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The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered e

The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures that represent mutation types that co-occur in the same tumours. However, it remains unclear how mutation processes change during cancer evolution due to the lack of reliable methods to reconstruct evolutionary trajectories of mutational signature activity. Here, as part o

We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions,

Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associate

In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mu

The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole g

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce th

In 2021, I had a residency in "Reaktorhallen" (The Reactor Hall, or "R1"), a former nuclear reactor hall on the campus of Kunliga Tekniska Högskolan (the Royal Institute of Technology, or "KTH"). I was there to make a work for the Skandia organ, a former cinema organ that is housed in R1. I also worked with the violin in the space, and played an improvisation from this material on the concert I di

The purpose of this study was to describe the epidemiology of patients presenting with acute burns and undergoing admission at Hospital Nacional Guido Valadares (HNGV) in Dili, Timor-Leste in the period 2013 to 2019. HNGV is the only tertiary referral hospital in Timor-Leste. This was a retrospective study involving all acute burn patients admitted to the surgical wards of HNGV from 2013 to 2019.

We present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I-(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Li

Science funders can enable responsible international collaboration by developing global norms for ethical research that appropriately respond to today’s geopolitical tensions.

The steel industry is a major contributor to emissions of CO2 and key air pollutants. Reducing air pollution has since long been a policy priority in China. Reducing CO2 emissions has more recently also become a key priority partially manifested through the signing of the Paris Agreement in 2015. Although there are often synergies between reducing CO2 emissions and air pollution, it may have impli

To investigate the associations of milk intake (non-fermented and fermented milk), lactase persistence (LCT-13910 C/T) genotype (a proxy for long-term non-fermented milk intake), and gene-milk interaction with risks of cardiovascular disease (CVD) and CVD mortality. Also, to identify the CVD-related plasma proteins and lipoprotein subfractions associated with milk intake and LCT-13910 C/T genotype

BACKGROUND: Epidemiological studies have demonstrated an association between the degree of food processing in our diet and the risk of various chronic diseases. Much of this evidence is based on the international Nova classification system, which classifies food into four groups based on the type of processing: (1) Unprocessed and minimally processed foods, (2) Processed culinary ingredients, (3)

In what ways are meetings a social form? How are meetings organized and how do organizations structure meetings to produce consensus around visions of the future? In this article, planning meetings, which gather representatives from the regional Public Transport Authority and the municipalities involved in public transport planning in Stockholm, Sweden, is probed as a social form. By structuring t