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

Giant Western Red Cedar Growth - Surprises

The book includes a description and illustration of a forest Western Red Cedar in it's growth and anatomy from bark to root. The young forest tree has grown from a branch that was attached to an adjacent tree not a seed. The attached branch grows and becomes unattached from the adjacent tree and forms a new tree.AlumniUnreviewedOthe

Heritage Eaters : Insects and Fungi in Heritage Collections

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Comparative Anatomy of Branches, Roots and Wood of Some North American Dicotyledonous and Coniferous Trees and Woody Shrubs Used in Ethnographic Artifacts : Identification and Conservation Concerns

This book deals with the comparative anatomy of the tissues of the bark, phloem, heartwood, sapwood, and pith in wood, branches, and roots of woody shrubs, hardwood trees and softwood coniferous trees, that were reported to have been used historically in making ethnographic and archaeological artifacts. The species researched in this book are endemic to Northwest Coast of North America. These species have generic anatomical characteristics that are also common in other genera of the same family. Thus, the information is applicable to tree genera in similar latitudinal environments in Canada, USA, Europe and Asia. The goal of the information is to assist; curators with their research and conservators with their care of artifacts made of these plant parts. Identification of a species is usually a curator’s job and is used to determine provenience. Conservators may obtain the species/genus identification by research or provenience. Relevant morphological, anatomical, and chemical features of plant parts are needed to interpret the physical changes and their influence on the stability of the artifact. Understanding the structure and inherent strengths or weaknesses of the plant part assist conservators in logical care for a specific object. These are presented throughout the text were possible. Also, throughout the text a few examples of the materials from artifacts are presented for comparison. The terminology used in the text is explained as it goes along and there is a glossary for further explanations. The terminology is easy because all plants have the same anatomical types of tissues, but the anatomical patterns of the cells are variable with species. A bibliography is supplied for further information on specific topics. Reviewed by Dr. Nancy Odegaard, Head of Preservation, Arizona State Museum and Professor, Univ. of Arizona School of Anthropology and Conservation; Dr. Robert Blanchette, Professor, Department of Plant Pathology, Univ. of Minnesota. The preparation of this book was made possible through a Samuel H. Kress Conservation Publication Fellowship, administered by the Foundation of the American Institute for Conservation., Washington DC. For which the author is most grateful.AlumniUnreviewedOthe