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.

Genomic context of NTRK1/2/3 fusion-positive tumours from a large real-world population.

Neurotrophic tropomyosin receptor kinase (NTRK) gene fusions are rare oncogenic drivers in solid tumours. This study aimed to interrogate a large real-world database of comprehensive genomic profiling data to describe the genomic landscape and prevalence of NTRK gene fusions. NTRK fusion-positive tumours were identified from the FoundationCORE® database of >295,000 cancer patients. We investigated the prevalence and concomitant genomic landscape of NTRK fusions, predicted patient ancestry and compared the FoundationCORE cohort with entrectinib clinical trial cohorts (ALKA-372-001 [EudraCT 2012-000148-88]; STARTRK-1 [NCT02097810]; STARTRK-2 [NCT02568267]). Overall NTRK fusion-positive tumour prevalence was 0.30% among 45 cancers with 88 unique fusion partner pairs, of which 66% were previously unreported. Across all cases, prevalence was 0.28% and 1.34% in patients aged ≥18 and <18 years, respectively; prevalence was highest in patients <5 years (2.28%). The highest prevalence of NTRK fusions was observed in salivary gland tumours (2.62%). Presence of NTRK gene fusions did not correlate with other clinically actionable biomarkers; there was no co-occurrence with known oncogenic drivers in breast, or colorectal cancer (CRC). However, in CRC, NTRK fusion-positivity was associated with spontaneous microsatellite instability (MSI); in this MSI CRC subset, mutual exclusivity with BRAF mutations was observed. NTRK fusion-positive tumour types had similar frequencies in FoundationCORE and entrectinib clinical trials. NTRK gene fusion prevalence varied greatly by age, cancer type and histology. Interrogating large datasets drives better understanding of the characteristics of very rare molecular subgroups of cancer and allows identification of genomic patterns and previously unreported fusion partners not evident in smaller datasets.

Acetone adsorption on ice investigated by X-ray spectroscopy and density functional theory.

Using a combination of X-ray photoemission and near-edge X-ray absorption spectroscopy (NEXAFS) as well as density-functional theory (DFT), we have investigated the adsorption of acetone on ice in the temperature range from 218 to 245 K. The adsorption enthalpy determined from experiment (45 kJ mol(-1)) agrees well with the adsorption energy predicted by theory (41 to 44 kJ mol(-1)). Oxygen K-edge NEXAFS spectra indicate that the presence of acetone at the ice surface does not induce the formation of a pre-melted layer at temperatures up to 243 K. DFT calculations show that the energetically most favored adsorption geometry for acetone on ice is with the molecular plane almost parallel to the surface.

Competitive reaction pathways for functionalization and volatilization in the heterogeneous oxidation of coronene thin films by hydroxyl radicals and ozone.

X-ray photoelectron spectroscopy (XPS) is used to monitor the heterogeneous reaction of hydroxyl radicals (OH) and ozone with thin films (∼5 Å) of coronene. Detailed elemental and functional group analysis of the XPS spectra reveals that there is a competition between the addition of oxygenated functional groups (functionalization) and the loss of material (volatilization) to the gas phase. Measurements of the film thickness and elemental composition indicate that carbon loss is as important as the formation of new oxygenated functional groups in controlling how the oxygen-to-carbon ratio (O/C) of the coronene film evolves during the surface reaction. When the O/C ratio of the film is small (∼0.1) the addition of functional groups dominates changes in film thickness, while for more oxygenated films (O/C > 0.3) carbon loss is an increasingly important reaction pathway. Decomposition of the film occurs via the loss of both carbon and oxygen atoms when the O/C ratio of the film exceeds 0.5. These results imply that chemically reduced hydrocarbons, such as primary organic aerosol, age in the atmosphere by forming new oxygenated functional groups, in contrast to oxygenated secondary organic aerosol, which decompose by a heterogeneous loss of carbon and/or oxygen.

High content imaging-based assay to classify estrogen receptor-α ligands based on defined mechanistic outcomes.

Estrogen receptor-α (ER) is an important target both for therapeutic compounds and endocrine disrupting chemicals (EDCs); however, the mechanisms involved in chemical modulation of regulating ER transcriptional activity are inadequately understood. Here, we report the development of a high content analysis-based assay to describe ER activity that uniquely exploits a microscopically visible multi-copy integration of an ER-regulated promoter. Through automated single-cell analyses, we simultaneously quantified promoter occupancy, recruitment of transcriptional cofactors and large-scale chromatin changes in response to a panel of ER ligands and EDCs. Image-derived multi-parametric data was used to classify a panel of ligand responses at high resolution. We propose this system as a novel technology providing new mechanistic insights into EDC activities in a manner useful for both basic mechanistic studies and drug testing.

Shape- and size-selective electrochemical synthesis of dispersed silver(I) oxide colloids.

Silver(I) oxide (Ag2O) micro- and nanoparticles were electrochemically synthesized by anodizing a sacrificial silver wire in a basic aqueous sulfate solution. Ag2O particles were released from the silver electrode surface during synthesis producing a visible sol "stream". The composition of these particles was established using selected area electron diffraction, X-ray diffraction, and X-ray photoelectron spectroscopy. The shape of Ag2O crystallites could be adjusted using the potential of the silver wire generator electrode. The generation of a dispersed Ag2O sol and the observed shape selectivity are both explained by a two-step mechanism involving the anodic dissolution of silver metal, Ag0 --> Ag+(aq) + 1e-, followed by the precipitation of Ag2O particles, 2Ag+ + 2OH- --> Ag2O(s) + H2O. Within 100 mV of the voltage threshold for particle growth, cubic particles with a depression in each face ("hopper crystals") were produced. The application of more positive voltages resulted in the generation of 8-fold symmetric "flower"-shaped particles formed as a consequence of fast growth in the <111> crystallographic direction. The diameter of flower particles was adjustable from 250 nm to 1.8 microm using the growth duration at constant potential.

Reversible resistance modulation in mesoscopic silver wires induced by exposure to amine vapor.

Ensembles of silver nanowires (AgNEs) with diameters ranging from 200 nm to 1.0 microm have been prepared by electrochemical step edge decoration. These AgNEs showed a rapid (< 5 s), reversible increase in resistance upon exposure to the vapor of ammonia, trimethylamine, and pyridine. The amplitude of the resistance change was up to +3000% (DeltaR/Ro)-more than 2 orders of magnitude larger than can be explained based on boundary layer scattering effects. We experimentally probe the mechanism for this resistance modulation in the case of ammonia, and we propose a model to describe it. Conductive tip atomic force microscopy was used to probe individual sections of nanowires in AgNEs; these data revealed that the resistance change caused by NH(3) exposure was concentrated within a minority (approximately 10%) of the 5-microm wire segments that were probed--not uniformly distributed along each nanowire. All AgNEs showed a temperature dependence of their resistance, alpha, that was smaller than expected for silver metal. Highly sensitive AgNEs sometimes showed a negative alpha, characteristic of semiconductors, but negative alpha values were never observed for AgNEs with a low sensitivity to NH3. AgNEs did not respond to hydrocarbons, O2, H2O, N2, CO, or Ar, but a large (DeltaR/Ro > |-50%|) irreversible decrease in resistance was seen upon exposures to acids including HCl, HNO3, and H2SO4. Based on these and other data, we propose a model in which oxidized constrictions in silver nanowires limit the conductivity of the wire and provide a means for "gating" conduction based on the protonation state of the oxide surface.

Molybdenum disulfide nanowires and nanoribbons by electrochemical/chemical synthesis.

Molybdenum disulfide nanowires and nanoribbons have been synthesized by a two-step, electrochemical/chemical synthetic method. In the first step, MoO(x) wires (a mixture of MoO(2) and MoO(3)) were electrodeposited size-selectively by electrochemical step-edge decoration on a highly oriented pyrolytic graphite (HOPG) surface. Then, MoO(x) precursor wires were converted to MoS(2) by exposure to H(2)S either at 500-700 degrees C, producing "low-temperature" or LT MoS(2) nanowires that were predominantly 2H phase, or above 800 degrees C producing "high-temperature" or HT MoS(2) ribbons that were predominantly 3R phase. The majority of these MoS(2) wires and ribbons were more than 50 microm in length and were organized into parallel arrays containing hundreds of wires or ribbons. MoS(2) nanostructures were characterized by X-ray photoelectron spectroscopy, scanning and transmission electron microscopy, selected area electron diffraction, X-ray diffraction, UV-visible absorption spectrometry, and Raman spectroscopy. HT and LT MoS(2) nanowires were structurally distinct: LT MoS(2) wires were hemicylindrical in shape and nearly identical in diameter to the MoO(x) precursor wires from which they were derived. LT MoS(2) wires were polycrystalline, and the internal structure consisted of many interwoven, multilayer strands of MoS(2); HT MoS(2) ribbons were 50-800 nm in width and 3-100 nm thick, composed of planar crystallites of 3R-MoS(2). These layers grew in van der Waals contact with the HOPG surface so that the c-axis of the 3R-MoS(2) unit cell was oriented perpendicular to the plane of the graphite surface. Arrays of MoS(2) wires and ribbons could be cleanly separated from the HOPG surface and transferred to glass for electrical and optical characterization. Optical absorption measurements of HT MoS(2) nanoribbons reveal a direct gap near 1.95 eV and two exciton peaks, A1 and B1, characteristic of 3R-MoS(2). These exciton peaks shifted to higher energy by up to 80 meV as the wire thickness was decreased to 7 nm (eleven MoS(2) layers). The energy shifts were proportional to 1/ L( parallel)(2), and the effective masses were calculated. Current versus voltage curves for both LT and HT MoS(2) nanostructures were probed as a function of temperature from -33 degrees C to 47 degrees C. Conduction was ohmic and mainly governed by the grain boundaries residing along the wires. The thermal activation barrier was found to be related to the degree of order of the crystallites and can be tuned from 126 meV for LT nanowires to 26 meV for HT nanoribbons.