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Showing 1–50 of 212 results
Advanced filters: Author: Sunil A. David Clear advanced filters
  • The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

    • Lauri A. Aaltonen
    • Federico Abascal
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 82-93
  • Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

    • Matthew A. Reyna
    • David Haan
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-17
  • Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

    • Esther Rheinbay
    • Morten Muhlig Nielsen
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 102-111
  • The transcription factor CREM is a pivotal regulator of NK cell function, making CREM a valuable target to increase the efficacy of anticancer immunotherapies based on this cell population and chimeric antigen receptors.

    • Hind Rafei
    • Rafet Basar
    • Katayoun Rezvani
    ResearchOpen Access
    Nature
    Volume: 643, P: 1076-1086
  • With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

    • Matthew H. Bailey
    • William U. Meyerson
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-27
  • The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

    • Marek Cmero
    • Ke Yuan
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-15
  • To address an evidence gap for the efficacy of hypertension therapy using dual drug combinations in patients of South Asian origin, a randomized clinical trial conducted in India found that three types of dual drug combinations, each administered in a single pill, had similarly large effects on reducing blood pressure.

    • Dorairaj Prabhakaran
    • Ambuj Roy
    • Neil R. Poulter
    ResearchOpen Access
    Nature Medicine
    Volume: 31, P: 3169-3175
  • Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

    • Yilong Li
    • Nicola D. Roberts
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 112-121
  • Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

    • Yulia Rubanova
    • Ruian Shi
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12
  • In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

    • Lina Sieverling
    • Chen Hong
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-13
  • Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

    • Moritz Gerstung
    • Clemency Jolly
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 122-128
  • Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

    • Marta Paczkowska
    • Jonathan Barenboim
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-16
  • In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

    • Yiqun Zhang
    • Fengju Chen
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-14
  • Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

    • Shimin Shuai
    • Federico Abascal
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12
  • Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

    • Wei Jiao
    • Gurnit Atwal
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12
  • Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

    • Claudia Calabrese
    • Natalie R. Davidson
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 129-136
  • Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

    • Marc Zapatka
    • Ivan Borozan
    • Christian von Mering
    ResearchOpen Access
    Nature Genetics
    Volume: 52, P: 320-330
  • Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

    • Vinayak Bhandari
    • Constance H. Li
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-10
  • The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

    • Ludmil B. Alexandrov
    • Jaegil Kim
    • Christian von Mering
    ResearchOpen Access
    Nature
    Volume: 578, P: 94-101
  • There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

    • Constance H. Li
    • Stephenie D. Prokopec
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-24
  • Pathogen diagnostics are strong determinants of azithromycin effects on diarrhea duration, but host factors may better predict benefits for severe outcomes. In this work, authors utilise a machine learning-based approach to evaluate personalized rules for the decision to treat watery diarrhea with azithromycin.

    • Sara S. Kim
    • Allison Codi
    • Elizabeth T. Rogawski McQuade
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12
  • Amyloid aggregation of mutant p53 contributes to its loss of tumor suppressor function and oncogenic gain-of-function. Here, the authors use a protein mimetic to abrogate mutant p53 aggregation and rescue p53 function, which inhibits cancer cell proliferation in vitro and halts tumor growth in vivo.

    • L. Palanikumar
    • Laura Karpauskaite
    • Mazin Magzoub
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-24
  • Chronic infection with SARS-CoV-2 leads to the emergence of viral variants that show reduced susceptibility to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma.

    • Steven A. Kemp
    • Dami A. Collier
    • Ravindra K. Gupta
    Research
    Nature
    Volume: 592, P: 277-282
  • Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.

    • Isidro Cortés-Ciriano
    • Jake June-Koo Lee
    • Christian von Mering
    ResearchOpen Access
    Nature Genetics
    Volume: 52, P: 331-341
  • Sera from vaccinated individuals and some monoclonal antibodies show a modest reduction in neutralizing activity against the B.1.1.7 variant of SARS-CoV-2; but the E484K substitution leads to a considerable loss of neutralizing activity.

    • Dami A. Collier
    • Anna De Marco
    • Ravindra K. Gupta
    Research
    Nature
    Volume: 593, P: 136-141
  • A diverse, multidisciplinary panel of 386 experts in COVID-19 response from 112 countries provides health and social policy actions to address inadequacies in the pandemic response and help to bring this public health threat to an end.

    • Jeffrey V. Lazarus
    • Diana Romero
    • Anne Øvrehus
    ResearchOpen Access
    Nature
    Volume: 611, P: 332-345
  • The identification of T cell epitopes is a critical step in understanding the immune response to infection and in designing vaccine based approaches. Here the authors introduce a frame work of antigen discovery called MHCvalidator and Epitrack to identify new antigenic features for T-cell COVID-19 vaccines and characterise a novel non-canonical epitope from a truncated Spike variant and mutation of an immunodominant epitope in the BNT162b4 vaccine.

    • Kevin A. Kovalchik
    • David J. Hamelin
    • Etienne Caron
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-22
  • Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

    • Yuan Yuan
    • Young Seok Ju
    • Christian von Mering
    ResearchOpen Access
    Nature Genetics
    Volume: 52, P: 342-352
  • A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.

    • Harald S. Vöhringer
    • Theo Sanderson
    • Moritz Gerstung
    ResearchOpen Access
    Nature
    Volume: 600, P: 506-511
  • The response to infectious and inflammatory challenges differs among people but the reasons for this are poorly understood. Here the authors explore the impact of variables such as age, sex, and the capacity for controlling inflammation and maintaining immunocompetence, linking this capacity to favourable health outcomes and lifespan.

    • Sunil K. Ahuja
    • Muthu Saravanan Manoharan
    • Weijing He
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-31
  • Inhibiting alpha-synuclein self-assembly into amyloid structures, associated with Parkinson’s disease, is a potential therapeutic intervention. Here, the authors identify the domains/sequences that are essential for alpha-synuclein aggregation and test the activity of foldamer-based antagonists to identify potential therapeutic targets.

    • Jemil Ahmed
    • Tessa C. Fitch
    • Sunil Kumar
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-17
  • Sakata et al. performed a prospective personalized mechanistic computational (digital twin) study focused on characterizing the arrhythmogenic properties of the atrial fibrotic substrate in patients with persistent atrial fibrillation, and they introduce here a novel mechanism-oriented strategy for optimal ablation.

    • Kensuke Sakata
    • Ryan P. Bradley
    • Natalia A. Trayanova
    ResearchOpen Access
    Nature Cardiovascular Research
    Volume: 3, P: 857-868
  • The CRISPR/Cas system known to aid bacterial defences by targeting invading DNA can also act to evade eukaryotic defences through a different class of small RNAs downregulating an endogenous immunogenic bacterial lipoprotein.

    • Timothy R. Sampson
    • Sunil D. Saroj
    • David S. Weiss
    Research
    Nature
    Volume: 497, P: 254-257
  • Artemisinin-resistantPlasmodium is an increasing problem. Here, using a medicinal chemistry programme, the authors identify a tetraoxane-based drug candidate that shows no cross-resistance with an artemisinin-resistant strain (PfK13-C580Y) and is efficient in Plasmodiummouse models.

    • Paul M. O’Neill
    • Richard K. Amewu
    • Stephen A. Ward
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-10
  • Turajlic and colleagues assess longitudinal antibody and cellular immune responses against SARS-CoV-2 variants of concern in patients with cancer, following either recovery from SARS-CoV-2 infection or vaccination, in two back-to-back reports from the CAPTURE study.

    • Annika Fendler
    • Scott T. C. Shepherd
    • Samra Turajlic
    ResearchOpen Access
    Nature Cancer
    Volume: 2, P: 1305-1320