scholarly journals The association of complex genetic background with the prognosis of acute leukemia with ambiguous lineage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jin Huang ◽  
Jing Zhou ◽  
Min Xiao ◽  
Xia Mao ◽  
Li Zhu ◽  
...  

AbstractAcute leukemia with ambiguous lineage (ALAL) is a rare and highly aggressive malignancy with limited molecular characterization and therapeutic recommendations. In this study, we retrospectively analyzed 1635 acute leukemia cases in our center from January 2012 to June 2018. The diagnose of ALAL was based on either EGIL or 2016 WHO criteria, a total of 39 patients were included. Four patients diagnosed as acute undifferentiated leukemia (AUL) by both classification systems. Among the patients underwent high-throughput sequencing, 89.5% were detected at least one mutation and the median number of gene mutation was 3 (0–8) per sample. The most frequently mutated genes were NRAS (4, 21%), CEBPA (4, 21%), JAK3 (3, 16%), RUNX1 (3, 16%). The mutations detected in mixed-phenotype acute leukemia (MPAL) enriched in genes related to genomic stability and transcriptional regulation; while AUL cases frequently mutated in genes involved in signaling pathway. The survival analysis strongly suggested that mutation burden may play important roles to predict the clinical outcomes of ALAL. In addition, the patients excluded by WHO criteria had even worse clinical outcome than those included. The association of the genetic complexity of blast cells with the clinical outcomes and rationality of the diagnostic criteria of WHO system need to be evaluated by more large-scale prospective clinical studies.

2020 ◽  
Author(s):  
Jin Huang ◽  
Min Xiao ◽  
Jing Zhou ◽  
Xia Mao ◽  
Li Zhu ◽  
...  

Abstract Background Acute leukemia with ambiguous lineage (ALAL) is a rare and heterogeneous group of highly aggressive malignancy with poor clinical outcome, limited molecular characterization and lack of general therapeutic recommendations. Results In this study, we retrospectively analyzed 1635 acute leukemia cases in our center from January 2012 to June 2018.The diagnose of ALAL was based on either EGIL or 2016 WHO criteria. Totally, 39 patients were included in this study and 30 patients satisfied the WHO criteria. Four patients diagnosed as acute undifferentiated leukemia (AUL) by both classification systems. Genetic analysis showed that mutations detected in bi-phenotypic acute leukemia enriched in genes related to genomic stability and transcriptional regulation; while AUL cases frequently mutated in genes involved in signaling pathway. Survival analysis of all patients included suggested that the prognosis of ALAL was independent of immunophenotype, chromosome karyotype, treatment, but significantly associated with the mutation complexity, also termed numbers of the mutations carried by each patient (Log rank p = 0.009 for progression-free survival [PFS] and Log rank p = 0.047 for overall survival [OS], respectively). Similar results were obtained when the WHO diagnostic system were applied. Among these patients, those excluded by WHO criteria had even worse clinical outcome than the patients included (Log rank p = 0.023 for PFS and Log rank p = 0.031 for OS). Conclusions Collectively, the complexity of genomic mutation of ALAL patients seems significantly related to the clinical outcomes. The rationality and clinical applicability of the diagnostic criteria of WHO system need to be evaluated by more large-scale clinical studies.


2021 ◽  
Author(s):  
Jin Huang ◽  
Min Xiao ◽  
Jing Zhou ◽  
Xia Mao ◽  
Li Zhu ◽  
...  

Abstract Acute leukemia with ambiguous lineage (ALAL) is a rare and highly aggressive malignancy with limited molecular characterization and therapeutic recommendations. In this study, we retrospectively analyzed 1635 acute leukemia cases in our center from January 2012 to June 2018.The diagnose of ALAL was based on either EGIL or 2016 WHO criteria, a total of 39 patients were included. Four patients diagnosed as acute undifferentiated leukemia (AUL) by both classification systems. The mutations detected in bi-phenotypic acute leukemia enriched in genes related to genomic stability and transcriptional regulation; while AUL cases frequently mutated in genes involved in signaling pathway. Survival analysis of all patients suggested that the prognosis of ALAL was independent of immunophenotype, chromosome karyotype, treatment, but significantly associated with the mutation complexity, also termed numbers of the mutations carried by each patient (Log rank p = 0.009 for progression-free survival [PFS] and Log rank p = 0.047 for overall survival [OS], respectively). Similar results were obtained when the WHO diagnostic system were applied (Log rank p < 0.001 for both PFS and OS). Among these patients, those excluded by WHO criteria had even worse clinical outcome than the patients included (Log rank p = 0.023 for PFS and Log rank p = 0.031 for OS). Collectively, the complexity of genomic mutation of ALAL patients is significantly associated with the clinical outcomes. The rationality and clinical applicability of the diagnostic criteria of WHO system need to be evaluated by more large-scale clinical studies.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4080-4080
Author(s):  
Matthew J. Oberley ◽  
Gerald Wertheim ◽  
Sunil S. Raikar ◽  
Jemily Malvar ◽  
Richard Sposto ◽  
...  

Abstract INTRODUCTION: Mixed phenotype acute leukemia (MPAL) is a category of acute leukemia established in the World Health Organization (WHO) 2001 classification, significantly modified in WHO2008, and again refined in the most recent WHO2016 update. The current WHO2016 iteration conceptualizes MPAL as a stem cell disorder whereby most cases will manifest heterogeneity of lineage-specific antigen expression by multi-parameter flow cytometry. The WHO2016 definition also urges caution for cases otherwise consistent with B-cell acute lymphoblastic leukemia (B-ALL) that express myeloperoxidase (MPO) as the sole representation of myeloid lineage. These cases met the WHO2008 definition but may not meet the newer WHO2016 criteria. There is limited data on the clinical impact of these recent changes in the WHO classification for MPAL. METHODS: Six institutions identified cases diagnosed as MPAL between 2008 and 2016 according to WHO criteria. The diagnostic flow cytometry was then reanalyzed by two independent hematopathologists blinded to clinical outcomes. The cases were evaluated as to whether they met criteria for WHO2008 MPAL and/or WHO2016 MPAL. Cases of WHO2008 MPAL were further subdivided into those that otherwise met criteria for B-ALL (including non-lineage specific expression of ±CD13, ±CD15, ±CD33) but qualified as MPAL due to MPO expression (MPO+MPAL) and all remaining cases of MPAL that demonstrated additional myeloid lineage specificity as described by the WHO criteria (MLS+MPAL). Data for a distinct cohort of pediatric B-ALL without significant MPO expression diagnosed during the same study period was submitted from one participating site to serve as a reference cohort (n=258). Endpoints of interest to evaluate clinical outcomes according to the WHO classification were event-free and overall survival (EFS, OS). All statistical tests were two-sided with significance set at p<0.05. RESULTS: The cohort consisted of 112 cases submitted for central review; 94/112 met the strict criteria for WHO2008 MPAL. Of these, 21/94 cases also had sufficiently comprehensive testing performed at diagnosis to meet criteria for WHO2016 MPAL. Five-year EFS and OS for patients identified as WHO2016 MPAL (63±11% and 69±11%) was significantly worse than the remainder meeting only the WHO2008 criteria (69±7% and 87±5%, p=0.024 and p<0.001, respectively). Patterns of failure occurred earlier for the WHO2016 MPAL subset (Figure 1). For those diagnosed with WHO2008 MPAL, 67/94 (71%) cases were found to be MPO+MPAL, and the remaining 27 were consistent with MLS+MPAL. Favorable prognostic features (age<10 years, WBC <50 K/uL, favorable cytogenetics) were significantly less prevalent at diagnosis in MLS+MPAL and MPO+MPAL versus B-ALL. Five-year EFS and OS for patients with MPO+MPAL (68±7% and 87±5%) or MLS+MPAL (68±9% and 72±9%) were significantly worse when compared to B-ALL overall (84±3% and 93±2%, Wilcoxon p<0.001 for EFS and OS) (Figure 2). However, on multivariable analysis inclusive of prognostic features, OS differed significantly from B-ALL for MLS+MPAL but not for MPO+MPAL (p=0.016 and p=0.629, respectively). There was no association between percentage of MPO+ blasts and EFS or OS. CONCLUSIONS: Reported survival rates for MPAL continue to vary with changes to the WHO classification. The subset fulfilling WHO2016 criteria demonstrated significantly worse EFS and OS than the WHO2008 cohort; WHO2016-defined MPAL may better represent the concept of MPAL as a stem cell disorder. Applying WHO2016 versus WHO2008 criteria to diagnostic flow cytometry in this retrospective cohort resulted in fewer patients classified as MPAL. As a retrospective study, the antigen combinations necessary to fulfill newer WHO2016 criteria for blast heterogeneity were not tested in many cases; however, it remains likely that the updated WHO2016 criteria will reduce apparent disease prevalence. While cases of WHO2008 MPAL otherwise meeting criteria for B-ALL apart from MPO expression were less likely to have favorable prognostic features at diagnosis, survival on multivariable analysis was similar to B-ALL; it remains unclear how best to categorize this group of MPO+ acute leukemia. Better understanding of the biology of MPAL is therefore essential to appropriately classify these rare leukemias and to develop optimal therapy. Disclosures O'Gorman: Becton Dickinson: Consultancy.


2020 ◽  
pp. 68-72
Author(s):  
V.G. Nikitaev ◽  
A.N. Pronichev ◽  
V.V. Dmitrieva ◽  
E.V. Polyakov ◽  
A.D. Samsonova ◽  
...  

The issues of using of information and measurement systems based on processing of digital images of microscopic preparations for solving large-scale tasks of automating the diagnosis of acute leukemia are considered. The high density of leukocyte cells in the preparation (hypercellularity) is a feature of microscopic images of bone marrow preparations. It causes the proximity of cells to eachother and their contact with the formation of conglomerates. Measuring of the characteristics of bone marrow cells in such conditions leads to unacceptable errors (more than 50%). The work is devoted to segmentation of contiguous cells in images of bone marrow preparations. A method of cell separation during white blood cell segmentation on images of bone marrow preparations under conditions of hypercellularity of the preparation has been developed. The peculiarity of the proposed method is the use of an approach to segmentation of cell images based on the watershed method with markers. Key stages of the method: the formation of initial markers and builds the lines of watershed, a threshold binarization, shading inside the outline. The parameters of the separation of contiguous cells are determined. The experiment confirmed the effectiveness of the proposed method. The relative segmentation error was 5 %. The use of the proposed method in information and measurement systems of computer microscopy for automated analysis of bone marrow preparations will help to improve the accuracy of diagnosis of acute leukemia.


Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 234 ◽  
Author(s):  
Eric A. Griffin ◽  
Joshua G. Harrison ◽  
Melissa K. McCormick ◽  
Karin T. Burghardt ◽  
John D. Parker

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.


2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Tianyun Wang ◽  
◽  
Kendra Hoekzema ◽  
Davide Vecchio ◽  
Huidan Wu ◽  
...  

Abstract Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case–control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E−06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E−07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype–genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.


Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 806
Author(s):  
Shambhu G. Aralaguppe ◽  
Anoop T. Ambikan ◽  
Manickam Ashokkumar ◽  
Milner M. Kumar ◽  
Luke Elizabeth Hanna ◽  
...  

The detection of drug resistance mutations (DRMs) in minor viral populations is of potential clinical importance. However, sophisticated computational infrastructure and competence for analysis of high-throughput sequencing (HTS) data lack at most diagnostic laboratories. Thus, we have proposed a new pipeline, MiDRMpol, to quantify DRM from the HIV-1 pol region. The gag-vpu region of 87 plasma samples from HIV-infected individuals from three cohorts was amplified and sequenced by Illumina HiSeq2500. The sequence reads were adapter-trimmed, followed by analysis using in-house scripts. Samples from Swedish and Ethiopian cohorts were also sequenced by Sanger sequencing. The pipeline was validated against the online tool PASeq (Polymorphism Analysis by Sequencing). Based on an error rate of <1%, a value of >1% was set as reliable to consider a minor variant. Both pipelines detected the mutations in the dominant viral populations, while discrepancies were observed in minor viral populations. In five HIV-1 subtype C samples, minor mutations were detected at the <5% level by MiDRMpol but not by PASeq. MiDRMpol is a computationally as well as labor efficient bioinformatics pipeline for the detection of DRM from HTS data. It identifies minor viral populations (<20%) of DRMs. Our method can be incorporated into large-scale surveillance of HIV-1 DRM.


2019 ◽  
Vol 3 (6) ◽  
pp. 922-933 ◽  
Author(s):  
Guillermo Montalban-Bravo ◽  
Rashmi Kanagal-Shamanna ◽  
Koji Sasaki ◽  
Keyur Patel ◽  
Irene Ganan-Gomez ◽  
...  

Abstract Nucleophosmin (NPM1) mutations are common in acute myeloid leukemia and are associated with high remission rates and prolonged survival with intensive chemotherapy. NPM1 mutations are rare in myelodysplastic syndromes (MDS) or myelodysplastic/myeloproliferative neoplasm (MDS/MPN), and the clinical outcomes of these patients, when treated with intensive chemotherapy, are unknown. We retrospectively evaluated the clinicopathologic characteristics and the impact of therapy in 31 patients with MDS or MDS/MPN and NPM1 mutations. Next-generation sequencing was performed at diagnosis in 22 patients. Median age was 62 years (range, 19-86). Twenty-four patients (77%) had normal karyotype, and all had multilineage dysplasia. Most patients could be classified as MDS with excess blasts (19/31, 61%). NPM1 mutations were detected at a median allele frequency of 0.38 (range, 0.09-0.49). Mutation burden did not correlate with bone marrow blast frequency, and its clearance seemed to be associated with decreased morphologic dysplasia. Ten of the 31 patients (32%) received cytotoxic chemotherapy, 20 (65%) hypomethylating agents, and 1 (4%) lenalidomide. Sequential sequencing was available in 16 (52%) patients, and mutation burden correlated with disease status and response to therapy. Patients treated with chemotherapy had higher complete response rates (90% vs 28%, P = .004), longer median progression-free survival (not reached vs 7.5 months, P = .023), and overall survival (not reached vs 16 months, P = .047). Intensive chemotherapy and allogeneic stem cell transplantation (SCT) may be associated with improved clinical outcomes in patients with NPM1-mutated MDS or MDS/MPN who are candidates for this form of therapy.


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