bayesian adaptive design & interim analysis

BAYESIAN ADAPTIVE DESIGN

& INTERIM ANALYSIS

BAYESIAN ADAPTIVE DESIGN

& INTERIM ANALYSIS

Donald A. [email protected]

Donald A. [email protected]

22

Some referencesSome references

Berry DA (2003). Statistical Innovations in Cancer Research. In Cancer Medicine e6. Ch 33. BC Decker. (Ed: Holland J, Frei T et al.)

Berry DA (2004). Bayesian statistics and the efficiency and ethics of clinical trials. Statistical Science.

Berry DA (2003). Statistical Innovations in Cancer Research. In Cancer Medicine e6. Ch 33. BC Decker. (Ed: Holland J, Frei T et al.)

Berry DA (2004). Bayesian statistics and the efficiency and ethics of clinical trials. Statistical Science.

33

BenefitsBenefits

Adapting; examples Stop early (or late!) Change doses Add arms Drop arms

Final analysis Greater precision (even full follow-up) Earlier conclusions

Adapting; examples Stop early (or late!) Change doses Add arms Drop arms

Final analysis Greater precision (even full follow-up) Earlier conclusions

44

GoalsGoals

Learn faster: More efficient trials

More efficient drug/device development

Better treatment of patients in clinical trials

Learn faster: More efficient trials

More efficient drug/device development

Better treatment of patients in clinical trials

55

OUTLINE: EXAMPLESOUTLINE: EXAMPLES

Extraim analysis Modeling early endpoints Seamless Phase II/III trial Adaptive randomization

Phase II trial in AML Phase II drug screening process Phase III trial



66

EXTRAIM ANALYSES*EXTRAIM ANALYSES* Endpoint: CR (detect 0.42 vs 0.32) 80% power: N = 800 Two extraim analyses, one at 800 Another after up to 300 added pts Maximum n = 1400 (only rarely) Accrual: 70/month Delay in assessing response

Endpoint: CR (detect 0.42 vs 0.32) 80% power: N = 800 Two extraim analyses, one at 800 Another after up to 300 added pts Maximum n = 1400 (only rarely) Accrual: 70/month Delay in assessing response

*Modeling due to Scott Berry<[email protected]>*Modeling due to Scott Berry<[email protected]>

77

After 800 pts accrued, have response info on 450 pts

Find pred prob of stat sig when full info on 800 pts available

Also when full info on 1400 Continue if . . . Stop if . . . If continue, n via pred prob Repeat at 2nd extraim analysis

After 800 pts accrued, have response info on 450 pts

Find pred prob of stat sig when full info on 800 pts available

Also when full info on 1400 Continue if . . . Stop if . . . If continue, n via pred prob Repeat at 2nd extraim analysis

Table 1: p0=0.42 p1 P(succ) meanSS sdSS P(800) P(1400) P(succ1) P(succ2) 0.37 0.0001 844.6 122.0 0.8707 0.0194 0.0001 0.0001 0.42 0.0243 1011.2 247.6 0.5324 0.2360 0.0084 0.0059 0.47 0.4467 1188.5 254.5 0.2568 0.5484 0.1052 0.0914 0.52 0.9389 1049.9 248.7 0.4435 0.2693 0.4217 0.2590 0.57 0.9989 874.2 149.1 0.7849 0.0268 0.7841 0.1729



vs 0.80vs 0.80

99

MODELING EARLY ENDPOINTS: LONGITUDINAL MARKERS

MODELING EARLY ENDPOINTS: LONGITUDINAL MARKERS

Example CA125 in ovarian cancer Use available data from trial (&

outside of trial) to model relationship over time with survival, depending on Rx

Predictive distributions Use covariates Seamless phases II & III

Example CA125 in ovarian cancer Use available data from trial (&

outside of trial) to model relationship over time with survival, depending on Rx

Predictive distributions Use covariates Seamless phases II & III

1010

CA125 data & predictive distributions of survival for two of many patients* ——>

CA125 data & predictive distributions of survival for two of many patients* ——>

*Modeling due to Scott Berry<[email protected]>*Modeling due to Scott Berry<[email protected]>

Days

Patient #1

Treatment

Patient #1

Days

Patient #2

Patient #2

1515

MethodsMethods

Analytical

Multiple imputation

Analytical

Multiple imputation

1616

SEAMLESS PHASES II/III*SEAMLESS PHASES II/III*

Early endpoint (tumor response, biomarker) may predict survival?

May depend on treatment Should model the possibilities Primary endpoint: survival But observe relationships

Early endpoint (tumor response, biomarker) may predict survival?

May depend on treatment Should model the possibilities Primary endpoint: survival But observe relationships

*Inoue, et al (2002 Biometrics)*Inoue, et al (2002 Biometrics)

1717

Goodresp

Goodresp

No respNo resp

SurvivaladvantageSurvival

advantage

No survivaladvantageNo survivaladvantage

Phase 2Phase 2 Phase 3Phase 3

Conventional drug developmentConventional drug development

6 mos6 mos 9-12 mos9-12 mos > 2 yrs> 2 yrs

StopStop

Seamless phase 2/3Seamless phase 2/3

< 2 yrs (usually)< 2 yrs (usually)

NotNot

MarketMarket

1818

Seamless phasesSeamless phases Phase 2: 1 or 2 centers; 10 pts/mo,

randomize E vs C If pred probs “look good,” expand to

Phase 3: Many centers; 50 pts/mo (Initial centers continue accrual)

Max n = 900

[Single trial: survival data combined in final analysis]

Phase 2: 1 or 2 centers; 10 pts/mo, randomize E vs C

If pred probs “look good,” expand to Phase 3: Many centers; 50 pts/mo (Initial centers continue accrual)

Max n = 900

[Single trial: survival data combined in final analysis]

1919

Early stoppingEarly stopping Use pred probs of stat sig Frequent analyses (total of 18)

using pred probs to: Switch to Phase 3 Stop accrual for

Futility Efficacy

Submit NDA

Use pred probs of stat sig Frequent analyses (total of 18)

using pred probs to: Switch to Phase 3 Stop accrual for

Futility Efficacy

Submit NDA

2020

Conventional Phase 3 designs: Conv4 & Conv18, max N = 900

(samepower as adaptive design)

Conventional Phase 3 designs: Conv4 & Conv18, max N = 900

(samepower as adaptive design)

ComparisonsComparisons

2121

Expected N under H0Expected N under H0

0

200

400

600

800

1000

431

855 884

Bayes Conv4 Conv18

2222

Expected N under H1Expected N under H1

0

200

400

600

800

1000

649

887 888

Bayes Conv4 Conv18

2323

BenefitsBenefits Duration of drug development is

greatly shortened under adaptive design: Fewer patients in trial No hiatus for setting up phase 3 All patients used for

Phase 3 endpoint Relation between response & survival

Duration of drug development is greatly shortened under adaptive design: Fewer patients in trial No hiatus for setting up phase 3 All patients used for

Phase 3 endpoint Relation between response & survival

2424

Possibility of large NPossibility of large N

N seldom near 900

When it is, it’s necessary!

This possibility gives Bayesian design its edge

[Other reason for edge is modeling response/survival]

N seldom near 900

When it is, it’s necessary!

This possibility gives Bayesian design its edge

[Other reason for edge is modeling response/survival]

2525

Troxacitabine (T) in acute myeloid leukemia (AML) combined with cytarabine (A) or idarubicin (I)

Adaptive randomization to:IA vs TA vs TI

Max n = 75 End point: Time to CR (< 50 days)

Troxacitabine (T) in acute myeloid leukemia (AML) combined with cytarabine (A) or idarubicin (I)

Adaptive randomization to:IA vs TA vs TI

Max n = 75 End point: Time to CR (< 50 days)

ADAPTIVE RANDOMIZATIONGiles, et al JCO (2003)

ADAPTIVE RANDOMIZATIONGiles, et al JCO (2003)

2626

Adaptive RandomizationAdaptive Randomization

Assign 1/3 to IA (standard) throughout (until only 2 arms)

Adaptive to TA and TI based on current results

Results

Assign 1/3 to IA (standard) throughout (until only 2 arms)

Adaptive to TA and TI based on current results

Results

2727

Patient Prob IA Prob TA Prob TI Arm CR<501 0.33 0.33 0.33 TI not2 0.33 0.34 0.32 IA CR3 0.33 0.35 0.32 TI not4 0.33 0.37 0.30 IA not5 0.33 0.38 0.28 IA not6 0.33 0.39 0.28 IA CR7 0.33 0.39 0.27 IA not8 0.33 0.44 0.23 TI not9 0.33 0.47 0.20 TI not

10 0.33 0.43 0.24 TA CR11 0.33 0.50 0.17 TA not12 0.33 0.50 0.17 TA not13 0.33 0.47 0.20 TA not14 0.33 0.57 0.10 TI not15 0.33 0.57 0.10 TA CR16 0.33 0.56 0.11 IA not17 0.33 0.56 0.11 TA CR

2828

Patient Prob IA Prob TA Prob TI Arm CR<5018 0.33 0.55 0.11 TA not19 0.33 0.54 0.13 TA not20 0.33 0.53 0.14 IA CR21 0.33 0.49 0.18 IA CR22 0.33 0.46 0.21 IA CR23 0.33 0.58 0.09 IA CR24 0.33 0.59 0.07 IA CR25 0.87 0.13 0 IA not26 0.87 0.13 0 TA not27 0.96 0.04 0 TA not28 0.96 0.04 0 IA CR29 0.96 0.04 0 IA not30 0.96 0.04 0 IA CR31 0.96 0.04 0 IA not32 0.96 0.04 0 TA not33 0.96 0.04 0 IA not34 0.96 0.04 0 IA CR

Compare n = 75

DropTI

2929

Summary of resultsSummary of results

CR < 50 days: IA: 10/18 = 56% TA: 3/11 =

27% TI: 0/5 = 0%

Criticisms . . .

CR < 50 days: IA: 10/18 = 56% TA: 3/11 =

27% TI: 0/5 = 0%

Criticisms . . .

3030

SCREENING PHASE II DRUGSSCREENING PHASE II DRUGS

Many drugsTumor responseGoals:

Treat effectively Learn quickly

Many drugsTumor responseGoals:

Treat effectively Learn quickly

3131

Standard designsStandard designs

One drug (or dose) at a time; no drug/dose comparisons

Typical comparison by null hypothesis: RR = 20%

Progress hopelessly slow!

One drug (or dose) at a time; no drug/dose comparisons

Typical comparison by null hypothesis: RR = 20%

Progress hopelessly slow!

3232

Standard 2-stage designStandard 2-stage design

First stage 20 patients: Stop if ≤ 4 or ≥ 9 responsesElse second set of 20

First stage 20 patients: Stop if ≤ 4 or ≥ 9 responsesElse second set of 20

3333

An adaptive allocationAn adaptive allocation

When assigning next patient, find r = P(rate ≥ 20%|data) for each drug

Assign drugs in proportion to r Add drugs as become available Drop drugs that have small r Drugs with large r phase 3

When assigning next patient, find r = P(rate ≥ 20%|data) for each drug

Assign drugs in proportion to r Add drugs as become available Drop drugs that have small r Drugs with large r phase 3

3434

Suppose 10 drugs, 200 patientsSuppose 10 drugs, 200 patients

9 drugs have mix of RRs 20% & 40%, 1 has 60%(“nugget”)


<70%<70%

>99%>99%

Identify nugget …

With probability: In average n:

Identify nugget …


110110

5050

Adaptive also better at finding “40%”, & soonerAdaptive also better at finding “40%”, & sooner

Sta

nd

ard

Ad

apti

ve

Ad

apti

ve

Sta

nd

ard

3535

Suppose 100 drugs, 2000 patientsSuppose 100 drugs, 2000 patients



Adaptive also better at finding “40%”, & soonerAdaptive also better at finding “40%”, & sooner

<70%<70%

>99%>99%

Identify nugget …


Identify nugget …


11001100

500500

Sta

nd

ard

Ad

apti

ve

Ad

apti

ve

Sta

nd

ard

3636

ConsequencesConsequences

Treat pts in trial effectivelyLearn quicklyAttractive to patients, in and

out of the trialBetter drugs identified

sooner; move through faster

Treat pts in trial effectivelyLearn quicklyAttractive to patients, in and

out of the trialBetter drugs identified

sooner; move through faster

3737

PHASE III TRIALPHASE III TRIAL Dichotomous endpoint Q = P(pE > pS|data)

Min n = 150; Max n = 600 After n = 50, assign to arm E

with probability Q Except that 0.2 ≤ P(assign E) ≤ 0.8

(Not “optimal,” but …)

Dichotomous endpoint Q = P(pE > pS|data)

Min n = 150; Max n = 600 After n = 50, assign to arm E

with probability Q Except that 0.2 ≤ P(assign E) ≤ 0.8

(Not “optimal,” but …)

3838

Recommendation to DSMB toRecommendation to DSMB to

Stop for superiority if Q ≥ 0.99

Stop accrual for futility if P(pE – pS < 0.10|data) > PF

PF depends on current n . . .

Stop for superiority if Q ≥ 0.99

Stop accrual for futility if P(pE – pS < 0.10|data) > PF

PF depends on current n . . .

3939

0.0

0.2

0.4

0.6

0.8

1.0

0 100 200 300 400 500 600

n

Futility stopping boundary

0.75

0.95

PF

4040

Common prior density for pE & pS

Common prior density for pE & pS

Independent

Reasonably non-informative

Mean = 0.30

SD = 0.20

Independent

Reasonably non-informative

Mean = 0.30

SD = 0.20

4141

0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1

p

Beta(1.275, 2.975) density

4242

UpdatingUpdating

After 20 patients on each arm

8/20 responses on arm 1


After 20 patients on each arm



4343

0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1

p

Beta(9.275, 14.975)

Beta(13.275, 10.975)

4444

AssumptionsAssumptions

Accrual: 10/month

50-day delay to assess response

Accrual: 10/month

50-day delay to assess response

4545

Need to stratify. But how?Need to stratify. But how?

Suppose probability assign to experimental arm is 30%, with these data . . .

Suppose probability assign to experimental arm is 30%, with these data . . .

4646

Proportions of Patients onExperimental Arm by Strata

Stratum 1Stratum 2

Small Big

Small 6/20 (30%) 10/20 (50%)

Big 6/10 (60%) 2/10 (20%)

Probability of Being Assigned toExperimental Arm for Above Example

Stratum 1Stratum 2

Small Big

Small 37% 24%

Big 19% 44%

4747

One simulation; pS = 0.30, pE = 0.45

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0 6 12 18 24 Months

Proportion Exp

Probability Exp is better 178/243

= 73%

FinalStd 12/38 19/60 20/65Exp 38/83 82/167 87/178

Superiority boundary

4848

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0.00 6 12 18 24 Months

Proportion Exp

Probability Exp is better

87/155 = 56%

Probability futility

9 mos. End FinalStd 8/39 15/57 18/68Exp 11/42 32/81 22/87

One simulation; pE = pS = 0.30

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0.00 6 12 18 24 Months

Proportion Exp

Probability Exp is better

87/155 = 56%

Futility boundary

4949

Operating characteristicsOperating characteristics

True ORR Mean # of patients (%)Std Exp

Probselect

exp Std Exp Total

Meanlength(mos)

Probmax n

0.3 0.2 <0.001 51 (34.9) 95 (65.1) 146 15 <0.0010.3 0.3 0.05 87 (43.1) 115 (56.9) 202 20 0.0030.3 0.4 0.59 87 (30.4) 199 (69.6) 286 29 0.050.3 0.45 0.88 79 (30.7) 178 (69.3) 257 26 0.020.3 0.5 0.98 59 (29.5) 141 (70.5) 200 20 0.0030.3 0.6 1.0 47 (30.1) 109 (69.9) 156 16 <0.001

5050

FDA: Why do this? What’s the advantage?

FDA: Why do this? What’s the advantage?

Enthusiasm of PIs

Comparison with standard design . . .

Enthusiasm of PIs

Comparison with standard design . . .

5151

Adaptive vs tailored balanced design w/same false-positive rate & power

(Mean number patients by arm)

Adaptive vs tailored balanced design w/same false-positive rate & power

(Mean number patients by arm)

ORR

Arm

pS = 0.20pE = 0.35

pS = 0.30pE = 0.45

pS = 0.40pE = 0.55

Std Exp Std Exp Std Exp

Adaptive 68 168 79 178 74 180

Balanced 171 171 203 203 216 216

Savings 103 3 124 25 142 36

5252

Consequences of Bayesian Adaptive Approach

Consequences of Bayesian Adaptive Approach

Fundamental change in way we do medical research

More rapid progressWe’ll get the dose right!Better treatment of patients . . . at less cost

Fundamental change in way we do medical research

More rapid progressWe’ll get the dose right!Better treatment of patients . . . at less cost

5353

OUTLINE: EXAMPLESOUTLINE: EXAMPLES





bayesian adaptive design & interim analysis

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