Abstract INTRODUCTION Mutations in genes such as TP53, SF3B1 and NOTCH1 are frequent in CLL and have been associated with outcome in previous studies. Whereas NOTCH1mut appeared to be a negative predictive factor in the context of chemotherapy combined with Rituximab, other mutations, e.g. SF3B1mut, TP53mut and BIRC3mut, were adverse prognostic factors in patient cohorts with different therapies. However, the impact on outcome among patients treated with non-chemotherapeutic agents is less clear. METHODS We assessed the incidence and impact of gene mutations in the CLL-009 trial (relapsed/refractory CLL, single-agent lenalidomide, Wendtner et al., Leuk Lymphoma 2016). Samples from study entry were available from 96 of 103 patients (93%). Analysis was performed via liquid chromatography (dHPLC) and sanger sequencing for TP53 and a customized targeted Next Generation Sequencing (tNGS) panel for ATM, BIRC3, EGR2, FBXW7, MYD88, TP53 (all exons), NOTCH1 (exon 34), SF3B1 (exon 14-16, 18) and XPO1 (exon 14, 15). All mutations with a variant allelic fraction > 5% were considered. RESULTS In total we identified 162 mutations across 11 genes in 79 of 96 patients with incidences of TP53mut 37.5%, SF3B1mut 33.3%, NOTCH1mut 21.9%, ATMmut 15.6%, XPO1mut 9.4%, FBXW7mut 7.3%, NFKBIEmut 6.3%, POT1mut 5.2%, BIRC3mut 3.1%, EGR2mut 2.0% and MYD88mut 2.0%. Twelve of 36 (33.3%) TP53mut patients had additional mutations within the same gene in contrast to only 2 of 32 (6.3%) SF3B1mut patients and 1 of 20 (5.0) NOTCH1mut patients. tNGS as compared to dHPLC and Sanger revealed 2 additional mutations in TP53 resulting in identification of 2 more TP53mut patients. We identified a variety of associations of subgroups defined by mutations with clinical and laboratory parameters, such as TP53mut with del17p (p 65 years more commonly had mutations in POT1 (p=0.02) and TP53 (p=0.02). Patients with NOTCH1mut (p Regarding response, OS and PFS, only the presence of NOTCH1mut showed a trend for reduced OS (HR=1.66, p=0.08). All other mutational subgroups, in particular TP53mut and SF3B1mut, had no significant association with PFS and OS. Three or more prior lines of therapy had the strongest impact on OS (HR 1.4, p To identify factors of independent prognostic impact, we performed multivariable Cox regressions for PFS and OS including number of prior lines of therapy, del17p, del11q, IGHV status and gene mutations. Only del17p (HR=2.81, p=0.01) was associated with decreased PFS, while for OS unmutated IGHV (HR 2.36 p=0.04), NOTCH1mut (HR 2.74 p =3 therapy lines (HR 3.3, p SUMMARY In this cohort, only del17p was associated with decreased PFS, while for OS unmutated IGHV, NOTCH1mut and >=3 therapy lines were identified as independent prognostic factors. The specific characteristics of the population under study and the treatment modality could explain not only the high incidence of recurrent mutations, but also uncommon associations of mutations to other characteristics or outcomes. Therefore, the associations of genetic prognostic factors may depend on the context of the particular trial population and the treatments administered, making a reassessment of prognostic markers and models mandatory in the era of novel treatments. Download : Download high-res image (358KB) Download : Download full-size image Figure . Disclosures Fraser: Lundbeck: Speakers Bureau; Celgene: Research Funding; Janssen: Consultancy, Honoraria, Research Funding, Speakers Bureau; AbbVie: Consultancy. Hillmen: Pharmacyclics LLC, an AbbVie Company: Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding; GSK: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; Alexion Pharmaceuticals, Inc.: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Celgene: Research Funding; Gilead: Consultancy, Honoraria, Research Funding. Durig: Lead Discovery Center: Research Funding. Gribben: Pharmacyclics: Honoraria; TG Therapeutics: Honoraria; Celgene: Honoraria; Acerta: Honoraria; Karyopharm: Honoraria; Kite: Honoraria; Janssen: Honoraria; Abbvie: Honoraria; Genentech/Roche: Honoraria. Kipps: Roche: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Oncternal: Research Funding; Pharmacyclics LLC, an AbbVie Company: Consultancy, Honoraria, Research Funding; Gilead: Consultancy, Speakers Bureau; Genentech: Consultancy, Research Funding; AbbVie: Consultancy, Honoraria, Research Funding. Purse: Celgene: Employment. Zhang: Celgene: Employment. De Bedout: Celgene: Employment. Hallek: AbbVie: Consultancy, Honoraria, Research Funding; Amgen: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; F. Hoffmann-LaRoche: Consultancy, Honoraria, Research Funding; Gilead: Consultancy, Honoraria, Research Funding; Janssen-Cilag: Consultancy, Honoraria, Research Funding; Mundipharma: Consultancy, Honoraria, Research Funding. Wendtner: Servier: Other: Grant, Personal Fees; Celgene: Consultancy, Research Funding; Mundipharma: Other: Grant, Personal Fees; Abbvie: Other: Personal Fees; Morphosys: Other: Personal Fees; Gilead: Other: Personal Fees; Novartis: Other: Personal Fees; Janssen-Cilag: Other: Personal Fees; Hoffmann La Roche: Other: Grant, Personal Fees. Stilgenbauer: Celgene: Consultancy, Honoraria, Research Funding; AbbVie: Consultancy, Honoraria, Research Funding; Mundipharma: Consultancy, Honoraria, Research Funding; Genzyme: Consultancy, Honoraria, Research Funding; Sanofi: Consultancy, Honoraria, Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria, Research Funding; Amgen: Consultancy, Honoraria, Research Funding; Hoffman La-Roche: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Pharmacyclics: Consultancy, Honoraria, Research Funding; GSK: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding; Gilead: Consultancy, Honoraria, Research Funding; Genentech: Consultancy, Honoraria, Research Funding.
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