Supplementary appendix

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1 Supplementary appendix This appendix formed part of the original submission and has been peer reviewed. We post it as supplied by the authors. Supplement to: Farooqui MZH, Valdez J, Martyr S, et al. Ibrutinib for previously untreated and relapsed or refractory chronic lymphocytic leukaemia with TP53 aberrations: a phase 2, single-arm trial. Lancet Oncol 2014; published online Dec 31.

2 Supplementary Index Farooqui et al Ibrutinib for previously untreated and relapsed or refractory chronic lymphocytic leukaemia with TP53 aberrations: a phase 2, single-arm trial Supplementary table S1. Reason for treatment discontinuation and disposition of patients who discontinued treatment by last follow-up. Enrollment deviation (ineligible diagnosis) Subject Age Cohort Time off study Pathologic diagnosis PCI B6 56 TN 6.3 Hodgkin s lymphoma* * Hodgkin s lymphoma diagnosed at 24 weeks, which on review of pre-treatment biopsy was already present pre-treatment but the CLL component predominated. Disease progression: Subject Age Cohort Time to progression Time to death PCI B12 62 TN PCI B24 66 RR PCI B30 57 RR PCI B2 66 RR PCI B23 56 TN Pathologic diagnosis No biopsy performed; presumed Richter s transformation. In retrospect, transformation likely present pre-enrollment, but no conclusive evidence was found that transformation had occurred Richter s transformation Prolymphocytic transformation. Pre-treatment pathologic evaluation was suspicious be not definitive for transformation. Prolymphocytic transformation Richter s transformation Death: Subject Age Cohort Time to death Cause of death PCI B29 62 TN 0.13 Died at home, presumed uro-sepsis. Not neutropenic. No cultures obtained. Autopsy without specific findings. PCI B11 59 RR 1.4 Biliary tract infection, sepsis. Not neutropenic. Suggestive laboratory data but no microbial cultures obtained. Treated at outside hospital. PCI B51 49 TN 7.8 Sudden, unexplained death at home. History of palpitations pre-dating study enrollment. Unremarkable cardiac workup prior to and during study participation. TN designates previously untreated patients, RR designates patients with relapsed or refractory disease. 1

3 Supplementary table S2. Response criteria. Response criteria based on the International Workshop on Chronic Lymphocytic Leukemia 2008, incorporating the 2012 and 2013 clarifications. 1-4 Response CR PR PRL PD Group A Lymphadenopathy 1 None > 1.5cm Decrease 50% Decrease 50% Increase 50% or any new lesion > 1.5 cm Hepatomegaly None Decrease 50% Decrease 50% Increase 50% or any new hepatomegaly Splenomegaly None Decrease 50% Decrease 50% Increase 50% or new splenomegaly Blood Lymphocytes 2 < 4000/µl Decrease 50% from Increase or <50% Increase 50% over Marrow 3 Normocellular, <30% lymphocytes, no B- lymphoid nodules. Hypocellular marrow defines CRi Group B Platelet count > 100,000/µL > 100,000/µL or increase Hemoglobin > 11.0 g/dl > 11.0 g/dl or increase 50% over baseline baseline decrease over baseline baseline or > 5000/µL Not applicable Not applicable Not applicable > 100,000/µL or increase 50% over baseline > 11.0 g/dl or increase Neutrophils > 1500/µL > 1500/µL or or increase Not applicable 1 Sum of the products of multiple lymph nodes as evaluated by CT scans 2 Patients with treatment-related lymphocytosis remain on study unless associated with other signs of progressive disease. 3 Complete response requires confirmation with bone marrow biopsy. Decrease 50% from baseline secondary to CLL Decrease 50% from baseline secondary to CLL Not applicable CR: Disease related constitutional symptoms resolved and all above criteria met, includes bone marrow biopsy. CRi: CR with incomplete hematopoietic recovery. PR: Two criteria from Group A if abnormal at baseline plus one of the criteria from Group B must be met, requires the absence of growth factor or transfusion support. PRL: All PR criteria met except blood lymphocyte count. SD: Failure to achieve a response and in the absence of PD PD: One criteria from Group A or B are met or development of transformation to a more aggressive histology 2

4 Overall Response Previously untreated Relapsed / Refractory Rai Stage 2 Rai Stage 3 < 65 years old 65 years old Lymph nodes < 5 cm Lymph nodes 5 cm Spleen volume < 315 ml Spleen volume 315 ml IGHV-mutated IGHV-unmutated β2 microglobulin < 3 mg/dl β2 microglobulin 3 mg/dl PR PRL Patients with response % Supplementary figure S1. Treatment response in subgroups defined by clinical and biologic criteria. Shown is the overall response divided into rate of partial response (PR) and partial response with lymphocytosis (PRL) for defined subgroups at 24 weeks. The rate of overall response rate was similar for all subgroups. However, patients with Rai stage 3 more often had partial response (60%) than partial response with lymphocytosis (28%), while patients with Rai stage 2 more often had partial response with lymphocytosis (69%) than partial response (31%). The difference in the type of response between these two subgroups was significant by Fischer s exact test (P = 0.029). This is consistent with the different kinetics of treatment-induced lymphocytosis we previously described in a partially overlapping cohort of patients. 5 3

5 Change from baseline (%) 100 * Supplementary figure S2. Change in the prevalence of subclones with deletion 17p13.1 at 24 weeks compared to baseline. The Waterfall plot summarizes the cytogenetic response at 24 weeks; red bars represent patients with relapsed or refractory disease, blue bars previously untreated patients. Five patients had complete resolution of the deletion 17p13 1 subclone. The % change for the patient marked with * was capped at 100% (the effective change was 634%). Supplementary references: 1. Hallek M, Cheson BD, Catovsky D, Caligaris-Cappio E, Dighiero G, Dohner H, et al. Response Assessment in Chronic Lymphocytic Leukemia Treated with Novel Agents Causing an Increase of Peripheral Blood Lymphocytes. Blood 2012; [e- Letter]( 2. Hallek M, Cheson BD, Catovsky D, Caligaris-Cappio E, Dighiero G, Dohner H, et al. Clarification Of iwcll Criteria For A Partial Response To Therapy. Blood. 2013; [e-letter]( 3. Hallek M, Cheson BD, Catovsky D, Caligaris-Cappio F, Dighiero G, Dohner H, et al. Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute-Working Group 1996 guidelines. Blood. 2008; 111(12): Cheson BD, Byrd JC, Rai KR, Kay NE, O'Brien SM, Flinn IW, et al. Novel targeted agents and the need to refine clinical end points in chronic lymphocytic leukemia. J Clin Oncol. 2012; 30(23): Herman SE, Niemann CU, Farooqui M, Jones J, Mustafa RZ, Lipsky A, et al. Ibrutinib-induced lymphocytosis in patients with chronic lymphocytic leukemia: correlative analyses from a phase II study. Leukemia. 2014; 28(11):