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

PU.1 expression is restored upon treatment of chronic myeloid leukemia patients

El pdf del artículo es el manuscrito de autor.The PU.1 transcription factor is a crucial regulator of hematopoiesis which expression is altered in various leukemic processes. Our previous work in chronic myeloid leukemia (CML) cells demonstrated that interferon-α upregulated PU.1 expression. Here we show that expression of PU.1 is severely impaired in patients with CML at diagnosis. However, the PU.1 suppression is abrogated in patients in remission, after interferon-α or imatinib treatment. These effects are not found in patients with other myeloproliferative diseases such as polycythemia vera or essential thrombocythemia. PU.1 could, therefore, be used as an additional marker of the response to the treatment of the CML. © 2008 Elsevier Ireland Ltd. All rights reserved.This work was supported by Grants FIS04/1083 from Spanish Ministerio de Sanidad y Consumo (M.D.D.) and CICYT SAF05-00461 from Spanish Ministerio de Educación y Ciencia (J.L.). M.R.G. is supported by a PhD fellowship from University of Cantabria.Peer Reviewe

Mathematics bridging education using an online, adaptive e-tutorial

This contribution describes and evaluates a postsecondary remediation program in mathematics, aiming to ease the transition from high school to university and to improve the success rates in the first year of bachelor studies. The remediation program consists of the administration of an entry test and the organisation of voluntary bridging education in the format of an online summer course, using the adaptive e-tutorial ALEKS. Participants are prospective students of the university programs business and economics of Maastricht University, and are mostly students with an international background. Effect analysis suggests a strong treatment effect of successful participation in the summer course. However, given the quasi-experimental setup of this study, with non-equivalent groups, selection effects may be responsible for part of that effect. Correction of the treatment effect by applying the propensity score method indicates that indeed a selection effect is present, but that a substantial treatment effect remains, of about 50% the size of the effect of being educated in advanced math versus basic math, in high school

A BCR-ABL1 cutoff of 1.5% at 3 months, determined by the GeneXpert system, predicts an optimal response in patients with chronic myeloid leukemia.

In chronic myeloid leukemia (CML) patients, 3-month BCR-ABL1 levels have consistently been correlated with further outcomes. Monitoring molecular responses in CML using the GeneXpert (Cepheid) platform has shown an optimal correlation with standardized RQ-PCR (IS) when measuring BCR-ABL1 levels lower than 10%, as it is not accurate for values over 10%. The aim of the present study was to determine the predictive molecular value at three months on different outcome variables using the Xpert BCR-ABL1 MonitorTM assay (Xpert BCR-ABL1). We monitored 125 newly diagnosed consecutive CML patients in the chronic phase (CML-CP) using an automated method: Xpert BCR-ABL1. Only 5% of patients did not achieve an optimal response at 3 months, and the 10% BCR-ABL1 cutoff defined by RQ-PCR (IS) methods was unable to identify significant differences in the probabilities of achieving a complete cytogenetic response (CCyR) (50% vs. 87%, p = 0.1) or a major molecular response (MMR) (60% vs. 80%, p = 0.29) by 12 months. In contrast, a cutoff of 1.5% more accurately identified differences in the probabilities of achieving CCyR (98% vs. 54%, p<0.001) and MMR (88% vs. 56%, p<0.001) by 12 months, as well as probabilities of treatment changes (p = 0.005). Therefore, when using the Xpert BCR-ABL1 assay, a cutoff of 1.5% at 3 months could with high probability identify patients able to achieve an optimal response at 12 months

Baseline characteristics.

<p>Baseline characteristics.</p

Probabilities of complete cytogenetic responses and major molecular responses at 12 months according to the molecular response (≤1.5%) at 3 months.

<p>Probabilities of complete cytogenetic responses and major molecular responses at 12 months according to the molecular response (≤1.5%) at 3 months.</p

Complete cytogenetic responses and major molecular response probabilities for each specific TKI used in first-line therapy.

<p>Complete cytogenetic responses and major molecular response probabilities for each specific TKI used in first-line therapy.</p

Molecular responses for each specific TKI at 3 months.

<p>Molecular responses for each specific TKI at 3 months.</p

Probabilities of complete cytogenetic response and major molecular response at 12 months according to the molecular response (≤10%) at 3 months.

<p>Probabilities of complete cytogenetic response and major molecular response at 12 months according to the molecular response (≤10%) at 3 months.</p