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

Green, Blue And Grey Water Footprints Of Primary Crops Production In Nepal

This study aims to estimate the green, blue and grey water footprints (WFs) of nine primary crops production in 75 districts, 5 developmental regions and 3 physiographic divisions of Nepal using local meteorological, agronomical and irrigation data at high spatial resolution. The estimates are based on the framework prescribed by the guideline of the Water Footprint Network. The green and blue WFs are calculated using a water balance model whereas the grey WF is estimated as the volume of freshwater needed to dilute nitrate pollution to an acceptable level. WF varies across different crops considered, different districts, development regions and physiographic divisions. WF of potato and wheat in Nepal is comparable to the world average; but paddy, barley and pulses have higher while sugarcane and maize have lower values compared to the world average. WFs of paddy, maize, potato and wheat are lower in Terai than the Hills and Mountains due to the accessibility of irrigation system and higher crop yield. Millet, pulses, oilseeds and barley have lower WFs and are suitable for Mountains. Similarly, sugarcane is suitable for both Terai and Mountain divisions because of its lower WF. Crops in Far Western Development Region generally have higher WFs due to the low crop productivity, and higher fertilizer use. © 2013 Springer Science+Business Media Dordrecht

Sudden unexplained death syndrome. A review and update

Tropical and Geographical Medicine444TGME