Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.

Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.

Colloidally Confined Crystallization of Highly Efficient Ammonium Phosphomolybdate Catalysts.

Nanodroplets in inverse miniemulsions provide a colloidal confinement for the crystallization of ammonium phosphomolybdate (APM), influencing the resulting particle size. The effects of the space confinement are investigated by comparing the crystallization of analogous materials both in miniemulsion and in bulk solution. Both routes result in particles with a rhombododecahedral morphology, but the ones produced in miniemulsion have sizes between 40 and 90 nm, 3 orders of magnitude smaller than the ones obtained in bulk solution. The catalytic activity of the materials is studied by taking the epoxidation of cis-cyclooctene as a model reaction. The miniemulsion route yields APM particles catalytically much more active than analogous samples produced in bulk solution, which can be explained by their higher dispersibility in organic solvents, their higher surface area, and their higher porosity. Inorganic phosphate salt precursors are compared with organic phosphate sources. APM nanoparticles prepared in miniemulsion from d-glucose-6-phosphate and O-phospho-dl-serine yield a conversion in the epoxidation reaction of more than 90% after only 1 h, compared to 30% for materials prepared in bulk solution. In addition, the catalysts prepared in miniemulsion display a promising recyclability.

Zirconium oxocluster/polymer hybrid nanoparticles prepared by photoactivated miniemulsion copolymerization.

The photoactivated free radical miniemulsion copolymerization of methyl methacrylate (MMA) and the zirconium oxocluster Zr4O2(methacrylate)12 is used as an effective and fast preparation method for polymer/inorganic hybrid nanoparticles. The oxoclusters, covalently anchored to the polymer network, act as metal-organic cross-linkers, thus improving the thermomechanical properties of the resulting hybrid nanoparticles. Benzoin carbonyl organic compounds were used as photoinitiators. The obtained materials are compared in terms of cross-linking, effectiveness of cluster incorporation, and size distribution with the analogous nanoparticles produced by using conventional thermally induced free radical miniemulsion copolymerization. The kinetics of the polymerization process in the absence and in the presence of the oxocluster is also investigated.