Extensive next-generation sequencing analysis in chronic lymphocytic leukemia at diagnosis: clinical and biological correlations

Abstract

BackgroundIn chronic lymphocytic leukemia (CLL), next-generation sequencing (NGS) analysis represents a sensitive, reproducible, and resource-efficient technique for routine screening of gene mutations.MethodsWe performed an extensive biologic characterization of newly diagnosed CLL, including NGS analysis of 20 genes frequently mutated in CLL and karyotype analysis to assess whether NGS and karyotype results could be of clinical relevance in the refinement of prognosis and assessment of risk of progression. The genomic DNA from peripheral blood samples of 200 consecutive CLL patients was analyzed using Ion Torrent Personal Genome Machine, a NGS platform that uses semiconductor sequencing technology. Karyotype analysis was performed using efficient mitogens.ResultsMutations were detected in 42.0 % of cases with 42.8 % of mutated patients presenting 2 or more mutations. The presence of mutations by NGS was associated with unmutated IGHV gene (p = 0.009), CD38 positivity (p = 0.010), risk stratification by fluorescence in situ hybridization (FISH) (p < 0.001), and the complex karyotype (p = 0.003). A high risk as assessed by FISH analysis was associated with mutations affecting TP53 (p = 0.012), BIRC3 (p = 0.003), and FBXW7 (p = 0.003) while the complex karyotype was significantly associated with TP53, ATM, and MYD88 mutations (p = 0.003, 0.018, and 0.001, respectively). By multivariate analysis, the multi-hit profile (≥2 mutations by NGS) was independently associated with a shorter time to first treatment (p = 0.004) along with TP53 disruption (p = 0.040), IGHV unmutated status (p < 0.001), and advanced stage (p < 0.001). Advanced stage (p = 0.010), TP53 disruption (p < 0.001), IGHV unmutated status (p = 0.020), and the complex karyotype (p = 0.007) were independently associated with a shorter overall survival.ConclusionsAt diagnosis, an extensive biologic characterization including NGS and karyotype analyses using novel mitogens may offer new perspectives for a better refinement of risk stratification that could be of help in the clinical management of CLL patients.Electronic supplementary materialThe online version of this article (doi:10.1186/s13045-016-0320-z) contains supplementary material, which is available to authorized users.

In chronic lymphocytic leukaemia with complex karyotype, major structural abnormalities identify a subset of patients with inferior outcome and distinct biological characteristics

“…IGHV genes were amplified from genomic DNA and sequenced according to standard methods with the cut‐off of 98% homology to the germline sequence to discriminate between mutated (<98%) and unmutated (≥98%) cases, as previously reported (Rigolin et al , ). Mutations of NOTCH1 , SF3B1 , BIRC3 and TP53 genes were analysed by next generation sequencing analysis using Ion Torrent PGM (Life Technologies, Foster City, CA), as described elsewhere (Rigolin et al , ). Details of GEP analysis are reported in Supplemental Methods (Appendix S1).…”

In CLL, comorbidities and the complex karyotype are associated with an inferior outcome independently of CLL-IPI

“…2 However, CLL is mainly a disease of the elderly with many patients presenting at diagnosis with significant comorbidities that may affect treatment decisions and outcome. 3 Moreover, in recent years, the complex karyotype (CK) emerged as a prognostic biomarker associated with an inferior outcome 4,5 and worse response to treatments including novel drugs. 6,7 We therefore set out to analyze the prognostic relevance of comorbidities and of CK in relation to the CLL-IPI.…”

“…The stability of the Cox model was internally validated using bootstrapping procedures. 4 Statistical analysis was performed using Stata 14.0 (Stata Corp, College Station, TX).…”

“…13 Furthermore, with the use of effective mitogens, cytogenetic abnormalities and, in particular, CK recently emerged as one of the novel biomarkers associated with an inferior outcome [4][5][6][7][8]12,20 and with the development of chemorefractoriness. 21 In conclusion, we showed for the first time that comorbidities and CK were associated with a worse outcome independently of CLL-IPI.…”

MYD88 in the driver’s seat of B-cell lymphomagenesis: from molecular mechanisms to clinical implications

“…83 Furthermore, MYD88(L265P) is absent in primary mediastinal large Bcell lymphoma 2,3,94 and primary cutaneous follicle center lymphoma, [71][72][73] and rarely present in hairy cell leukemia (1.1%), 22,30,[57][58][59] plasma cell myeloma (1.5%), 18,22,23,43,106,107 Burkitt lymphoma (1.5%), 2,74 follicular lymphoma (1.9%), 18,22,23,67,68 and CLL (2.5%). 18,[22][23][24]28,[38][39][40][41][42][43][44][45][46][47][48][49][50][51][52]…”