Refined cytogenetic IPSS-R evaluation by the use of SNP array in a cohort of 290 MDS patients

Genetic testing plays a central role in myelodysplastic neoplasms (MDS) diagnosis, prognosis, and therapeutic decisions. The widely applied cytogenetic revised international prognostic scoring system (IPSS-R) was based on chromosome banding analysis (CBA). However, subsequently developed genetic methodologies, such as single nucleotide polymorphism (SNP) array, demonstrated to be a valid alternative test for MDS. SNP array is, in fact, able to detect the majority of MDS-associated cytogenetic aberrations, by providing further genomic information due to its higher resolution. In this study, 290 samples from individuals with a confirmed or suspected diagnosis of MDS were tested by both CBA and SNP array, in order to evaluate and compare their cytogenetic IPSS-R score in the largest MDS cohort reported so far. A concordant or better refined cytogenetic IPSS-R array-based score was obtained for 95% of cases (277). Therefore, this study confirms the effective applicability of SNP array toward the cytogenetic IPSS-R evaluation and consequently, toward the molecular international prognostic scoring system for MDS (IPSS-M) assessment, which ensures an improved MDS risk stratification refinement. Considering the advent of additional genetic technologies interrogating the whole genome with increased resolutions, counting cytogenetic abnormalities based on their size may result in a simplistic approach. On the contrary, assessing overall genomic complexity may provide additional crucial information. Independently of the technology used, genetic results should indeed aim at ensuring a highly refined stratification for MDS patients.

Comparison of the International Consensus and 5th WHO edition classifications of adult myelodysplastic syndromes and acute myeloid leukemia

Several editions of the World Health Organization (WHO) classifications of lympho-hemopoietic neoplasms in 2001, 2008, and 2016 served as the international standard for diagnosis. Since the 4th WHO edition, here referred as WHO-HAEM4, significant clinico-pathological, immunophenotypic, and molecular advances have been made in the field of myeloid neoplasms, which have contributed to refine diagnostic criteria, to upgrade entities previously defined as provisional and to identify new entities. This process has resulted in two recent classification proposals of myeloid neoplasms: the International Consensus Classification (ICC) and the 5th edition of the WHO classification (WHO-HAEM5). In this paper, we review and compare the two classifications in terms of diagnostic criteria and entity definition, with a focus on adult myelodysplastic syndromes/neoplasms (MDS) and acute myeloid leukemia (AML). The goal is to provide a tool to facilitate the work of pathologists, hematologists and researchers involved in the diagnosis and treatment of these hematological malignancies.

The International Consensus Classification of acute myeloid leukemia

Acute myeloid leukemias (AMLs) are overlapping hematological neoplasms associated with rapid onset, progressive, and frequently chemo-resistant disease. At diagnosis, classification and risk stratification are critical for treatment decisions. A group with expertise in the clinical, pathologic, and genetic aspects of these disorders developed the International Consensus Classification (ICC) of acute leukemias. One of the major changes includes elimination of AML with myelodysplasia-related changes group, while creating new categories of AML with myelodysplasia-related cytogenetic abnormalities, AML with myelodysplasia-related gene mutations, and AML with mutated TP53. Most of recurrent genetic abnormalities, including mutations in NPM1, that define specific subtypes of AML have a lower requirement of ≥ 10% blasts in the bone marrow or blood, and a new category of MDS/AML is created for other case types with 10-19% blasts. Prior therapy, antecedent myeloid neoplasms or underlying germline genetic disorders predisposing to the development of AML are now recommended as qualifiers to the initial diagnosis of AML. With these changes, classification of AML is updated to include evolving genetic, clinical, and morphologic findings.

Diagnosis of rare subtypes of acute myeloid leukaemia and related neoplasms

The diagnosis of acute myeloid leukaemia and related neoplasms in adults is challenging as this requires the integration of clinical findings, morphology, immunophenotype, cytogenetics, and molecular genetic findings. Lack of familiarity with rare subtypes of acute leukaemia hinders the diagnosis. In this review, we will describe diagnostic findings of several rare acute myeloid leukaemias and related neoplasms that primarily occur in adults including information on presentation, morphology, immunophenotype, genetics, differential diagnosis, and prognosis. Leukaemias discussed include blastic plasmacytoid dendritic cell neoplasm, acute myeloid leukaemia with t(6;9) (p23;q34.1); DEK-NUP214, acute myeloid leukaemia with inv(3)(q21.3q26.2) or t(3;3)(q21.3;q26.2); GATA2, MECOM, acute myeloid leukaemia with BCR-ABL1, acute leukaemias of ambiguous lineage, acute myeloid leukaemia with mutated RUNX1, pure erythroid leukaemia, acute panmyelosis with myelofibrosis, and acute basophilic leukaemia. Case studies with morphological features of the nine subtypes of acute myeloid leukaemia and related neoplasms have been included, and additional evidence available since publication of the 2016 World Health Organization Classification has been added to each subtype.

Comprehensive genetic diagnosis of acute myeloid leukemia by next-generation sequencing

Differential induction therapy of all subtypes of acute myeloid leukemia other than acute promyelocytic leukemia is impeded by the long time required to complete complex and diverse cytogenetic and molecular genetic analyses for risk stratification or targeted treatment decisions. Here, we describe a reliable, rapid and sensitive diagnostic approach that combines karyotyping and mutational screening in a single, integrated, next-generation sequencing assay. Numerical karyotyping was performed by low coverage whole genome sequencing followed by copy number variation analysis using a novel algorithm based on in silico-generated reference karyotypes. Translocations and DNA variants were examined by targeted resequencing of fusion transcripts and mutational hotspot regions using commercially available kits and analysis pipelines. For the identification of FLT3 internal tandem duplications and KMT2A partial tandem duplications, we adapted previously described tools. In a validation cohort including 22 primary patients’ samples, 9/9 numerically normal karyotypes were classified correctly and 30/31 (97%) copy number variations reported by classical cytogenetics and fluorescence in situ hybridization analysis were uncovered by our next-generation sequencing karyotyping approach. Predesigned fusion and mutation panels were validated exemplarily on leukemia cell lines and a subset of patients’ samples and identified all expected genomic alterations. Finally, blinded analysis of eight additional patients’ samples using our comprehensive assay accurately reproduced reference results. Therefore, calculated karyotyping by low coverage whole genome sequencing enables fast and reliable detection of numerical chromosomal changes and, in combination with panel-based fusion-and mutation screening, will greatly facilitate implementation of subtype-specific induction therapies in acute myeloid leukemia.