The insufficient standardization of diagnostic next-generation sequencing (NGS) still limits its implementation in clinical practice, with the correct detection of mutations at low variant allele frequencies (VAF) facing particular challenges. We address here the standardization of sequencing coverage depth in order to minimize the probability of false positive and false negative results, the latter being underestimated in clinical NGS. There is currently no consensus on the minimum coverage depth, and so each laboratory has to set its own parameters. To assist laboratories with the determination of the minimum coverage parameters, we provide here a user-friendly coverage calculator. Using the sequencing error only, we recommend a minimum depth of coverage of 1,650 together with a threshold of at least 30 mutated reads for a targeted NGS mutation analysis of ≥3% VAF, based on the binomial probability distribution. Moreover, our calculator also allows adding assay-specific errors occurring during DNA processing and library preparation, thus calculating with an overall error of a specific NGS assay. The estimation of correct coverage depth is recommended as a starting point when assessing thresholds of NGS assay. Our study also points to the need for guidance regarding the minimum technical requirements, which based on our experience should include the limit of detection (LOD), overall NGS assay error, input, source and quality of DNA, coverage depth, number of variant supporting reads, and total number of target reads covering variant region. Further studies are needed to define the minimum technical requirements and its reporting in diagnostic NGS.

The significance of positron emission tomography/computed tomography (PET/CT) in chronic lymphocytic leukemia (CLL) has not yet been systematically studied. This prospective study was aimed at assessing the benefit of PET/CT in patients with newly diagnosed or relapsed CLL and Richter transformation (RT). PET/CT examination was performed in 23 patients with newly diagnosed disease, 13 with relapsed disease and eight with suspected or histopathologically confirmed RT. In all patients, the maximum standardized uptake value (SUV(max)) was calculated. The median SUV(max) was 3.4 (range: 1.5-6.3) and 3.1 (range: 1.2-5.9) in newly diagnosed and relapsed patients, respectively. The median SUV(max) of patients with suspected or confirmed RT reached 16.5 (range: 7.2-25.3), a value different from that of the previous groups (p < 0.001). 2-[18F]fluoro- 2-deoxy-D-glucose ((18)F-FDG) PET/CT revealed inflammatory lesions in seven patients (16%) and synchronous tumors in two newly diagnosed patients. (18)F-FDG PET/CT may be a beneficial imaging method when used in individuals with CLL and suspected RT.

Inhibitors of B-cell receptor signaling, ibrutinib and idelalisib, and BCL-2 antagonist, venetoclax, have become the mainstay of treatment for chronic lymphocytic leukemia (CLL). Despite significant efficacy in most CLL patients, some patients develop resistance to these agents and progress on these drugs. We provide a state-of-the-art overview of the acquired resistance to novel agents. In 80% of patients with ibrutinib failure, acquired mutations in BTK and PLCG2 genes were detected. No distinct unifying resistance-associated mutations or deregulated signaling pathways have been reported in idelalisib failure. Acquired mutations in the BCL2 gene were detected in patients who had failed on venetoclax. In most cases, patients who have progressed on ibrutinib and venetoclax experience resistance-associated mutations, often present at low allelic frequencies. Resistance-associated mutations tend to occur between the second and fourth years of treatment and may already be detected several months before clinical relapse. We also discuss the development of next-generation agents for CLL patients who have acquired resistant mutations to current inhibitors.