ANNUALREPORT2014-15

GFCC ANNUAL REPORT

UnderstandingPrecisionMedicineandGeneSequencingforNeuroblastoma

January20,2018MeredithIrwin,MD

SickKids SequencingProgram

PrecisionTherapy

Whatisprecisionmedicine?

• “personalized”vs.“individualized”vs.precision

• isanapproachfordiseasetreatment(andprevention)thattakesintoaccountindividualvariabilityingenes,environment,andlifestyleforeachperson.

• useofgenes/molecularcharacterization(+/- inconjunctionwithclassictumorclinicalandbiologicalfeatures)toinformtreatment

PrecisionCancerTherapy

Earlyprecisionmedicine:Low,intermediateandhighriskneuroblastoma

Whatcausescancer?

• Whatcausescancer?

– Changesingenesthatgivecellstheabilitytogrow

fast,continuouslydivide,spreadandformtumors

• GENETICS101

Whatiscancer?

Mutations/alterationsingenescausecancer

(1)Mutation

(2)Extracopies- oncogenes

(3)Missingcopies-suppressorgenes

DNA

mRNA

protein

AUGGAGCCAACUAUUGAUGAA

FlowofgeneticinformationDNA RNA Protein

Met- Glu - Pro- Thr - Ile- Asp - Glu

ATGGAGCCAACTATTGATGAA

Genes

DNA

mRNA

protein

AUGGAGCCAACUAUUGAUGAA

FlowofgeneticinformationDNA RNA Protein

Met- Glu - Pro - Thr - Ile- Asp - Glu

ATGGAGCCAACTATTGATGAA

Genes

X

DNA

mRNA

protein

AUGGAGCCAACUAUUGAUGAA

FlowofgeneticinformationDNA RNA Protein

Met- Glu - Pro - Thr - Ile- Asp - Glu

ATGGAGCCAACTATTGATGAA

Genes

MUTANT WILD-TYPE

DNA

mRNA

protein

AUGGAGCCAACUAUUGAUGAA

FlowofgeneticinformationDNA RNA Protein

Met- Glu - Pro - Thr - Ile- Asp - Glu

ATGGAGCCAACTATTGATGAA

Genes

MUTANT WILD-TYPEPrecisionTherapy

Rolesforgenealterationsinpediatriccancer?

– Unlikeadultcancersitisraretogetpediatriccancerfromanexposuretosomethingtoxic(cigarettesmoke,sun)

– Althoughitcanbeinheritedfromparentsmostofthetimeitisnot

– Changesincancercellgenesleadtopropertiessuchasgrowth/survival,proliferation,invasion/metastasis…...

Genemutationscanbeinheritedornew-what’sthedifference?

Howtosequencegenes

• Sequencing=codeofgenesACTG…..

• Previously- checkonegeneafteranotherforalterations/mutations

• Nowcansequenceallgenes(DNAandRNA)

Breakthrough:nextgenerationsequencing

• Cansequenceallofthegenesinacancercell

ratherthanoneatatime

Thehumangenomestats

• 23chromosomepairs– 1x/y,other22

• Entiregenome=over3billionbasepairs– ACTG…..

• Approx20,000genesthatcodeforproteinsmadeincells– Alotmoreimportantinfointheothermillionsofbasepairs

0

5,000

10,000

15,000

20,000

25,000

30,000

Cost per Human Genome

20122011 2013

$ R

eage

nt C

ost

Cost range

• ‘$ Cost’ of exome sequencing 1,000-2,000

Genome wide sequencing is becoming less expensive than existing genetic tests

Existing Genetic Dx Tests

Sequencing ALK ~ $1500

MutationsinNeuroblastoma

• Mutation- changesinoneormoreDNAbases(eg A->C)resultingindifferentaminoacidthatchangestheprotein

• Veryheterogeneous• IncomparisontosomecancerswherethereisacommonmutationinmostpatientsinNBvarietyofdifferentgenemutations– ALK- mostcommonmutation(10%)– Others- ATRX,Ras,NF1,PTPN11,…..

Targetedtherapiesbasedongenetics

– Chemotherapiesattackcancerandnormalcells

causingincreasedsideeffects

– “target”thedifferentgenes/proteinsonthe

cancercellthathelpittogrowandsurvive

SickKids SequencingProgram

PrecisionTherapy

KICSprogram

• 2016:sequenced–almost200completed• Someledtoidentificationoftargetedtherapiesandotherguidancefortreatmentdecisions– ALKinhibitordrugs,others

• DiscoveryofnewgenesinvolvedinNB• ExpandingtoallCanadiansites(PROFYLE)

KiCS StudyObjectives• Establishtheutilityofsequencingforpatientcare(relapsedandrefractory)– PatientDiagnosticsandMonitoringDiseaseResponse– Prognosis– Guidingtherapeuticdecisions:

• suggestnewtargetsfortherapeuticinterventionbasedontumor-specificgeneticalterations

• Establishthevalueofsequencinginidentifyinginheritedgenes

KiCS Consent- Overview• ReferraltoKiCS → eligible→ consent

• Consent– EntryPoint1(tumour andgermline/blood)

• Twopartconsentavailable– PartA– samples– PartB– sequencing

– EntryPoint2(germline only)– Parentconsentformsandassent

• Averageconsent:~90minutes

Whywedorepeatbiopsiesatrelapse?

• Evidencethattherearemore(anddifferent)mutationsatrelapse(clonalevolution)– MostcommontargetablemutationinNB(ALK)increasedattimeofrelapsevs.diagnosis

Ramaswamy andTaylor,NatureGenetics2015

NGSPlatformsandAnalyses

Tumour DNA+RNA

Non-tumour DNA

Focused, deep sequencing

Broad, shallowsequencing

HiSeq 2500NextSeq 500

800+genes Wholegenome

HiSeq XTen

Libraryprep:2daysSequencing:1day

Libraryprep:2daysSequencing:3day

+6to30hrs

SickKidsChildhoodCancerPanel

18,950exonannotations

Covering3.9millionbases

Focuseddeepsequencingof886genes

SickKidsChildhoodCancerPanel

18,950exonannotations

Covering3.9millionbases

MOLECULARTUMORBOARD

TheKiCS MolecularTumorBoard• Multi-disciplinaryandweekly• AtMeeting:

– datapresented,interpretedanddiscussed:• “actionability”determined

– linktopotentialagentsortrialsmade– challengesornextstepsreviewed– directcommunicationwithprimaryoncologistàfamily

• Attendance:– CoreKiCS team(oncologists,geneticists,pathologists,genomescientists,bioinformaticians,geneticcounsellors,researchassociates,MRP,etc)

Drivervs.passengermutations

- Manygenevariantsthatcanbeconsidered- Teamincludingbioinformaticians needtoidentifypossible

“drivermutations”sincemanyarejustpassengers

- DRIVER:mutationthatgivesthecancercellaselectivemutation(togrowfaster,spreadetc)=ENGINE

- PASSENGER:manyothermutationsorvariantsincancercellsthatarealongforridebuthavenofunctionaleffect

ALK,MYCN

ResearchReportsfromCancerPanel

30

Ledia Brunga

0

2

4

6

8

10

12

14

AMLrelapse

ALL

CMLandALL

Undiffe

rentiatedleukem

iaPe

riphe

ralTCellLym

phom

aMPA

LAM

KLRe

nalcellcarcino

ma

Wilm

stum

orRe

lapsed

hep

atob

lastom

aParagangliomaw/n

euroblastic…

Metastaticpapillarythyroidcarcinom

a…Follicular-Va

riantPapillaryThyroidCA

Prim

itivehem

atologicneo

plasm,…

NF1and

GBM

Embryonalrhabd

omyosarcom

aSyno

vialsa

rcom

a,and

pasth

istoryof…

Myofib

roblasticsa

rcom

aFron

toparie

talrhabd

oidmen

ingiom

a…NF1.M

etastaticrhabd

omyosarcom

a.Astrocytom

aGliosarcom

aNeu

roblastomaandCN

Stumor

Epen

dymom

aGB

MGlioma

Med

ulloblastoma

AT/RT

Intracranialund

ifferen

tiatedsarcom

aCo

loncancer

ProstateRMS

Chordo

ma

Osteo

sarcom

aCh

ondrob

lasticosteo

sarcom

aGIST

Undiffe

rentiatedsarcom

aAlveolarRhabd

omyosarcom

aYo

lkSacTum

orMyofib

roblasticsa

rcom

aEW

S-rearranged

prim

itivesa

rcom

Ewingsarcom

ametastaticto

thelungs

Desm

oidtumou

rMPN

STNeu

roblastoma

Ovaria

nmucinou

scarcino

ma

Ovaria

nsertolileydigtumou

rBreastcancer

Epith

eloidsarcom

aParagangliomaandpo

ssiblere

nalcell…

PapillaryThyroidCA

SampleCo

unt

Tumourtype

121patientsenrolled

Incorporatinggeneticsintotreatmentandcareofpatients

- Insteadofpathology(neuroblastoma,sarcomaetc)treatmentisbasedonageneabnormalityintumorthatcanbetargeted

- PhaseIandIItrialsforonedrugorcombinationthatrequireagenemutation/alterationtoenroll

- Trialswithmanyregimensthatusebiopsyresultstoassignpatientstodifferentarmsofathetrial

6monthslater

TargetingALKmutationwithALKinhibitor

protein

MUTANT WILD-TYPE

1275mutation

ALKi

ALKinhibitor

CLINICALTRIALS

Umbrella Trial UMBRELLA and BASKET TRIALS rial.

Woodcock J, LaVange LM. N Engl J Med 2017;377:62-70

Woodcock J, LaVange LM. N Engl J Med 2017;377:62-70

-One(orfewtumortypes)

-themutationidentifieddetermineswhichtreatment

-commoninbreast,lung

Umbrella Trial UMBRELLA and BASKET TRIALS rial.

Woodcock J, LaVange LM. N Engl J Med 2017;377:62-70

Woodcock J, LaVange LM. N Engl J Med 2017;377:62-70

-One(orfewtumortypes)

-themutationidentifieddetermineswhichtreatment

-commoninbreast,lung

-Multiplecancerseligible(histologyagnostic)

-mutationidentifiedallowseligibility

-CAPTUR,MATCH,many

NCIPediatricMATCHMolecularAnalysisforTherapyCHoice

• BaskettrialforrelapsedsolidtumorsandlymphomasinUS– 200- 300/year;estimated5-10%Match

• Biopsyandsmall%willhavegeneabnormalityandcanenrollon1of8trialsofsingleagentthattargetsmutation

NCIPediatricMATCHschema

MASTERPROTOCOL

Sub-protocols

40

totransformthecareofCAYApatientsacrossCanadaby

usingnext-generationmoleculartoolsandcancermodel

systemstoidentifydisease- andpatient-specificbiomarkers

thataretractabletargetsfortherapytoimproveoutcomes.

ThePROFYLEPrecisionMedicinePlatform

POG

KiCS

MUGQICandTRICEPS

Buildingonthesuccessof3regionalprograms

Dec2015enrollment Sept2017enrollment

POG(Vancouver) 32 (incl.21youngadults)

98 (incl.29youngadults)

TRICEPS(Montreal) 21 (upto 21yrs.) 81 (upto 21yrs.)

KiCS (Toronto) 33 158 (incl.10youngadults)

157newcasesin13months~12permonth

AdamShlien

43

Goals:

• Enroll and molecularly profile 450 patients over 5 years

• Analyze the tumour genome, transcriptome, and proteome to look for treatment targets

• Develop strategies to access therapies for CAYAs with ‘hard to treat’ cancers

4444

MolecularProfiling&

PrecisionMedicineClinicalTrials

Biospecimen

EfficacyofPrecisionMedicine

IMPROVEOUTCOMESFORHARD-TO-TREAT

CAYACANCERS

Children,Adolescents,andYoungAdults(CAYA)withHard-to-TreatCancers

Modelsof

CAYACancers

•DiscoverNewTargets•DevelopTherapies• UnderstandBiology

CanadianCAYACancerBiobank

&

DataRepository

•BiomarkersofResponse•NewProfilingTools• FuelFutureDiscoveries

ThePROFYLEPrecisionMedicinePlatform

Toestablishanationalmulti-institutional

cooperativenetworkforgenomics,withthe

goaltoensurethatALLeligiblepatientsinthe

countrywillhaveaccesstothisresource.

Identify,screen,consent/assent

Tissuecollection,pathologyreview,

Biobanking

MolecularTumourProfiling,Data

Analysis

MolecularTumourBoard

QualityAssuranceandEthicsOversight

PROFYLE CLINICAL NODE

ActionableGenomicFinding(s)

NoactionableGenomicFinding

≥18y <18y

CAPTURclinicaltrial

CAPTURpediatriccohort

CAPTURadultcohort

CAPTURdrugs

ALKinhibitorPDGFRinhibitormTORinhibitorBRAFinhibitorMEKinhibitor?Checkpointinhibitor

HealthCanadanof1trialconcept

Compassionate/SAPaccess

PediatricphaseI/IItrials

PR,CR,SDPD

Continuetherapy

Sequencingalsoidentifiesgermlinemutations(inherited)

• Mayhavesomeimplicationsfortreatment• Mayhaveimplicationsforotherfamilymembers– Counselling– Screening/surveillance

• Newscientificdiscoveries

Howtousegenomics/sequencingtoguidetreatment

Modified from Lillian L. Siu et al. Clin Cancer Res 2015;21:4536-4544

“OMICS”tofindtarget-genomics(DNA,RNA)-proteomics-other

Molecular+clinical,radiology,histology,…

1. Othertrials2. SpecialAccess3. Nof14. Informtherapy

ChallengestoPrecisionMedicineinChildren,AYA

• Pediatriccancersarerare(relatively)• Eachsubset– byhistologyand/orbygeneticalterationisevenrarer• ClinicaltrialschallengesofsmallN,endpoints,controls

• Drugaccessforchildren<18yo (<12)• Regulatory

– US,EUsomelegislationtohelpfacilitate• Pharma• Formulation

• Ethics• (Gen)omics

– Differentsetsofalterationsthatmaynotbeeasytointerrogatesincemostdataisadult

- Needresearchtounderstandnewvariants

TheFuture• MorebaskettrialsandphaseI/IItrialsinwhicheligibilityisthegeneticorothermolecularalteration(histologyagnostic)

• Usesequencingmoreatdiagnosis,beforerelapse

• CellFreeDNA– DNAthattumorsshedintheperipheralbloodthatcanbeisolatedfromafewmlofblood

• Usetodetectmutationandtoquanitfy before/aftertreatment

• Abilitytomakemodelsusingpatientsamplesandtestdrugsinrealtime…..

THANKS!

NEUROBLASTOMARESEARCHPROGRAMS