Haplotype Inference on Pedigrees with Recombinations, Errors, and Missing Genotypes via SAT solvers

The Minimum-Recombinant Haplotype Configuration problem (MRHC) has been highly successful in providing a sound combinatorial formulation for the important problem of genotype phasing on pedigrees. Despite several algorithmic advances and refinements that led to some efficient algorithms, its applicability to real datasets has been limited by the absence of some important characteristics of these data in its formulation, such as mutations, genotyping errors, and missing data. In this work, we propose the Haplotype Configuration with Recombinations and Errors problem (HCRE), which generalizes the original MRHC formulation by incorporating the two most common characteristics of real data: errors and missing genotypes (including untyped individuals). Although HCRE is computationally hard, we propose an exact algorithm for the problem based on a reduction to the well-known Satisfiability problem. Our reduction exploits recent progresses in the constraint programming literature and, combined with the use of state-of-the-art SAT solvers, provides a practical solution for the HCRE problem. Biological soundness of the phasing model and effectiveness (on both accuracy and performance) of the algorithm are experimentally demonstrated under several simulated scenarios and on a real dairy cattle population.Comment: 14 pages, 1 figure, 4 tables, the associated software reHCstar is available at http://www.algolab.eu/reHCsta

Thyroid Hormone Profile in Patients Ingesting Soft Gel Capsule or Liquid Levothyroxine Formulations with Breakfast

Background. Recently, it has been shown that liquid L-T4 formulation can be ingested with breakfast. This study looked to extend these findings by investigating whether a soft gel capsule formulation of L-T4 could also be ingested at breakfast time. Methods. 60 patients (18–65 yrs), previously submitted to thyroidectomy for proven benign goitre in stable euthyroidism receiving liquid L-T4 therapy ingested with breakfast, were enrolled. TSH, fT4, and fT3 levels were assessed in all the patients who were switched from liquid L-T4 to a soft gel capsule formulation at the same dosage of L-T4. After 6 months, TSH, fT4, and fT3 levels were determined again. Results. There were no differences in TSH levels, but fT3 and fT4 levels during treatment with the soft gel capsule were significantly lower than those at enrolment with the liquid L-T4 formulation (TSH median (min–max): 1.9 (0.5–4.0) versus 2.2 (0.5–4.5) mIU/L, fT3: 2.5 (2.4–3.1) versus 2.7 (2.4–3.3) pg/mL, p<0.05, and fT4: 9.9 (8.0–13) versus 10.6 (8.6–13.8) pg/mL, p<0.0001). Conclusion. Both liquid and soft gel formulations of L-T4 can be taken with breakfast. However, liquid L-T4 would be the preferred formulation for patients in whom even small changes in fT4 and fT3 levels are to be avoided

A New Frontier of Photocatalysis Employing Micro-Sized TiO2: Air/Water Pollution Abatement and Self-Cleaning/ Antibacterial Applications

This chapter presents the use of a commercial micro-sized TiO2 powder as an alternative to the traditional nano-powders as semiconductors in photocatalytic processes. Results of the photocatalytic efficiency towards the photodegradation of the traditional pollutant molecules both in gas phase (nitrogen oxides (NOx) and volatile organic compounds (VOCs)) and in water phase (phenol) are presented and compared to the results obtained with two nano-sized reference powders. Micro-sized TiO2 is also industrially coated at the surfaces of porcelain grés tiles (Active Clean Air and Antibacterial Ceramic™). The possibility to have a photocatalytic material, strongly stuck at the surface of a vitrified tile, increases the use of photocatalysis in real conditions: no problem of filtration of the semiconductor from the liquid medium after use and no risks of leakage of nanoparticles in the atmosphere. Tests were performed using reactors equipped with UV-A lamps and with suitable analytical systems, depending on the final purpose. Characterization data from both powders and coated tiles are put in correlation with the photocatalytic results to understand the semiconductor action during the photocatalytic process. Polluting molecules were chosen in order to cover all the common aspects of environmental pollution: NOx and some VOCs represent the model molecules to test the efficiency of the micro-sized TiO2 (degradation from the pristine molecule to CO2 or inorganic salts) in gas phase. As for the water pollution, phenol was chosen as common pollutant in worldwide rivers. Moreover, tests on self-cleaning and antibacterial properties are also reported. The positive results of micro-sized TiO2 both in powder and coated onto the surface of porcelain grés tiles open the way to new photocatalytic products that do not make use of nanoscale powders avoiding problems to human safety caused by the inherent toxicity of the nanoparticles

SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub

SETBP1 variants occur as somatic mutations in several hematological malignancies such as atypical chronic myeloid leukemia and as de novo germline mutations in the Schinzel-Giedion syndrome. Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. Genes controlled by SETBP1 such as MECOM are significantly upregulated in leukemias containing SETBP1 mutations. Gene ontology analysis of deregulated SETBP1 target genes indicates that they are also key controllers of visceral organ development and brain morphogenesis. In line with these findings, in utero brain electroporation of mutated SETBP1 causes impairment of mouse neurogenesis with a profound delay in neuronal migration. In summary, this work unveils a SETBP1 function that directly affects gene transcription and clarifies the mechanism operating in myeloid malignancies and in the Schinzel- Giedion syndrome caused by SETBP1 mutations.Peer reviewe

De novo UBE2A mutations are recurrently acquired during chronic myeloid leukemia progression and interfere with myeloid differentiation pathways

Despite the advent of tyrosine kinase inhibitors, a proportion of chronic myeloid leukemia patients in chronic phase fails to respond to Imatinib or to second generation inhibitors and progress to blast crisis. Limited improvements in the understanding of the molecular mechanisms responsible for chronic myeloid leukemia transformation from chronic phase to the aggressive blast crisis were achieved until now. We present here a massive parallel sequencing analysis of 10 blast crisis samples and of the corresponding autologous chronic phase controls which reveals, for the first time, recurrent mutations affecting the ubiquitin-conjugating enzyme E2A gene (UBE2A, formerly RAD6A). Additional analyses on a cohort of 24 blast crisis, 41 chronic phase as well as 40 acute myeloid leukemia and 38 atypical chronic myeloid leukemia patients at onset confirmed that UBE2A mutations are specifically acquired during chronic myeloid leukemia progression with a frequency of 16.7% in advanced phases. In vitro studies show that the mutations here described cause a decrease in UBE2A activity, leading to an impairment of myeloid differentiation in chronic myeloid leukemia cells

Integrated Genomic, Functional, and Prognostic Characterization of Atypical Chronic Myeloid Leukemia

Atypical chronic myeloid leukemia (aCML) is a BCR-ABL1-negative clonal disorder, which belongs to the myelodysplastic/myeloproliferative group. This disease is characterized by recurrent somatic mutations in SETBP1, ASXL1 and ETNK1 genes, as well as high genetic heterogeneity, thus posing a great therapeutic challenge. To provide a comprehensive genomic characterization of aCML we applied a high-throughput sequencing strategy to 43 aCML samples, including both whole-exome and RNA-sequencing data. Our dataset identifies ASXL1, SETBP1, and ETNK1 as the most frequently mutated genes with a total of 43.2%, 29.7 and 16.2%, respectively. We characterized the clonal architecture of 7 aCML patients by means of colony assays and targeted resequencing. The results indicate that ETNK1 variants occur early in the clonal evolution history of aCML, while SETBP1 mutations often represent a late event. The presence of actionable mutations conferred both ex vivo and in vivo sensitivity to specific inhibitors with evidence of strong in vitro synergism in case of multiple targeting. In one patient, a clinical response was obtained. Stratification based on RNA-sequencing identified two different populations in terms of overall survival, and differential gene expression analysis identified 38 significantly overexpressed genes in the worse outcome group. Three genes correctly classified patients for overall survival