We delineated and analyzed directly oriented paralogous low-copy repeats (DP-LCRs) in the most recent version of the human haploid reference genome. The computationally defined DP-LCRs were cross-referenced with our chromosomal microarray analysis (CMA) database of 25,144 patients subjected to genome-wide assays. This computationally guided approach to the empirically derived large data set allowed us to investigate genomic rearrangement relative frequencies and identify new loci for recurrent nonallelic homologous recombination (NAHR)-mediated copy-number variants (CNVs). The most commonly observed recurrent CNVs were NPHP1 duplications (233), CHRNA7 duplications (175), and 22q11.21 deletions (DiGeorge/velocardiofacial syndrome, 166). In the~25% of CMA cases for which parental studies were available, we identified 190 de novo recurrent CNVs. In this group, the most frequently observed events were deletions of 22q11.21 (48), 16p11.2 (autism, 34), and 7q11.23 (Williams-Beuren syndrome, 11). Several features of DP-LCRs, including length, distance between NAHR substrate elements, DNA sequence identity (fraction matching), GC content, and concentration of the homologous recombination (HR) hot spot motif 59-CCNCCNTNNCCNC-39, correlate with the frequencies of the recurrent CNVs events. Four novel adjacent DP-LCR-flanked and NAHR-prone regions, involving 2q12.2q13, were elucidated in association with novel genomic disorders. Our study quantitates genome architectural features responsible for NAHR-mediated genomic instability and further elucidates the role of NAHR in human disease.

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The slags generated in the conventional copper conversion process are mainly composed of Cu2O–Fe2O3–SiO2 with CaO, Al2O3, and MgO compounds—in concentrations up to 10 wt %. The present work contributes to the knowledge of the conversion process, generating experimental data for the phase diagrams of the Cu2O–Fe2O3–SiO2–Al2O3 and Cu2O–Fe2O3–SiO2–CaO systems. The experiments were carried out in a tubular furnace at temperatures of 1150 °C and 1200 °C, under a condition of saturation with tridymite and spinel. Once the equilibrium was reached, the samples were immediately quenched in water. The phases in the samples were observed through a scanning electron microscope (SEM) and the elemental composition of the phases were analyzed by means of energy-dispersive X-ray spectroscopy (EDS) detectors. The addition of Al2O3 and CaO into the Cu2O–Fe2O3–SiO2 system resulted in an appreciable displacement of the liquidus lines, corresponding to an expansion of the liquid in the tridymite primary phase field. The addition of CaO and Al2O3 combined was evaluated on industrial slags and from samples obtained in a Peirce–Smith furnace, with increasing amounts of CaO in the flux.

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