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 soft donor atom on the mutual separation of zinc and cadmium

Extraction behavior of zinc and cadmium in the systems of bis(1,1,3, 3-tetramethylbutyl) phosphinic acid (HMBP)/cyclohexane-nitric acid and bis(1,1,3, 3-tetramethylbutyl) monothiophosphinic acid (HMTP)/cyclohexane-nitric acid was systematically investigated. The extraction mechanism was proposed through the log-log plot analysis, and the extracted species of zinc and cadmium might be Zn[H (MBP)(2)](2), Cd[H(MBP)(2)](2) in HMBP/C6H12-HNO3 system and Zn[H(MTP)(2)](2), Cd[H(MTP)(2)](2) in HMTP/C6H12-HNO3 system. Experimental results showed that the selectivity of HMBP to cadmium was remarkably improved by introducing the soft donor atom sulfur into HMBP molecule, and the quantitative mutual separation of cadmium from zinc could be achieved by a single extraction with HMTP as an extractant. This method may be expected to be useful for the determination of trace cadmium in high purity zinc