamplehasbeentaken.A
fearofgeneticdiscrimination,forexamplebyinsurancecompanies,mayalsopreventpeopleundergoinggenetic
testingwhenitwouldbeofbenefit(1820).Ownershipofdonatedsamplesbecomesaparticularissuewhenthe
samplesproducescientificbreakthroughsofusetothebiotechindustry.Onefamousexampleofcontroversialuseof
apatienttissueisHeLacells,thefirstimmortalisedcellline,whichwereisolatedfromacervicalcancerbiopsytaken
withoutconsentfromthepatientHenriettaLacksinthe1950s(21).
ArelatedcaseinvolvinggeneticinformationisthatofGreenbergv.MiamiChildrensResearchInstitute(2003).The
plaintiffsinthiscasewereagroupoffamiliesaffectedbyCanavandisease,aninheriteddegenerativebraincondition
resultingfromaninabilitytoprocesstheaminoacidAsparticacid.ThefamilieshadpreviouslypersuadedDrReuben
Matalontoconductresearchtoidentifythegeneresponsibleforthediseaseandhadsetupatissuebankwiththeaim
offindinganaffordablediagnostictest.Theydidindeedfindthegeneanddevelopatest.However,Matalonwent
ontoobtainapatentforthegenewithoutthefamiliesconsent,sohisemployer,MiamiChildrensResearchInstitute,
gainedcontroloftestingforthedisease.Thefamiliesbelievedthattheseactionsdisagreedwiththeoriginalpurpose
ofthedonations.Thecourtdidnotfindthatthefamilieshadapropertyrighttothetissue,however,statingthatthe
propertyrightinbloodandtissuesamplesevaporatesoncethesampleisvoluntarilygiventoathirdparty(22,23)
Thegeneralfeelingbythecourtsappearedtobethatthereisadangerifpeoplecanexploittheirbodiesforfinancial
gain,andthatthismaynegativelyimpactonthebiotechindustryandthereforeonthedevelopmentofresearchand
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healthcare.Somearguefortissuedonorstobenamedasinventorsonpatentsarisingfromtheirtissueasunique
material,whichmayincentivisetissuedonation(23).Theargumentagainstthisisthatapatentrequiresaninventive
stepandthereforedetailedknowledgeofhowtoadvancetheresearchusingthedonatedsample..Theargumentis
lessthanclearwiththeGreenbergcase,asthefamilieswishedtheirtissuetobeusedforresearch.However,they
maynothavetheknowledgetoconducttheexperimentsneededtoidentifythegeneanddevelopthediagnostic
procedures.Aninnovativemother,SharonTerry,whosetwochildrenareaffectedbytheinheritedcondition
pseudoxanthomaelasticum(PXE)wasnamedascoinventorforthepatentforthePXEgene(ABCC6)whichaffects
connectivetissueintheskin,retinaandthecardiovascularsystem.ShefoundedPXEinternationalwithherhusband,
settingupacentralizedtissuebankandcoordinatinggenetic,epidemiologicalandotherstudies.MrsTerryisalso
nowCEOoftheGeneticAlliance(2325).
Personalisedmedicineandthefuture
Sequencingtechnologyhasadvancedmassivelysinceitsbirthinthe1970s,withmanytechnologiesreleasedthisyear
potentiallyallowingsequencingofwholegenomesinadayforlessthan$1,000,agoalthatcouldonlybedreamed
aboutafewyearsago.
Thetechnologicaldevelopmentsraiseimportantethicalissues,whichareslowlybeingaddressed.Rapid
interpretationofthemassesofdataproducedcurrentlyrequireshighlyspecializedsoftware,andrepresentsoneofthe
nextchallengestobringingwholegenomesequencingroutinelytotheclinic.Theareaofpharmacogenomics
lookingatgeneticcombinationsorbarcodesofanindividualfortargetingtherapy,asopposedtohominginona
specificgeneislikelytobeanimportantfocusfordeterminingpeopleatriskofcommondiseases.Identificationof
the10typesofbreastcancerearlierthisyearrepresentsanexampleofhowthisareaisprogressing(6).The
developmentsmayalsotransformthewaythepharmaceuticalindustryworks.EliLilly,forexample,arenow
developingmanyoftheirnewtherapiesbasedonspecificbiomarkers(28).
Thenextstepandacurrenthottopicistoprovidefurtherinsightintotheworkingsofthebodyinhealthanddisease
bylookingattheproteinsactiveinparticularcelltypes.Thiscanbeachievedinpartbylookingatthemessenger
RNA(transcriptomics)andnoncodingRNAsshowinghowgeneticsaffectsthecellsystemincombinationwith
environmentalinfluences.Withthespeedatwhichtechnologyisdevelopingperhapseventhesehurdleswillsoonbe
overcometoincreasetheefficiencyandefficacyofsequencingandpersonalisedmedicineintheclinic.Thereisno
doubt,however,thattherapidprogresswehaveseensincethefirstsequencingtechnologiesisalreadyhighly
remarkable.

References
(1)http://www.sciencedaily.com/releases/2012/02/120228123847.htm
(2)http://www.bbc.co.uk/news/scienceenvironment17191398
(3)www.nature.com/news/microbiomesequencingoffershopefordiagnostics1.10299)
(4)http://www.sanger.ac.uk/genetics/CGP/
(5)http://www.sciencenews.org/view/generic/id/38320/title/First_complete_cancer_genome_sequenced
(6)Curtisetal(2012),Thegenomicandtranscriptomicarchitectureof2,000breasttumoursrevealsnovelsubgroups,
Nature,publishedonlineApril2012,doi:10.1038/nature10983
(7)http://news.sciencemag.org/scienceinsider/2012/05/worldslargesthubforcancer.html?ref=hp
(8)http://blogs.nature.com/news/2012/05/uscancergenomerepositoryhopestospeedresearch.html
(9)Pressrelease:http://www.nanoporetech.com/news/pressreleases/view/39
(10)http://www.nature.com/news/norwaytobringcancergeneteststotheclinic1.9949
(11)HutchinsonIII,C.A.(2007)DNAsequencing:BenchtoBedsideandBeyond.NucleicAcidsResearch,35:18
(62276237)doi.10.1093/nar/gkm688
(12)http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1980/
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(13)http://www.wellcome.ac.uk/Educationresources/Teachingandeducation/Animations/DNA/WTX056046.htm
(14)http://wellcome.ac.uk/Educationresources/Teachingandeducation/Animations/DNA/WTX056051.htm
(15)Youtubevideo:http://www.youtube.com/watch?v=Sx6FbYoFGmM
(16)http://www.nanoporetech.com/technology/introductiontonanoporesensing/introductiontonanoporesensing
(17)http://www.nature.com/news/nanoporegenomesequencermakesitsdebut1.10051
(18)www.nature.com/news/dnadonorrightsaffirmed1.10275
(19)http://news.sciencemag.org/scienceinsider/2012/03/biobanksaskedtohelpdeliver.html?ref=hp
(20)Robertson,(2003)The$1000Genome:EthicalandLegalIssuesinWholeGenomeSequencingofIndividuals.
TheAmericanJournalofBioethics,InFocus.
(21)RebeccaSkloot(2010),TheImmortalLifeofHenriettaLacks,CrownBooks,February2,20101stEdition,
ISBN9781400052172
(22)Roche(2010),TheProperty/PrivacyConundrumoverHumanTissue,HECForum22:197209DOI
10.1007/s1073001091372
(23)Coryell(2011)PatentLawasanIncentivetoInnovatenotDonate:TheRoleoftheUSPatentSystemin
regulatingOwnershipofHumanTissue,PhDThesis?
(24)http://www.sciencemag.org/content/305/5688/1226.2.full.pdf
(25)http://content.healthaffairs.org/content/22/5/166.full
(26)http://www.science20.com/news_articles/nextgeneration_sequencing_leads_personalized_medicine_win_teenager
80079
(27)http://www.nature.com/news/2011/110615/full/news.2011.368.html
(28)http://www.pharmamanufacturing.com/articles/2008/007.html
Thispostwaswrittenby:

SarahEtheridgeViewauthorbio
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