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

Effect of non-linear adsorption on the transport behaviour of Brilliant Blue in a field soil

The food dye Brilliant Blue FCF (Color Index 42090) is often used as dye tracer in field studies for visualizing the flow pathways of water in soils. Batch studies confirmed findings of other researchers that non-linear sorption is important for Brilliant Blue, especially at small concentrations (< 10 g l(-1) for our soil), and that retardation increases with decreasing concentrations as well as with increasing ionic strength of solutions. Therefore, it is not obvious if it can be used as an indicator for water flow paths as is often done. In this study, we compared the mobility of Brilliant Blue in a field soil (gleyic Luvisol) with that of bromide. Brilliant Blue and potassium bromide were simultaneously applied as a 6-mm pulse on a small plot in the field, and the tracers were displaced with 89 mm of tracer-free water using a constant intensity of 3.9 +/- 0.2 mm hour(-1) . Both tracer concentrations were determined on 144 soil cores taken from a 1 m x 1 m vertical soil profile. The transport behaviour differed in both (i) mean displacement and (ii) spatial concentration pattern. We found the retardation of Brilliant Blue could not be neglected and, in contrast to the bromide pattern, a pulse splitting was observed at the plough pan. Numerical simulations with a particle tracking code revealed that the one-dimensional concentration profile of bromide was represented fairly well by the model, but the prediction of the double peak in the Brilliant Blue concentration profile failed. With additional assumptions, there were indications that Brilliant Blue does not follow the same flow paths as bromide. However, the question of Brilliant Blue taking the same flow pathways as bromide cannot be adequately answered by comparing both concentration distributions, because we look at two different transport distances due to the retardation of Brilliant Blue. It became obvious, however, that Brilliant Blue is not a suitable compound for tracing the travel time of water itself