SUPPLEMENTARY MATERIALS

Supplementary methods

Plasma samples were analyzed using the FOUNDATIONACT® platform (Clark et al, 2018;

Foundation Medicine, Inc 2017) and tissue samples were analyzed using

FOUNDATIONONE® (Frampton et al, 2013; Foundation Medicine, Inc 2017).

FOUNDATIONACT® works by analyzing circulating-tumor DNA (ctDNA), which is found in

the peripheral blood of patients with NSCLC; through analysis of the ctDNA using proprietary

FragTag™ technology it is possible to identify clinically relevant genomic alterations.

FOUNDATIONONE® can identify somatic genomic alterations in genes known to be drivers

of solid tumours. Both FOUNDATIONACT® and FOUNDATIONONE® identify four classes of

genomic alterations; base substitutions, insertions and deletions, copy number alterations

and rearrangements. Test results were provided in an interpretive report approved by board-

certified pathologists.

Supplementary figures and tables

FIGURE S1. Patient disposition. Flow diagram summarizing screening, enrolment, patient

randomization, and follow-up. Intention-to-treat (ITT) population includes all patients who

were randomized to study treatment. Data cut-off: December 1, 2017

FIGURE S2. Duration of response in the response-evaluable population.

NE, not estimable

FIGURE S3. Investigator-assessed best overall response according to baseline CNS metastases: (A) alectinib patients with baseline CNS

metastases; (B) crizotinib patients with baseline CNS metastases; (C) alectinib patients without baseline CNS metastases; (D) crizotinib

patients without baseline CNS metastases.

BOR, best overall response; CNS, central nervous system; CR, complete response; NE, not evaluable; PD, progressive disease; PR, partial

response; SD, stable disease.

FIGURE S4. Overall survival in the intent-to-treat population.

FIGURE S5. Overview of ALK rearrangements, SNVs and CNAs detected in baseline

samples from ALEX by NGS (FoundationOne®)

CNA, circulating nucleic acids; NGS, next-generation sequencing

SNV, single-nucleotide variant

FIGURE S6. Investigator-assessed PFS in the EML4-ALK variant 1, 2 and 3a/b biomarker evaluable populations

BEP, biomarker-evaluable population; CI, confidence interval; HR, hazard ratio; INV, investigator

PFS, progression-free survival

FIGURE S7. Objective duration of response (INV, confirmed) by EML4-ALK fusion variant in both the tissue and plasma BEP subgroups for

alectinib and crizotinib

BEP: biomarker evaluable population; DOR: duration of response; EML4-ALK, echinoderm microtubule-associated protein like 4-anaplastic lymphoma kinase; INV: investigator assessment

TABLE S1. Baseline characteristics of the EML4-ALK variants in plasma and tissue BEP subgroups by treatment arm compared to ITT

Plasma BEPCrizotinib (EML4-ALK variant) Alectinib (EML4-ALK variant)

ITT population

(N=303)v1

(n=28)v2

(n=12)v3a/b(n=24)

v1(n=22)

v2(n=10)

v3a/b(n=25)

Age, median, years (range)

<65 (n, %)≥65 (n, %)

56 (18–91)233 (76.9)70 (23.1)

48 (18–77)25 (89.3)3 (10.7)

54.5 (46–76)8 (66.7)4 (33.3)

53 (28–91)21 (87.5)3 (12.5)

54 (37–70)19 (86.4)3 (13.6)

57.5 (44–69)9 (90.0)1 (10.0)

57 (29–75)20 (80.0)5 (20.0)

Ethnicity (n, %)Hispanic/LatinoNot Hispanic/LatinoNot stated

16 (5.3)274 (90.4)

13 (4.3)

0 (0)25 (89.3)3 (10.7)

0 (0)12 (100.0)

0 (0)

2 (8.3)21 (87.5)

1 (4.2)

2 (9.1)20 (90.9)

0 (0)

0 (0)10 (100.0)

0 (0)

0 (0)23 (92.0)

2 (8.0)Race (n, %)

AsianBlackNative AmericanWhiteUnknown

138 (45.5)4 (1.3)4 (1.3)

151 (49.8)4 (1.3)

15 (53.6)1 (3.6)0 (0)

`12 (42.9)0 (0)

6 (50.0)0 (0)0 (0)

6 (50.0)0 (0)

9 (37.5)0 (0)0 (0)

15 (62.5)0 (0)

13 (59.1)0 (0)0 (0)

9 (40.9)0 (0)

4 (40.0)0 (0)0 (0)

6 (60.0)0 (0)

13 (52.0) 0 (0)

1 (4.0)‡

10 (40.0)1 (4.0)

Smoking status, n (%)Active smokerNon-smokerPast smoker

17 (5.6)190 (62.7)96 (31.7)

1 (3.6)15 (53.6)12 (42.9)

0 (0)8 (66.7)4 (33.3)

0 (0)16 (66.7)8 (36.3)

0 (0)14 (63.6)8 (36.4)

0 (0)6 (60.0)4 (40.0)

1 (4.0)20 (80.0)4 (16.0)

ECOG PS, n (%)0 or 12

283 (93.4)20 (6.6)

26 (92.9)2 (7.1)

10 (83.3)2 (16.7)

22 (91.7)2 (8.33)

19 (86.4)3 (13.6)

9 (90.0)1 (10.0)

23 (92.0)2 (8.0)

CNS lesions*, n (%)NoYes

181 (59.7)122 (40.3)

18 (64.3)10 (35.7)

5 (41.7)7 (58.3)

16 (66.7)8 (33.3)

13 (59.1)9 (40.9)

7 (70.0)3 (30.0)

14 (56.0)11 (44.0)

*Measurable and non-measurable;‡Native Hawaiian or other Pacific Islander

Tissue BEPCrizotinib (EML4-ALK variant) Alectinib (EML4-ALK variant)

ITT population

(N=303)v1

(n=28)v2

(n=5)v3a/b(n=25)

v1(n=25)

v2(n=8)

v3a/b(n=21)

Age, median, years (range)

<65 (n, %)≥65 (n, %)

56 (18–91)233 (76.9)70 (23.1)

51 (18–78)24 (85.7)4 (14.3)

53 (37–73)4 (80.0)1 (20.0)

50 (34–79)21 (84.0)4 (16.0)

60 (37–78)19 (76.0)6 (24.0)

59.5 (28–72)6 (75.0)2 (25.0)

60 (29–75)16 (76.2)5 (23.8)

Ethnicity (n, %)Hispanic/LatinoNot Hispanic/LatinoNot stated

16 (5.3)274 (90.4)

13 (4.3)

0 (0)27 (96.4)

1 (3.6)

0 (0)3 (60.0)2 (40.0)

1 (4.0)23 (92.0)

1 (4.0)

1 (4)24 (96.0)

0 (0)

0 (0)8 (100.0)

0 (0)

0 (0)20 (95.2)

1 (4.8)Race (n, %)

AsianBlackNative AmericanWhiteUnknown

138 (45.5)4 (1.3)4 (1.3)

151 (49.8)4 (1.3)

16 (57.1)0 (0)0 (0)

12 (42.9)0 (0)

1 (20.0)0 (0)0 (0)

4 (80.0)0 (0)

13 (52.0)1 (4.0)0 (0)

11 (44.0)0 (0)

13 (52.0)0 (0)

1 (4.0)‡

11 (44.0)0 (0)

4 (50.0)0 (0)0 (0)

4 (50.0)0 (0)

14 (66.7)0 (0)

1 (4.8)¶

6 (28.6)0 (0)

Smoking status, n (%)Active smokerNon-smokerPast smoker

17 (5.6)190 (62.7)96 (31.7)

4 (14.3)17 (60.7)7 (25.0)

0 (0)2 (40.0)3 (60.0)

0 (0)17 (68.0)8 (32.0)

2 (8.0)17 (68.0)6 (24.0)

1 (12.5)4 (50.0)3 (37.5)

1 (4.8)13 (61.9)7 (33.3)

ECOG PS, n (%)0 or 12

283 (93.4)20 (6.6)

25 (89.3)3 (10.7)

5 (100.0)0 (0)

24 (96.0)1 (4.0)

23 (92.0)2 (8.0)

8 (100.0)0 (0)

21 (100.0)0 (0)

CNS lesions*, n (%)NoYes

181 (59.7)122 (40.3)

17 (60.7)11 (39.3)

2 (40.0)3 (60.0)

19 (76.0)8 (24.0)

17 (68.0)8 (32.0)

4 (50.0)4 (50.0)

13 (61.9)8 (38.1)

*Measurable and non-measurable;‡American Indian or Alaska native;¶Native Hawaiian or other Pacific Islander

BEP: biomarker-evaluable population; CNS, central nervous system; ECOG PS, Eastern Cooperative Oncology Group performance status; ITT: intent to treat; EML4-ALK, echinoderm microtubule-associated protein like 4-anaplastic lymphoma kinase

TABLE S2. Investigator-assessed objective response rate (ITT Population)

Crizotinib

(N=151)

Alectinib

(N=152)

Responders, n 114 126

%, (95% CI) 75.5 (67.84–82.12) 82.9 (75.95–88.51)

Difference in ORR

(95% CI)

7.40

(–1.71–16.50)

Stratified Analysis

p-value (Mantel-Haenszel Test) 0.0936

Odds ratio (95% CI) 1.62 (0.92–2.84)

Unstratified Analysis

p-value (Mantel-Haenszel Test) 0.1132

Odds ratio (95% CI) 1.57 (0.90–2.76)

Complete response, % (95% CI) 2.0 (0.41–5.70) 4.6 (1.87–9.26)

Partial response, % (95% CI) 73.5 (65.72–80.35) 78.3 (70.88–84.56)

Stable disease, % (95% CI) 15.9 (10.46–22.72) 5.9 (2.74–10.94)

Progressive disease, % (95% CI) 6.6 (3.22–11.84) 5.3 (2.30–10.11)

Missing or unevaluable, % 2.0 5.9

CI, confidence interval; ITT, intent-to-treat; ORR, objective response rate.

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TABLE S3. Percentage tumor reduction in the ITT population and CNS subgroups

Responders, n (%)

Crizotinib

(N=151)

Alectinib

(N=152)

>25% tumor reduction 125 (82.8) 126 (82.9)

>50% tumor reduction 76 (50.3) 114 (75.0)

>75% tumor reduction 30 (19.9) 55 (36.2)

Responders with CNS lesions at baseline

Crizotinib

(N=58)

Alectinib

(N=64)

>25% tumor reduction 46 (79.3) 52 (81.3)

>50% tumor reduction 21 (36.2) 45 (70.3)

>75% tumor reduction 10 (17.2) 18 (28.1)

Responders without CNS lesions at baseline

Crizotinib

(N=93)

Alectinib

(N=88)

>25% tumor reduction 79 (84.9) 74 (84.1)

>50% tumor reduction 55 (59.1) 69 (78.4)

>75% tumor reduction 20 (21.5) 37 (42.0)

CNS, central nervous system; ITT, intent-to-treat.

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TABLE S4. Grade 3–5 adverse events reported in ≥2 patients in either treatment arm (safety

population)

n (%) Crizotinib (N=151) Alectinib (N=152)

Total number of patients with grade 3–5 AEs 77 (51.0) 68 (44.7)

ALT increased 24 (15.9) 7 (4.6)

AST increased 16 (10.6) 8 (5.3)

Blood CPK 2 (1.3) 5 (3.3)

ECG QT prolonged 5 (3.3) 0

Blood bilirubin increased 0 3 (2.0)

Blood creatinine increased 1 (0.7) 2 (1.3)

Gamma-glutamyltransferase increased 2 (1.3) 1 (0.7)

Neutrophil count decreased 2 (1.3) 0

Anemia 1 (0.7) 8 (5.3)

Neutropenia 6 (4.0) 0

Pulmonary embolism 5 (3.3) 2 (1.3)

Pleural effusion 2 (1.3) 2 (1.3)

Pneumonia 3 (2.0) 4 (2.6)

Pneumonitis 4 (2.6) 0

Pneumothorax 0 2 (1.3)

Urinary tract infection 1 (0.7) 4 (2.6)

Hyponatremia 3 (2.0) 3 (2.0)

Hypokalemia 1 (0.7) 2 (1.3)

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Hypoalbuminemia 2 (1.3) 0

Lung infection 0 3 (2.0)

Bronchitis 0 2 (1.3)

Nausea 5 (3.3) 1 (0.7)

Vomiting 5 (3.3) 0

Diarrhea 3 (2.0) 1 (0.7)

Acute kidney injury 0 4 (2.6)

Confusional state 2 (1.3) 1 (0.7)

Rash 0 3 (2.0)

Death 0 2 (1.3)

Pyrexia 2 (1.3) 0

Hyperbilirubinemia 0 2 (1.3)

Deep vein thrombosis 2 (1.3) 0

Arthralgia 2 (1.3) 1 (0.7)

AE, adverse event; ALT, alanine aminotransferase; AST, aspartate aminotransferase;

CPK, creatinine phosphokinase; ECG, echocardiogram.

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TABLE S5. Fatal adverse events (safety population)

n (%)

Crizotinib

(N=151)

Alectinib

(N=152)

All fatal AEs 7 (4.6) 6 (3.9)

Cardiac arrest 1 (0.7) 1 (0.7)

Acute kidney injury 0 1 (0.7)

Blood creatinine increase 0 1 (0.7)

Lung infection 0 1 (0.7)

Death 0 2 (1.3)

Sudden death 1 (0.7) 0

Cerebral hemorrhage 1 (0.7) 0

Necrotizing fasciitis 1 (0.7) 0

Dyspnea 1 (0.7) 0

Pneumonitis 1 (0.7) 0

Respiratory failure 1 (0.7) 0

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TABLE S6. Adverse events with an incidence ≥10% in either treatment arm (safety

population)

n (%)

Crizotinib

(N=151)

Alectinib

(N=152)

Gastrointestinal disorders

Constipation 51 (33.8) 54 (35.5)

Nausea 75 (49.7) 24 (15.8)

Diarrhea 70 (46.4) 20 (13.2)

Vomiting 62 (41.1) 14 (9.2)

General disorders and administration site conditions

Edema peripheral 48 (31.8) 28 (18.4)

Fatigue 25 (16.6) 31 (20.4)

Investigations

Alanine aminotransferase increased 50 (33.1) 26 (17.1)

Aspartate aminotransferase increased 40 (26.5) 24 (15.8)

Blood bilirubin increased 2 (1.3) 29 (19.1)

Nervous system disorders

Dizziness 23 (15.2) 13 (8.6)

Dysgeusia 30 (19.9) 5 (3.3)

Headache 16 (10.6) 11 (7.2)

Musculoskeletal and collective tissue disorders

Arthralgia 13 (8.6) 18 (11.8)

Myalgia 3 (2.0) 25 (16.4)

Back pain 10 (6.6) 16 (10.5)

Blood and lymphatic system disorders

Anemia 11 (7.3) 34 (22.4)

Skin and subcutaneous tissue disorders

Rash 14 (9.3) 20 (13.2)

16

Infections and infestations

Upper respiratory tract infection 14 (9.3) 17 (11.2)

Psychiatric disorders

Insomnia 9 (6.0) 18 (11.8)

Eye disorders

Visual impairment 18 (11.9) 3 (2.0)

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TABLE S7. Adverse events related to study treatment occurring in ≥5% of patients in either

treatment arm (safety population)

n (%)

Crizotinib

(N=151)

Alectinib

(N=152)

Gastrointestinal disorders

Nausea 65 (43.0) 12 (7.9)

Constipation 33 (21.9) 41 (27.0)

Diarrhea 58 (38.4) 9 (5.9)

Vomiting 45 (29.8) 6 (3.9)

Dyspepsia 8 (5.3) 4 (2.6)

Investigations

Alanine aminotransferase increased 46 (30.5) 22 (14.5)

Aspartate aminotransferase increased 35 (23.2) 24 (15.8)

Blood bilirubin increased 2 (1.3) 24 (15.8)

Blood creatinine increased 5 (3.3) 10 (6.6)

Blood creatinine phosphokinase increased 5 (3.3) 8 (5.3)

Weight increased 0 9 (5.9)

Gamma–glutamyltransferase increased 8 (5.3) 0

General disorders and administration site conditions

Edema peripheral 38 (25.2) 14 (9.2)

Fatigue 19 (12.6) 24 (15.8)

Nervous system disorders

Dysgeusia 29 (19.2) 3 (2.0)

Skin and subcutaneous tissue disorders

Rash 9 (6.0) 14 (9.2)

Photosensitivity reaction 0 8 (5.3)

Eye disorders

Visual impairment 16 (10.6) 1 (0.7)

18

Vision blurred 9 (6.0) 2 (1.3)

Photopsia 9 (6.0) 0

Cardiac disorders

Bradycardia 12 (7.9) 10 (6.6)

Sinus bradycardia 8 (5.3) 8 (5.3)

Blood and lymphatic system disorders

Anemia 6 (4.0) 19 (12.5)

Neutropenia 8 (5.3) 3 (2.0)

Musculoskeletal and connective tissue disorders

Myalgia 3 (2.0) 17 (11.2)

Metabolism and nutrition disorders

Decreased appetite 11 (7.3) 5 (3.3)

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TABLE S8. Adverse events leading to study treatment discontinuation occurring in ≥3% of

patients in either treatment arm (safety population)

n (%)

Crizotinib

(N=151)

Alectinib

(N=152)

Investigations

Alanine aminotransferase increased 9 (6.0) 2 (1.3)

Aspartate aminotransferase increased 6 (4.0) 2 (1.3)

Respiratory, thoracic, and mediastinal disorders

Pneumonitis 5 (3.3) 1 (0.7)

AE, adverse event

20