Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Aqueous and solid phase interactions of radionuclides with organic complexing agents

Characterising the geochemistry and speciation of major contaminant radionuclides is crucial in order to understand their behaviour and migration in complex environmental systems. Organic complexing agents used in nuclear decontamination have been found to enhance migration of radionuclides at contaminated sites; however, the mechanisms of the interactions in complex environments are poorly understood. In this work, radionuclide speciation and sorption behaviour were investigated in order to identify interactions between four key radionuclides with different oxidation states (Cs(I) and Sr(II) as important fission products; Th(IV) and U(VI) as representative actinides), three anthropogenic organic complexing agents with different denticities (EDTA, NTA and picolinic acid as common co-contaminants), and natural sand (as simple environmental solid phase). A UV spectrophotometric and an IC method were developed to monitor the behaviour of EDTA, NTA and picolinic acid in the later experiments. The optimised methods were simple, applied widely-available instrumentation and achieved the necessary analytical figures of merit to allow a compound specific determination over variable background levels of DOC and in the presence of natural cations, anions and radionuclides. The effect of the ligands on the solubility of the radionuclides was studied using a natural sand matrix and pure silica for comparison of anions, cations and organic carbon. In the silica system, the presence of EDTA, NTA and, to a lesser extent, picolinic acid, showed a clear net effect of increasing Th and U solubility. Conversely, in the sand system, the sorption of Th and U was kinetically controlled and radionuclide complexation by the ligands enhanced the rate of sorption, by a mechanism identified as metal exchange with matrix metals. Experiments in which excess EDTA, NTA and picolinic acid (40 – 100 fold excess) were pre-equilibrated with Th and U prior to contact with the sand, to allow a greater degree of radionuclide complex formation, resulted in enhanced rates of sorption. This confirmed that the radionuclide complexes interacted with the sand surface more readily than uncomplexed Th or U. Overall this shows that Th and U mobility would be lowered in this natural sand by the presence of organic co-contaminants. In contrast, the complexation of Sr with the complexing agents was rapid and the effect of the ligands was observed as a net increase on Sr solubility (EDTA, picolinic acid) or sorption (NTA). As expected, Cs did not interact with the ligands, and showed rapid sorption kinetics. Finally, ESI-MS was used to study competitive interactions in the aqueous Th-Mn-ligand ternary system. Quantification presented a challenge, however, the careful approach taken to determine the signal correction allowed the competitive interactions between Mn and Th for EDTA to be studied semi-quantitatively. In an EDTA limited system, Th displaced Mn from the EDTA complex, even in the presence of a higher Mn concentration, which was consistent with the higher stability constant of the Th-EDTA complex.EThOS - Electronic Theses Online ServiceNexia Solutions Limited (Agreement Number 1002373)GBUnited Kingdo

Seasonal Variations in Interstitial Water Transuranium Element Concentrations

The porewater concentrations of the transuranium elements Np, Pu, and Am have been measured over time at a salt marsh in west Cumbria, U.K., and all three show seasonal variations. Pu follows the pattern previously observed at this site very closely, with concentrations reaching a maximum of 3.2 mBq L-1 and a minimum of 0.8 mBq L-1 in 1996, compared with 3.5 mBq L-1 and 1.1 mBq L-1, respectively, in 1994. However, no relationship with dissolved Fe and Mn concentrations was observed in this study. Plutonium and Am concentrations follow similar patterns from April to September, but there are fluctuations in the Am concentration in February which are not observed for Pu. Neptunium concentrations, measured by accelerator mass spectrometry, follow a less clear pattern, although they are at a marked maximum of 0.56 mBq L-1 in February. Changes in Pu and Am concentrations between April and September can be related to changes in the microbial community and suggest that these elements are taken up in biosorption processes. When biomass is low, no relationship is observed between Pu and Am concentrations. There is no correlation between the microbiological data and Np concentrations at any time of year