Search

• Changes in the clonal composition of acute myeloid leukemia occur during therapy. • Rare cases of outgrowth of clones related to nonmalignant, but clonal hematopoiesis unrelated to the leukemic clone can be seen on regeneration after chemotherapy. • In cases in which changes occur in the proportions of leukemic subclones, the largest subclone is not necessarily the one with relapse-initiating potential. • Caution is warranted when correlating residual disease levels to prognosis in patients whose leukemic subclones exhibit differential responses to chemotherapy. • It remains to be seen whether these findings can be extrapolated to the minimal residual disease setting when overall reduction of leukemic subclones is much greater. Next-generation sequencing (NGS) is an excellent methodology for measuring residual disease in acute myeloid leukemia and surveying several subclones simultaneously. There is little experience with interpretation of differential clonal responses to therapy. We hypothesized that differential clonal response could best be studied in patients with residual disease at the time of response evaluation. We performed targeted panel sequencing of paired diagnostic and first treatment evaluation samples in 69 patients with residual disease by morphology or measurable residual disease (MRD) level >0.02. Five patients had a rising clone at the time of evaluation. In a representative case, the rising clone was present only in the putative healthy stem cells (CD45lowCD34+CD38–CD123–CD7–) and not in the putative leukemic stem cells (CD34+CD38–CD123+CD7+) cells, thus indicating nonmalignant clonal hematopoiesis. In contrast, 17 of 43 evaluable patients exhibited a differential response in genes related to the leukemic clone. Twenty-six of 43 patients exhibited a clonal response that followed the overall treatment response. Patients with a differential response had better event-free survival (EFS) and overall survival (OS) than those in whom the clonal response followed the overall response (log-rank test, EFS: p = 0.045, OS: p = 0.050). This indicates that when following multiple leukemia-related clones, the less chemotherapy-responsive clone could, in some cases, have lower relapse potential, contrary to what is known when using standard mutation or fusion transcript-based disease surveillance. In conclusion, our results confirm the potential of refining MRD assessments by following multiple clones and warrants further studies on the precise interpretations of multiclone NGS–MRD assays. [ABSTRACT FROM AUTHOR]

The future of clinical diagnosis and treatment of hematologic diseases will inevitably involve the integration of artificial intelligence (AI)-based systems into routine practice to support the hematologists' decision making. Several studies have shown that AI-based models can already be used to automatically differentiate cells, reliably detect malignant cell populations, support chromosome banding analysis, and interpret clinical variants, contributing to early disease detection and prognosis. However, even the best tool can become useless if it is misapplied or the results are misinterpreted. Therefore, in order to comprehensively judge and correctly apply newly developed AI-based systems, the hematologist must have a basic understanding of the general concepts of machine learning. In this review, we provide the hematologist with a comprehensive overview of various machine learning techniques, their current implementations and approaches in different diagnostic subfields (e.g., cytogenetics, molecular genetics), and the limitations and unresolved challenges of the systems. [ABSTRACT FROM AUTHOR]

The diagnosis of haematological malignancies requires a plethora of methods to evaluate primarily the morphology, but also immunophenotypic and genetic markers. However, intratumoural and interpatient tumour heterogeneity present a challenge when it comes to achieve early diagnosis and informed treatment decisions. Here, the clinical potential of personalized genome and transcriptome sequencing as a comprehensive diagnostic approach is just beginning to be realized, whereas the analysis and clinical interpretation of the acquired data requires a solid knowledge base and sophisticated bioinformatics workflows. Personalized sequencing is already clinically applied and offers the possibility to refine molecular diagnostics, to more accurately assess disease risk and to optimize and personalize treatment decisions. This article reflects the current status of whole genome and transcriptome sequencing as a diagnostic tool for haematological neoplasms, describes pre-analytical and analytical considerations and discusses the current challenges and limitations of the approach. [ABSTRACT FROM AUTHOR]

• To define the biological differences in acute myeloid leukaemia (AML) with KMT2A gene involvement and their prognostic impact, we compared 190 de novo AML patients at diagnosis, 95 harbouring KMT2A -rearrangement (KMT2A r) and 95 KMT2A -PTD, performing cytogenetic and molecular genetic analyses. Both AML subtypes had an unfavourable outcome, particularly in patients older than 60. Patients with KMT2A r were younger compared to patients with KMT2A -PTD (mean 52 vs 65 years, p < 0.001) and had a higher rate of additional cytogenetic abnormalities (ACA) (46% vs 25% of cases). • In both groups, occurrence of ACA did not influence the overall survival (OS). Regarding molecular genetics, 66% of patients with KMT2A r and 99% of patients with KMT2A -PTD had additional gene mutations. In multivariate analysis, KRAS mutations and 10p12 rearrangement resulted as adverse prognostic factors in KMT2A r subgroup. In the KMT2A -PTD group, apart from age, only the occurrence of DNMT3A non-R882 mutations correlated with shorter OS. To define the biological differences in acute myeloid leukaemia (AML) with KMT2A gene involvements and their prognostic impact, we compared 190 de novo AML patients at diagnosis, 95 harbouring KMT2A -rearrangement (KMT2A r) and 95 KMT2A -PTD by performing cytogenetic and molecular genetic analyses. Both AML subtypes had an unfavourable outcome, particularly in patients > 60 years. Patients with KMT2A r were younger compared to patients with KMT2A -PTD (mean 52 vs 65 years, p < 0.001) and had a higher rate of additional cytogenetic abnormalities (ACA) (46% vs 25% of cases). In both groups, occurrence of ACA did not influence the overall survival (OS). Regarding molecular genetics, 66% of patients with KMT2A r and 99% of patients with KMT2A -PTD had additional gene mutations. In multivariate analysis, KRAS mutations and 10p12 rearrangement resulted as adverse prognostic factors in KMT2A r subgroup. In the KMT2A -PTD group, apart from age, only the occurrence of DNMT3A non-R882 mutations correlated with shorter OS. [ABSTRACT FROM AUTHOR]

• Assessing translocations involving the IGH locus we observed a 96% concordance of FISH (fluorescence in situ hybridization) and WGS results. • Assessing copy number alterations (CNA) we observed and a 92% overall concordance of FISH and WGS. • WGS analysis resulted in the identification of 17 additional MYC -translocations that were missed by the initial FISH based workup. • RNA-Seq followed by supervised clustering grouped patients in their expected genetically defined subgroup and prompted the assessment of WGS data in cases that were not congruent with conventional FISH. • The simultaneous analysis of CNA, SV and small nucleotide variants (SNV) allowed the evaluation of mutations in relation to common cytogenetic findings. The diagnosis and risk stratification of multiple myeloma (MM) is based on clinical and cytogenetic tests. Magnetic CD138 enrichment followed by interphase FISH (fluorescence in situ hybridisation) is the gold standard to identify prognostic translocations and copy number alterations (CNA). Although clinical implications of gene expression profiling (GEP) or panel based sequencing results are evident, those tests have not yet reached routine clinical application. We set up a single workflow to analyse MM of 211 patients at first diagnosis by whole genome sequencing (WGS) and RNA-Seq and validate the results by FISH analysis. We observed a 96% concordance of FISH and WGS results when assessing translocations involving the IGH locus and an overall concordance of FISH and WGS of 92% when assessing CNA. WGS analysis resulted in the identification of 17 additional MYC -translocations that were missed by FISH analysis. RNA-Seq followed by supervised clustering grouped patients in their expected genetically defined subgroup and prompted the assessment of WGS data in cases that were not congruent with FISH. This allowed the identification of additional IGH-translocations and hyperdiploid cases. We show the reliability of WGS an RNA-Seq in a clinical setting, which is a prerequisite for a novel routine diagnostic test. [ABSTRACT FROM AUTHOR]

Trisomy 8 is the most frequent cytogenetically gained aberration in AML. We compared 79 adult de novo AML with trisomy 8 as the sole cytogenetic abnormality (+8sole) to 511 normal karyotype AML patients (NK). +8sole patients were older ( p = 0.013), presented lower WBC counts ( p = 0.010), harbored more often ASXL1 mutations ( p < 0.001) and RUNX1 mutations ( p = 0.009), but less frequent FLT3 -ITD ( p = 0.038), NPM 1 mutations ( p < 0.001) and double-mutated CEBPA ( p = 0.038) than NK patients. No prognostic difference was found between +8sole and NK. With respect to genetic stability we found +8sole was instable, and molecular markers were either stable or gained in number and diversity. [ABSTRACT FROM AUTHOR]

• We defined Complex Karyotype (CK) in T-ALL as the presence of ≥3 cytogenetic alterations. • T-ALL cases with CK ≥ 3 accounted for 16 % (22/139) of all evaluable karyotypes. • T-ALL patients with CK ≥ 3 showed a significantly inferior response to initial therapy. • CK ≥ 3 showed an adverse prognostic value in a multivariable test, independently of MRD. • The mutational profile CK ≥ 3 patients suggested a molecular mechanism of resistance. The potential prognostic value of conventional karyotyping in adult T-cell acute lymphoblastic leukemia (T-ALL) remains an open question. We hypothesized that a modified cytogenetic classification, based on the number and type of cytogenetic abnormalities, would allow the identification of high-risk adult T-ALL patients. Complex karyotype defined by the presence of ≥3 cytogenetic alterations identified T-ALL patients with poor prognosis in this study. Karyotypes with ≥3 abnormalities accounted for 16 % (22/139) of all evaluable karyotypes, corresponding to the largest poor prognosis cytogenetic subgroup of T-ALL identified so far. Patients carrying karyotypes with ≥3 cytogenetic alterations showed a significantly inferior response to therapy, and a poor outcome in terms of event-free survival (EFS), overall survival (OS) and cumulative incidence of relapse (CIR), independently of other baseline characteristics and the end-induction minimal residual disease (MRD) level. Additional molecular analyses of patients carrying ≥3 cytogenetic alterations showed a unique molecular profile that could contribute to understand the underlying molecular mechanisms of resistance and to evaluate novel targeted therapies (e.g. IL7R directed) with potential impact on outcome of adult T-ALL patients. [ABSTRACT FROM AUTHOR]