Detection of kinase domain mutations in BCR::ABL1 leukemia by ultra-deep sequencing of genomic DNA

The screening of the BCR::ABL1 kinase domain (KD) mutation has become a routine analysis in case of warning/failure for chronic myeloid leukemia (CML) and B-cell precursor acute lymphoblastic leukemia (ALL) Philadelphia (Ph)-positive patients. In this study, we present a novel DNA-based next-generation sequencing (NGS) methodology for KD ABL1 mutation detection and monitoring with a 1.0E−4 sensitivity. This approach was validated with a well-stablished RNA-based nested NGS method. The correlation of both techniques for the quantification of ABL1 mutations was high (Pearson r = 0.858, p < 0.001), offering DNA-DeepNGS a sensitivity of 92% and specificity of 82%. The clinical impact was studied in a cohort of 129 patients (n = 67 for CML and n = 62 for B-ALL patients). A total of 162 samples (n = 86 CML and n = 76 B-ALL) were studied. Of them, 27 out of 86 harbored mutations (6 in warning and 21 in failure) for CML, and 13 out of 76 (2 diagnostic and 11 relapse samples) did in B-ALL patients. In addition, in four cases were detected mutation despite BCR::ABL1 < 1%. In conclusion, we were able to detect KD ABL1 mutations with a 1.0E−4 sensitivity by NGS using DNA as starting material even in patients with low levels of disease.Tis project was funded in part by CRIS CANCER FOUNDATION

Outcomes of control and monitoring of a widespread riparian invader (Tamarix spp.): a comparison of synthesis approaches

Effective ecological restoration requires empirical assessment to determine outcomes of projects, but conclusions regarding the effects of restoration treatments on the whole ecosystem remain rare. Control of invasive shrubs and trees in the genus Tamarix and associated riparian restoration in the American Southwest has been of interest to scientists and resource managers for decades; dozens of studies have reported highly variable outcomes of Tamarix control efforts, as measured by a range of response variables, temporal and spatial scales and monitoring strategies. We conducted a literature search and review, meta-analysis and vote count (comparison of numerical outcomes lacking reported variances and/or sample sizes) on published papers that quantitatively measured a variety of responses to control of Tamarix. From 96 publications obtained through a global search on terms related to Tamarix control, we found 52 publications suitable for a meta-analysis (n = 777 comparisons) and 63 publications suitable for two vote counts (n = 1,460 comparisons total; 622 comparisons reported as statistically significant) of response to Tamarix control. We estimated responses to control by treatment type (e.g. cut-stump treatment, burning, biocontrol) and ecosystem component (e.g. vegetation, fauna, fluvial processes). Finally, we compared results of the various synthesis methods to determine whether the increasingly stringent requirements for inclusion led to biased outcomes. Vegetation metrics, especially measures of Tamarix response, were the most commonly assessed. Ecosystem components other than vegetation, such as fauna, soils and hydrogeomorphic dynamics, were under-represented. The meta-analysis showed significantly positive responses by vegetation overall to biocontrol, herbicide and cut-stump treatments. This was primarily due to reduction of Tamarix cover; impacts on replacement vegetation were highly variable. We found concordance amongst our varied synthesis approaches, indicating that increased granularity from stricter quantitative techniques does not come at the cost of a biased sample. Overall, our results indicate that common control methods are generally effective for reducing Tamarix, but the indirect effects on other aspects of the ecosystem are variable and remain understudied. Given that this is a relatively well-studied invasive plant species, our results also illustrate the limitations of not only individual studies, but also of reviews for measuring the impact of invasive species control. We call on researchers to investigate the less commonly studied responses to Tamarix control and riparian restoration including the effects on fauna, soil and hydrogeomorphic characteristics

Effects of ants on riparian poplars: an ex situ experiment of biotic interaction

International audiencePoplars establish on alluvial bars within sand and gravel-bed rivers. Alluvial bars also provide particularly suitable habitatsfor the proliferation of ants. We hypothesized that ants, by modifying substrate structure and resource availability in fluvialhabitats, positively influence poplar growth during its establishment stage. We conducted a preliminary nine-month ex situgreenhouse experiment with one ant species (Lasius niger L.) and six different genotypes of poplar cuttings (Populus nigraL.), both collected on the Garonne River, SW France. Three main treatments: ‘P. nigra alone’, ‘P. nigra without ants and withant food’ and ‘P. nigra with ants and ant food’ were applied. After one growing season, we tested differences in branchinglength and biomass of stems, roots and leaves. Certain genotypes showed significant differences in growth, but there wereno significant differences in stem length, dry mass of stems and roots between the three treatments. The total biomass ofpoplars after the first growing season was positively affected by the initial size of the cuttings and was modulated by thegenotype independently from the treatments. However, an increased poplar growth for the treatment without ants and withant food was observed according to significant differences in dry weight of leaves and total biomass (i.e. dry mass of stems,roots and leaves) for the pooled genotypes across treatments. We discuss our results with the aim of serving as a referencefor future in situ and ex situ experiments and field measurements exploring interactions between ants and poplars, specificallyin riparian ecosystems

Effects of ants on riparian poplars: an ex situ experiment of biotic interaction

International audiencePoplars establish on alluvial bars within sand and gravel-bed rivers. Alluvial bars also provide particularly suitable habitats for the proliferation of ants. We hypothesized that ants, by modifying substrate structure and resource availability in fluvial habitats, positively influence poplar growth during its establishment stage. We conducted a preliminary nine-month ex situ greenhouse experiment with one ant species (Lasius niger L.) and six different genotypes of poplar cuttings (Populus nigra L.), both collected on the Garonne River, SW France. Three main treatments: ‘P. nigra alone’, ‘P. nigra without ants and with ant food’ and ‘P. nigra with ants and ant food’ were applied. After one growing season, we tested differences in branching length and biomass of stems, roots and leaves. Certain genotypes showed significant differences in growth, but there were no significant differences in stem length, dry mass of stems and roots between the three treatments. The total biomass of poplars after the first growing season was positively affected by the initial size of the cuttings and was modulated by the genotype independently from the treatments. However, an increased poplar growth for the treatment without ants and with ant food was observed according to significant differences in dry weight of leaves and total biomass (i.e. dry mass of stems, roots and leaves) for the pooled genotypes across treatments. We discuss our results with the aim of serving as a reference for future in situ and ex situ experiments and field measurements exploring interactions between ants and poplars, specifically in riparian ecosystems

Effects of ants on riparian poplars: an ex situ experiment of biotic interaction

International audiencePoplars establish on alluvial bars within sand and gravel-bed rivers. Alluvial bars also provide particularly suitable habitatsfor the proliferation of ants. We hypothesized that ants, by modifying substrate structure and resource availability in fluvialhabitats, positively influence poplar growth during its establishment stage. We conducted a preliminary nine-month ex situgreenhouse experiment with one ant species (Lasius niger L.) and six different genotypes of poplar cuttings (Populus nigraL.), both collected on the Garonne River, SW France. Three main treatments: ‘P. nigra alone’, ‘P. nigra without ants and withant food’ and ‘P. nigra with ants and ant food’ were applied. After one growing season, we tested differences in branchinglength and biomass of stems, roots and leaves. Certain genotypes showed significant differences in growth, but there wereno significant differences in stem length, dry mass of stems and roots between the three treatments. The total biomass ofpoplars after the first growing season was positively affected by the initial size of the cuttings and was modulated by thegenotype independently from the treatments. However, an increased poplar growth for the treatment without ants and withant food was observed according to significant differences in dry weight of leaves and total biomass (i.e. dry mass of stems,roots and leaves) for the pooled genotypes across treatments. We discuss our results with the aim of serving as a referencefor future in situ and ex situ experiments and field measurements exploring interactions between ants and poplars, specificallyin riparian ecosystems

Comparison of the 2022 and 2017 European LeukemiaNet risk classifications in a real-life cohort of the PETHEMA group

Abstract Next-Generation Sequencing is needed for the accurate genetic risk stratification of acute myeloid leukemia according to European LeukemiaNet (ELN) guidelines. We validated and compared the 2022 ELN risk classification in a real-life cohort of 546 intensively and 379 non-intensively treated patients. Among fit patients, those aged ≥65 years old showed worse OS than younger regardless risk classification. Compared with the 2017 classification, 14.5% of fit patients changed the risk with the 2022 classification, increasing the high-risk group from 44.3% to 51.8%. 3.7% and 0.9% FLT3-ITD mutated patients were removed from the favorable and adverse 2017 categories respectively to 2022 intermediate risk group. We suggest that midostaurin therapy could be a predictor for 3 years OS (85.2% with vs. 54.8% without midostaurin, P = 0.04). Forty-seven (8.6%) patients from the 2017 intermediate group were assigned to the 2022 adverse-risk group as they harbored myelodysplasia (MDS)-related mutations. Patients with one MDS-related mutation did not reach median OS, while patients with ≥2 mutations had 13.6 months median OS (P = 0.002). Patients with TP53 ± complex karyotype or inv(3) had a dismal prognosis (7.1 months median OS). We validate the prognostic utility of the 2022 ELN classification in a real-life setting providing supportive evidences to improve risk stratification guidelines

Networking for advanced molecular diagnosis in acute myeloid leukemia patients is possible: the PETHEMA NGS-AML project

Next-Generation Sequencing has recently been introduced to efficiently and simultaneously detect genetic variations in acute myeloid leukemia. However, its implementation in the clinical routine raises new challenges focused on the diversity of assays and variant reporting criteria. To overcome this challenge, the PETHEMA group established a nationwide network of reference laboratories aimed to deliver molecular results in the clinics. We report the technical cross-validation results for next-generation sequencing panel genes during the standardization process and the clinical validation in 823 samples of 751 patients with newly diagnosed or refractory/relapse acute myeloid leukemia. Two cross-validation rounds were performed in seven nationwide reference laboratories in order to reach a consensus regarding quality metrics criteria and variant reporting. In the pre-standardization cross-validation round, an overall concordance of 60.98% was obtained with a great variability in selected genes and conditions across laboratories. After consensus of relevant genes and optimization of quality parameters the overall concordance rose to 85.57% in the second cross-validation round. We show that a diagnostic network with harmonized next-generation sequencing analysis and reporting in seven experienced laboratories is feasible in the context of a scientific group

Networking for advanced molecular diagnosis in acute myeloid leukemia patients is possible: the PETHEMA NGS-AML project

Next-Generation Sequencing has recently been introduced to efficiently and simultaneously detect genetic variations in acute myeloid leukemia. However, its implementation in the clinical routine raises new challenges focused on the diversity of assays and variant reporting criteria. To overcome this challenge, the PETHEMA group established a nationwide network of reference laboratories aimed to deliver molecular results in the clinics. We report the technical cross-validation results for next-generation sequencing panel genes during the standardization process and the clinical validation in 823 samples of 751 patients with newly diagnosed or refractory/relapse acute myeloid leukemia. Two cross-validation rounds were performed in seven nationwide reference laboratories in order to reach a consensus regarding quality metrics criteria and variant reporting. In the pre-standardization cross-validation round, an overall concordance of 60.98% was obtained with a great variability in selected genes and conditions across laboratories. After consensus of relevant genes and optimization of quality parameters the overall concordance rose to 85.57% in the second cross-validation round. We show that a diagnostic network with harmonized next-generation sequencing analysis and reporting in seven experienced laboratories is feasible in the context of a scientific group