© F e r r a t a S t o r t i F o u n d a t i o ntreatment. However, the relative frequency and clinical significance of ATM and BIRC3 abnormalities is unclear. This study addresses this issue in a large cohort of 11q-deleted patients detected by SNP6 profiling and screened for ATM and BIRC3 mutations. As a consequence, in the context of a phase III clinical trial of chemotherapy, we show that ATM mutational status remains the most clinically informative genomic lesion in 11q-deleted CLL, identifying cases with outcome comparable to TP53 deletion and/or mutation patients, and that the presence of BIRC3 deletion and/or mutation is associated with outcome comparable to other 11q-deleted CLL cases.
Methods
Patients and molecular diagnostic assaysA total of 166 untreated CLL patients diagnosed according to standard morphological and immunophenotypic criteria were included in this study (Table 1 and Online Supplementary Table S1). This cohort principally included patients from the UK LRF CLL4 trial 9 (n=133) which allowed accurate clinical correlations to bemade. An additional 33 11q-deleted patients were also included to allow more significant associations between the 11q deletion and other genomic variables to be made, such as with mutational status of ATM and BIRC3. The additional del11q patients were sampled subsequent to the development of progressive disease, with a median time from diagnosis of 3.2±5.2 years (±1 standard deviation (SD); range 1 month-27 years). For the entire cohort of 166 patients, mutational data were available for TP53 (n=125), SF3B1 (n=140) and NOTCH1 (n=146). 28,29 Details on the molecular diagnostic assays 30,31 are available in the Online Supplementary Methods. Informed consent was obtained from all patients in accordance with the Declaration of Helsinki and our local ethics committee gave their approval for the study.
DNA extraction, SNP6 array hybridization, data extraction and analysisGenomic DNA was extracted from CLL B cells (n=166) and buccal swabs (n=32), prior to being purified, amplified, labeled and hybridized to the Affymetrix SNP6.0 platform (Affymetrix, Santa Clara, CA, USA) as previously described 32 (Online Supplementary Methods).11q23 deletions, ATM and BIRC3 mutations in CLL haematologica | 2014; 99(4) 737
© F e r r a t a S t o r t i F o u n d a t i o n
Mutational analysis of ATM and BIRC3 genesThe presence or absence of somatically-acquired single nucleotide variants (SNVs or mutations) in ATM and BIRC3 were successfully ascertained in 105 (CLL4 cases: n=79 of 133) and 162 (CLL4 cases: n=131 of 133) patients, respectively. Denaturing high-performance liquid chromatography (DHPLC), high-resolution melt (HRM) polymerase chain reaction (PCR) analysis and Sanger sequencing were utilized. 20,26,27,29 More details of methods and the strategy adopted for assigning the somatic nature of each SNV are provided in the Online Supplementary Methods and Online Supplementary Table S2.
Statistical analysisStatistical analysis was performed using SPSS (v.20
Results
Incidence ...