Clinical and technical validation of a genomic classifier (ColoPrint) for predicting outcome of stage II colon cancer patients

Josep Tabernero, Vall d’Hebron University Hospital, Barcelona, Spain

and Victor Moreno2, Robert Rosenberg3, Ulrich Nitsche3, Thomas Hoffmann-Bachleitner4, Giovanni Lanza5, Jeroen van Akker6, Paul Roepman6, Iris Simon6, Ramon Salazar2

2IDIBELL, Institut Català d'Oncologia, L'Hospitalet de Llobregat, Spain; 3Department of Surgery, Klinikum rechts der Isar,T echnische University Munich, Munich, Germany;

4Department of Surgery, Medical University of Vienna, Vienna, Austria; 5Istituto di Anatomia e Istologia Patologica, University di Ferrara, Ferrara, Italy;

6Agendia BV, Amsterdam, Netherlands and Agendia Inc. , Irvine, CA, US

Treatment of stage II patients is still debatable

Quasar Collaborative Group, Lancet. 2007; 370(9604):2020-9

Chemo Observation5 year survival 82.5% 80.6%

ASCO recommendation• “direct evidence from randomized controlled trials does not support the

routine use of adjuvant chemotherapy for patients with stage II colon cancer.• Features associated with an increased risk of recurrence include inadequate

lymph node sampling, T4 disease, perforation and a poorly differentiated histology

NCCN guidelines • consider 5FU or clinical trial or observation for low risk patients (T3, no high risk

features)• Consider 5FU/oxaliplatin or clinical trial or observation for high risk patients• High risk features: T4, less than 12 LN assessed, perforation, obstructions,

positive margins, high grade, lymphatic/vascular invasion

Guidelines for Risk Assessment

Whole Genome Array

Training Set (stage I-IV) (n=188) Netherlands Cancer Institute, Leiden Medical Center, Slotervaart

Selection of Final 18-Gene Set & Algorithm

Clinical Validation Study 1 (stage I-III)Institut Catala d’Oncologia Barcelona (J Clin Oncol. 2011;29:17-24)

Standardization of Analytical Methods

In-silico Validation Study (stage I-III) public datasets (n=322)

Deve

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ent

Valid

ation

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Clinical Validation Study 2 (stage II)Munich Hospital Rechts der Isar (J Clin Oncol 28:15s (abstract 3513)

Clinical Validation Study 3 (stage II)Vall d’Hebron, MedUni Vienna, University of Ferrara

PARSC Prospective Study (stage II + III) - ongoingUS, Asian, and European Center (N ~600 stage II)

Clinical Validation Study 4 (stage II-III)MD Anderson (ongoing)

Stag

e II

pool

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sis

STAGE II PATIENTS (N=320)

Pooled Analysis

Variable

Total

ColoPrint

Low High p-value

N=320 % N=209 % N=111 % Median Age 68.4 67.3 69.3 0.583

Age > 70 No 195 60.9 130 62.2 65 58.6 0.525 Yes 125 39.1 79 37.8 46 41.4

Localization Left 144 56.9 92 55.1 52 60.5 0.413 Right 109 43.1 75 44.9 34 39.5

Grade Low (1,2) 254 82.2 170 82.1 84 82.3 0.897 High (3,4) 55 17.8 37 17.9 18 17.7

Gender Male 186 58.1 116 55.5 70 63.1 0.192 Female 134 41.9 93 44.5 41 36.9

Median LN assessed 19.0 19.0 18.0 0.147

LN> 12 No 70 21.9 41 19.6 29 26.1 0.180 Yes 250 78.1 168 80.4 82 73.9

T-stage 3 283 88.4 182 87.1 101 91.0 0.298 4 37 11.6 27 12.9 10 9.0

MSI status* MSS 253 79.1 156 74.6 97 87.4 0.008MSI-H 67 20.9 53 25.4 14 12.6

Patient Characteristics

*MSI-status based on PCR (n=170) and Genomic Profile (n=150) – see Poster BRD.B37 (R. Salazar et al)

Patient Characteristics (cont’)

Variable

Total

ColoPrint

Low High p-value

N=320 % N=209 % N=111 %

DM No 280 87.5 193 92.3 87 78.4

0.000 Yes 40 12.5 16 7.7 24 21.6

Median Time to DM 68.5 77.2 53.1 0.000 Local, regional, distant Relapse

No 273 85.3 188 90.0 85 76.60.001

Yes 47 14.7 21 10.0 26 23.4

Time to Relapse 64.0 73.0 49.0 0.006

Survival Time 70.6 77.4 63.6 0.031

Adjuvant treatmentNo 229 72.0 157 75.5 72 65.5

0.058 Yes 89 28.0 51 24.5 38 34.5

ASCO Low 170 53.1 113 54.1 57 51.4

0.643 High 150 46.9 96 45.9 54 48.6

NCCN Low 166 51.9 111 53.1 55 49.5

0.544 High 154 48.1 98 46.9 56 50.5

ColoPrint identifies patients at risk of distant and local-regional relapse (RFS)

Local, Regional and Distant Relapse

5-year RFSLow Risk = 88% (83-93%)High Risk = 71% (62-80.5%)

3-year RFSLow Risk = 91% (86-95%)High Risk = 74% (64-83%)

Univariate analysis: 3-yr Relapse-free Survival

Variable HR 95% CI p-value

ColoPrint high vs low risk 2.9 1.55 5.39 0.001Age continuous 1.01 0.98 1.04 0.469Localization right vs. left 1.19 0.58 2.43 0.638Grade high vs. low 0.92 0.38 2.25 0.273Gender Female vs male 0.57 0.29 1.12 0.104LN assessed continuous 0.97 0.94 1.00 0.078LN>12 yes/no 0.72 0.35 1.47 0.365pT ( 3 vs 4) 4 vs 3 1.45 0.64 3.27 0.372MSI MSI-H vs MSS 0.42 0.15 1.18 0.101

ASCO high vs low risk 1.4 0.76 2.59 0.283

NCCN high vs low risk 1.5 0.81 2.77 0.200

Clinical Risk Factors distinguish risk groups but are not sufficient

p-value for uncensored time

Subgroup analysis in T3-MSS patients (n=227)

Variable HR 95% CI P-value

ColoPrint 3.04 1.45-6.34 0.003

Age 1.01 0.97-1.05 0.59

Localization 1.34 0.59-3.06 0.48

Grade 0.71 0.22-2.26 0.27

Gender 0.46 0.19-1.061 0.07

LN > 12 0.83 0.37-1.85 0.65

Univariate Analysis of 3-year RFS

3-year RFSLow Risk = 91% (86-96%)High Risk = 73% (63-83%)

Clinical risk factors are even less sufficient to distinguish low and high risk patients in the T3-MSS subgroup

ColoPrint in combination with clinical factors might give best risk stratification

3-year RFS 93 % Low Risk ColoPrint, low risk NCCN 88 % Low Risk ColoPrint, high risk NCCN 76 % High Risk ColoPrint, low risk NCCN 71 % High Risk ColoPrint, high risk NCCN

ColoPrint + NCCN clinical factorsAll patients T3 MSS

3-year RFS 93% 89% 76% 70%

ColoPrint and MSI-status

• MSI-High patients have a better prognosis than MSS patients and may suffer worse adverse effects from 5-FU

• ColoPrint indentifies low risk patients beyond MSI-high status– 67 patients were classified as MSI-H (20.9%)–MSI-H patients are mainly ColoPrint Low Risk (53/67 =

80%)

Technical Validation of ColoPrint as a reproducible and standardized test

ColoPrint uses the same technology, methods and QC as FDA-cleared MammaPrint assay

Repeated runs of three samples over 20 days performed by different operators

= less than 5% variation

Summary

• The 18-gene genomic signature for patients with colon cancer distinguishes populations with different outcomes

• The signature was validated in an in-silico study and with independent cohorts

• In stage II patients:– Over 60% of patients were identified as Low Risk with a 3-

year RFS of 91%– It identifies patients at High Risk of developing

metastases and who are more likely to benefit from adjuvant CTx

– It is better at identifying High Risk patients than any clinical risk factor alone

• ColoPrint complements clinical-pathological factors for better treatment decisions

PARSC: Prospective Assessment of Risk Stratification by ColoPrint

• Aim 575 eligible stage 2 patients• Status January 2012:

– 32 sites open (EU 15, Asia 2, US 15) – 340 eligible stage 2– 300 eligible stage 3

• Expected last patient enrollment: Dec’12

Patient Information

&InformedConsent

Surgery

RNARetainSampleAgendia

Treatment at discretion of investigator

Quality check

sample

CRF 2 - 4If eligible:CRF1

Year 1Year 3Year 5

ColoPrint analysis

± 4 weeks after surgery

See also Poster BRD. G15

Acknowledgements

• To all patients and participating Institutions