Randomized, Placebo-Controlled, Phase 2 Study of Veliparib, a PARP Inhibitor, in Combination

1 Supplemental Tables

Table S1. Summary of Adverse Events in All Randomized Patients and Recent Smoker Group Placebo BID and Veliparib BID and Carbo/Paclitaxel Carbo/Paclitaxel All randomized Recent All randomized Recent patients smokers patients smokers (n=52) (n=30) (n=105) (n=64) Any grade AE, n (%) 46 (88.5) 28 (93.3) 101 (96.2) 61 (96.3) Any grade 3/4 AE, n (%) 26 (50.0) 12 (40.0) 68 (64.8) 42 (65.6)a Any SAE 12 (23.1) 8 (26.7) 28 (26.7) 17 (26.6) All-grade AEs in ≥15% of all patients, n (%) Alopecia 22 (42.3) 10 (33.3) 41 (39.0) 23 (35.9) Anemia 21 (40.4) 12 (40.0) 33 (31.4) 20 (31.3) Neutropenia 15 (28.8) 8 (26.7) 38 (36.2) 26 (40.6) Peripheral neuropathy 13 (25.0) 6 (20.0) 25 (23.8) 14 (21.9) Nausea 13 (25.0) 6 (20.0) 29 (27.6) 14 (21.9) Fatigue 13 (25.0) 7 (23.3) 24 (22.9) 11 (17.2) Anorexia 9 (17.3) 5 (16.7) 14 (13.3) 6 (9.4) Thrombocytopenia 8 (15.4) 4 (13.3) 13 (12.4) 9 (14.1) Diarrhea 8 (15.4) 4 (13.3) 13 (12.4) 8 (12.5) Arthralgia 7 (13.5) 4 (13.3) 20 (19.0) 14 (21.9) Dyspnea 6 (11.5) 3 (10.0) 16 (15.2) 9 (14.1) Grade 3/4 AEs in ≥5% of all patients, n (%) Neutropenia 12 (23.1) 6 (20.0) 20 (19.0) 12 (18.8) Anemia 5 (9.6) 3 (10.0) 11 (10.5) 9 (14.1) Alopecia 3 (5.8) 0 (0) 7 (6.7) 5 (7.8) Thrombocytopenia 3 (5.8) 3 (10.0) 5 (4.8) 4 (6.3) Leukopenia 0 (0) 0 (0) 6 (5.7) 2 (3.1) ap<0.05 versus recent smoker placebo group. AE, adverse event; BID, twice daily; Carbo, carboplatin. 2

Table S2. Paclitaxel Plasma Concentrations (ng/mL) by Cotinine Level Patients with Cotinine ≤10 ng/mL Patients with Cotinine >10 ng/mL C1D3 C2D3 C3D3 C4D3 C1D3 C2D3 C3D3 C4D3 Placebo BID N=29 N=29 N=24 N=21 N=21 N=18 N=15 N=13 6133 ± 5868 ± 7185 ± 7001 ± 4182 ± 9227 ± 5810 ± 7992 ± 2700 2345 5035 3754 2499 12482 4596 9530 (5960) (5810) (6290) (6570) (4300) (6380) (4760) (5780) Veliparib 120 mg BID N=58 N=46 N=38 N=35 N=40 N=37 N=32 N=32 12842 ± 5926 ± 5824 ± 8809 ± 13441 ± 10041 ± 6584 ± 6798 ± 39061 3024 2656 16544 41487 22330 5693 3198 (5565) (5310) (5635) (5930) (6680) (6350) (5615) (5865) Data are mean ± SD (median) plasma concentrations of paclitaxel just before ending paclitaxel infusion (2 hr 55 min after start of paclitaxel infusion) in patients with cotinine concentrations ≤10 ng/mL and >10 ng/mL at screening. BID, twice daily; C, cycle; D, day; SD, standard deviation. 4 5

2 Table S3. Carboplatin Plasma Concentrations (µg/mL) by Cotinine Level Patients with Cotinine ≤10 ng/mL Patients with Cotinine >10 ng/mL C1D3 C2D3 C3D3 C4D3 C1D3 C2D3 C3D3 C4D3 Placebo BID N=29 N=28 N=24 N=21 N=21 N=18 N=15 N=13 29.6 ± 33.5 ± 56.2 ± 37.8 ± 30.7 ± 29.1 ± 13 30.6 ± 39.9 ± 18.3 21.8 103.3 16.4 14.3 (30.9) 14.3 17.9 (31.6) (38.5) (35.2) (31.8) (35.2) (37.9) (35.0) Veliparib 120 mg BID N=58 N=46 N=39 N=36 N=40 N=39 N=33 N=34 31.2 ± 31.3 ± 27.9 ± 42.6 ± 33.6 ± 38.0 ± 34.9 ± 34.5 ± 14.1 18.5 15.3 46.4 15.6 42.9 16.2 15.0 (32.7) (33.0) (32) (35.1) (30.7) (33.3) (35.5) (32.4) Data are mean ± SD (median) plasma concentrations of carboplatin just before ending carboplatin infusion (25 min after start) in patients with cotinine concentrations ≤10 ng/mL and >10 ng/mL at screening. BID, twice daily; C, cycle; D, day; SD, standard deviation. 6 7 8

3 9 Table S4. Summary of Primary and Secondary Endpoints by Smoking History Placebo BID and Veliparib BID and HR Adjusted HRa Carbo/Paclitaxel Carbo/Paclitaxel Median PFS, months (95% CI) 4.2 (3.1–5.6) 5.8 (4.2–6.1) 0.74 (0.46–1.17) 0.57 (0.35–0.92) Recent 3.3 (1.4–4.2) 5.6 (4.1–7.0) 0.38 (0.21–0.67) 0.37 (0.21–0.68) Former NA (3.3–NA) 6.0 (2.4–NA) 2.10 (0.66–6.65) 0.77 (0.20–3.06) Never 5.6 (1.4–8.2) 6.4 (1.0–NA) 1.03 (0.27–3.85) 0.96 (0.21–4.46) Median OS, months (95% CI) 9.1 (5.4–12.3) 11.7 (8.8–13.7) 0.80 (0.54–1.18) 0.72 (0.49–1.07) Recent 5.4 (3.8–8.8) 12.5 (9.9–16.6) 0.43 (0.26–0.70) 0.45 (0.27–0.76) Former 14.6 (9.2–NA) 8.6 (5.9–17.5) 1.62 (0.73–3.6) 0.72 (0.27–1.92) Never NA (3.6–NA) 13.2 (5.0–NA) 1.34 (0.40–4.44) 0.71 (0.18–2.74) ORR, % (95% CI) 32 (20–46) 32 (24–42) ------Recent 26 (12–45) 31 (20–44) Former 43 (18–71) 39 (22–59) Never 38 (9–76) 23 (5–54) Median DOR, months (95% CI) 3.3 (2.7–5.3) 6.9 (4.4–7.0) 0.11 (0.03–0.50) ----- Recent 4.3 (1.5–NA) 6.9 (4.4–7.0) 0.39 (0.09–1.66) Former NA (2.9–NA) 5.5 (4.6–NA) 0.51 (0.07–3.67) Never NA (2.8–NA) NA (5.0–NA) 0.51 (0.07–3.67) aFrom Cox proportional hazard model, adjusted for gender and baseline ECOG PS. BID, twice daily; Carbo, carboplatin; CI, confidence interval; DOR, duration of overall response; ECOG PS, Eastern Cooperative Oncology Group performance status; HR, hazard ratio; NA, not available; ORR, objective response rate; OS, overall survival; PFS, progression-free survival. 10 11

4 12 Table S5. Impact of Smoking During Study Treatment in Recent Smokers

Placebo BID and Veliparib BID and Carbo/Paclitaxel Carbo/Paclitaxel HR Cotinine high: n=22 Cotinine high: n=41 Cotinine low: n=8 Cotinine low: n=23

Median PFS, months (95% CI)

Cotinine-high 3.5 (1.3–5.6) 5.6 (4.3–5.9) 0.38 (0.19–0.75) recent smokers

Cotinine-low 3.1 (0.0–5.0) 5.8 (2.5–8.4) 0.43 (0.15–1.23) recent smokers

Median OS, months (95% CI)

Cotinine-high 5.7 (3.6–11.1) 12.5 (9.5–17.0) 0.50 (0.27–0.90) recent smokers

Cotinine-low recent smokers 4.9 (0.0–8.4) 12.8 (7.9–17.7) 0.22 (0.08–0.61)

BID, twice daily; Carbo, carboplatin; CI, confidence interval; HR, hazard ratio; OS, overall survival; PFS, progression-free survival. 13

Table S6. Hazard Ratios in Smoking Status Subgroup Based on a Multivariate Cox Proportional Hazards Model for Overall Survival Endpoint

From Multivariate Modela HR 95% CI of HR

V vs P in current smokers 0.4541 0.2157–0.9560

V vs P in past smokers 1.4416 0.5916–3.5125

V vs P in never smokers 0.9663 0.2421–3.8562

aModel includes treatment, smoking history, histology, age, ECOG, gender, geographic region. CI, confidence interval; ECOG, Eastern Cooperative Oncology Group; HR, hazard ratio; P, placebo; V, veliparib. 15 16

Table S7. Hazard Ratios in Smoking Status Subgroup Based on a Multivariate Cox PH Model for Progression Free Survival Endpoint

From Multivariate Model** HR 95% CI of HR

V vs P in Current smokers 0.4090 0.1744–0.9593

V vs P in Past Smokers 1.3352 0.3755–4.7482

V vs P in never smoked 0.7245 0.1535–3.4192

**Model includes treatment, smoking status, Histology, age group, ECOG, gender, Region. CI, confidence interval; HR, hazard ratio; P, placebo; V, veliparib. 18 19

7 20 21 Supplemental Figures 22

23 Figure S1. Case Report Form Example 24

9 27 Supplemental Methods

28 DNA Extraction, Exome Sequencing, and Variant Calling

30 Genomic DNA (and RNA) was extracted using Qiagen AllPrep kit. Profiling aimed to achieve a

31 150X mean on-target coverage for tumor (and 100X for germline DNA). Alignment was

32 performed using OSA (http://omicsoft.com/downloads/whitepaper/OmicsoftAligner.pd). Somatic

33 call was performed by Array Studio module “Summarize Matched Pair Variation Data” (the

34 same algorithm as Varscan2) to identify somatic mutations. A one-sided Fisher exact test is

35 done for the somatic mutation test. For variants called by ArrayStudio, filters include: Base

36 Quality Cutoff is 13, Map Quality Cutoff is 0, Minimal coverage in normal samples is 8, Minimal

37 coverage in Tumor samples is 6, Minimal Mutation Hit is 2, Frequency Difference Cutoff is 0.20,

38 Filtering Significance Level=0.05, Maximal Frequency Cutoff is 0.10. In order to remove false

39 positive calls due to sequencing or alignment-related artifacts, a set of filters were set up

40 (Koboldt D.K. et al, Genome Research, 2012). These include: Read Position Cutoff is 0.10,

41 Strandness Cutoff is 0.9, Homopolymer Cutoff is 5, Mapping Quality Difference Cutoff is 30,

42 Read Length Difference Cutoff is 25, Mmqs Difference (Difference in average mismatch quality

43 sum between variant and reference reads) Cutoff is 100. There are two categories in the variant

44 calls –high confidence or low confidence, only high confidence somatic calls were kept to make

45 somatic mutational signature and mutational burden calculation. Variants in protein coding

46 regions and splicing sites were used to calculate mutational signature (Alexandrov L.B. et al.,

47 Nature, 2013). These are the so called “tier 1” mutations in whole exome sequencing data

48 analysis (Mardis E.R. et al, N Engl J Med. 2009;361). Certain germline variants still leaked

49 through after somatic calling. Common SNPs (defined as variants with population frequency =

50 or >1% in dbSNP database or ExAC database) were further filtered out. When calculating

51 somatic mutational signature, functional significance of the variants were not evaluated as even

52 silent mutations (or neutral mutations) could be informative for the underlying mutagenesis

10 53 processes (Alexandrov L.B. et al., Nature 2013; Helleday T. et al., Nat Rev Genet 2014;

54 Alexandrov L.B. and Stratton M.R., Curr Opin Genet Dev 2014). Since only high quality exome

55 pairs (defined as of more than 90% of target exome region being sequenced more than 10

56 times) were used for our analysis and exomic region coverage is comparable across these high

57 quality exome pairs, no further normalization was done when comparing mutational burden.

59 Determination of Molecular Signatures

61 The deconvolution method as described in Rosenthal et al, 2016 was followed. To validate the

62 methodology, we downloaded TCGA ovarian and lung cancer somatic mutational data,

63 calculated somatic mutational signatures for each patient, and re-established the reported

64 correlation between age of onset and signature 1, smoking exposure and signature 4, and

65 BRCA1/2 mutational status and signature 3 (Alexandrov L.B. et al., Nature 2013; Helleday T. et

66 al., Nat Rev Genet 2014; Alexandrov L.B. and Stratton M.R., Curr Opin Genet Dev 2014).

67 This deconvolution method returned a numeric value for each somatic signature in each patient

68 tumor. We define scores of “zero” as “negative”, any value “more than zero” as “positive”.

11 70 List of supplemental materials 71

72 Supplemental Table 1. Word document file. 73 Supplemental Table 2. Word document file. 74 Supplemental Table 3. Word document file. 75 Supplemental Table 4. Word document file. 76 Supplemental Table 5. Word document file. 77 Supplemental Figure 1. Word documents file. 78 Supplemental Methods. Word document file. 79