Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project.

BACKGROUND: Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications. MATERIALS AND METHODS: Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values. RESULTS: Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples. CONCLUSIONS: Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available.

Superparamagnetic iron oxides nanoparticles from municipal solid waste incinerators.

During their production, management, and landfilling, bottom (BA) and fly (FA) ashes from municipal solid waste incineration may liberate Fe-bearing, ultrafine particles and easily enter different environmental sinks of the biosphere. We aim to explore a collection of BA and FA samples from Italian incinerators to probe magnetic mineralogy and the fraction of harmful superparamagnetic (SP) nanoparticles (d<30nm). X-ray diffraction, electron microscopy observation, temperature- and frequency-dependent magnetometry, and Mossbauer analysis are performed. The integration of information from our rock magnetic and non-magnetic techniques leads us to conclude that the dominant magnetic carrier in our samples is magnetite and its intermediate/impure forms, while sulphides (i.e., monoclinic pyrrhotite) are important ancillary magnetic phases. The SP fraction fluxing from the BA and FA outputs of a single incinerator is detected and estimated in 103tons/year. This work stresses the need to calibrate the current technologies towards a safer management of combustion ashes and certainly to inform the environmental impact assessment by using a combination of different methods.

Metal removal from Municipal Solid Waste Incineration fly ash: A comparison between chemical leaching and bioleaching.

Bio- and hydrometallurgical experimental setups at 2-l reactor scale for the processing of fly ash from municipal waste incinerators were explored. We aimed to compare chemical H2SO4 leaching and bioleaching; the latter involved the use of H2SO4 and a mixed culture of acidophilic bacteria. The leaching yields of several elements, including some of those considered as critical (Mg, Co, Ce, Cr, Ga, Nb, Nd, Sb and Sm), are provided. At the end of the experiments, both leaching methods resulted in comparable yields for Mg and Zn (>90%), Al and Mn (>85%), Cr (∼65%), Ga (∼60%), and Ce (∼50%). Chemical leaching showed the best yields for Cu (95%), Fe (91%), and Ni (93%), whereas bioleaching was effective for Nd (76%), Pb (59%), and Co (55%). The two leaching methods generated solids of different quality with respect to the original material as we removed and significantly reduced the metals amounts, and enriched solutions where metals can be recovered for example as mixed salts for further treatment. Compared to chemical leaching the bioleaching halved the use of H2SO4, i.e., a part of agent costs, as a likely consequence of bio-produced acid and improved metal solubility.

Elevated interleukin-6 levels in peritoneal fluid of patients with pelvic pathology.

OBJECTIVE: To determine if interleukin 6 (IL-6) is a normal constituent of peritoneal fluid (PF), and if various types of pelvic pathology influence its presence within the PF microenvironment. STUDY DESIGN: Peritoneal fluid from 73 women obtained at the time of laparoscopy was examined for the presence of IL-6 using an IL-6 specific sandwich enzyme-linked immunosorbent assay. Thirty-nine patients had pelvic endometriosis, 17 had nonendometriotic pelvic adhesive disease, and 17 subjects undergoing tubal sterilization without evidence of pelvic pathology served as controls. RESULTS: Immunoreactive IL-6 was observed in the PF of all 73 subjects (range 0.26 to 11.16 ng/mL). The mean concentration of IL-6 was higher in women with nonendometriotic pelvic adhesions as compared with control subjects (1.28 +/- 0.16 versus 0.80 +/- 0.06 ng/mL, P less than 0.03). There was no difference in the mean peritoneal concentrations of IL-6 between women with endometriosis (1.16 +/- 0.28 ng/mL) and controls, P = 0.38. Twenty-seven of 73 patients (37%) demonstrated elevated levels (greater than 1.0 ng/mL) of IL-6. Patients with pelvic adhesions were significantly more likely to have elevated concentrations of IL-6 than controls (10/17 [59%] versus 3/17 [18%], P less than 0.02). Alternatively, the percentage of patients with elevated IL-6 concentrations did not differ between patients with endometriosis or controls (14/39 [36%] versus 3/17 [18%], P greater than 0.10). CONCLUSIONS: These findings demonstrate that IL-6 is a normal constituent of PF and that elevated levels are found in many patients with pelvic adhesions.