Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels

Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma

(2022) Jenette Creaney et al.   Genome Medicine

First-line nivolumab plus ipilimumab in unresectable malignant pleural mesothelioma (CheckMate 743): a multicentre, randomised, open-label, phase 3 trial

(2021) Paul Baas et al.   LANCET

Comparative study of whole exome sequencing-based copy number variation detection tools

(2020) Lanling Zhao et al.   BMC BIOINFORMATICS

Larotrectinib in patients with TRK fusion-positive solid tumours: a pooled analysis of three phase 1/2 clinical trials

(2020) David S Hong et al.   LANCET ONCOLOGY

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

(2020) Bernardo Rodriguez-Martin et al.   NATURE GENETICS

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

(2020) Yiqun Zhang et al.   Nature Communications

Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage

(2020) Yury A. Barbitoff et al.   Scientific Reports

Use of an Integrated Pan-Cancer Oncology Enrichment Next-Generation Sequencing Assay to Measure Tumour Mutational Burden and Detect Clinically Actionable Variants

(2020) Valerie Pestinger et al.   Molecular Diagnosis & Therapy

ESMO recommendations on microsatellite instability testing for immunotherapy in cancer, and its relationship with PD-1/PD-L1 expression and tumour mutational burden: a systematic review-based approach

(2019) C Luchini et al.   ANNALS OF ONCOLOGY

Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers

(2019) K Nones et al.   ANNALS OF ONCOLOGY

Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets

(2019) Felicity Newell et al.   Nature Communications

Tumor mutational burden analysis of 2,000 Japanese cancer genomes using whole exome and targeted gene panel sequencing

(2018) Keiichi HATAKEYAMA et al.   BIOMEDICAL RESEARCH-TOKYO

Measuring coverage and accuracy of whole-exome sequencing in clinical context

(2018) Sek Won Kong et al.   GENETICS IN MEDICINE

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

(2018) Pauline Robbe et al.   GENETICS IN MEDICINE

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

(2018) David Tamborero et al.   Genome Medicine

Size Matters: Dissecting Key Parameters for Panel-Based Tumor Mutational Burden (TMB) Analysis

(2018) Ivo Buchhalter et al.   INTERNATIONAL JOURNAL OF CANCER

Blood-based tumor mutational burden as a predictor of clinical benefit in non-small-cell lung cancer patients treated with atezolizumab

(2018) David R. Gandara et al.   NATURE MEDICINE

Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome

(2018) Michael Rusch et al.   Nature Communications

Integrative Molecular Characterization of Malignant Pleural Mesothelioma

(2018) Julija Hmeljak et al.   Cancer Discovery

Non–Small Cell Lung Cancer, Version 5.2017, NCCN Clinical Practice Guidelines in Oncology

(2017) David S. Ettinger et al.   Journal of the National Comprehensive Cancer Network

OA20.01 Tumor Mutation Burden (TMB) is Associated with Improved Efficacy of Atezolizumab in 1L and 2L+ NSCLC Patients

(2017) Marcin Kowanetz et al.   Journal of Thoracic Oncology

Whole-genome landscape of pancreatic neuroendocrine tumours

(2017) Aldo Scarpa et al.   NATURE

Whole-genome landscapes of major melanoma subtypes

(2017) Nicholas K. Hayward et al.   NATURE

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Clinical sequencing: is WGS the better WES?

(2016) Janine Meienberg et al.   HUMAN GENETICS

Phase II Study of WEE1 Inhibitor AZD1775 Plus Carboplatin in Patients With TP53-Mutated Ovarian Cancer Refractory or Resistant to First-Line Therapy Within 3 Months

(2016) Suzanne Leijen et al.   JOURNAL OF CLINICAL ONCOLOGY

Can you teach old drugs new tricks?

(2016) Nicola Nosengo   NATURE

Genomic analyses identify molecular subtypes of pancreatic cancer

(2016) Peter Bailey et al.   NATURE

Whole–genome characterization of chemoresistant ovarian cancer

(2015) Ann-Marie Patch et al.   NATURE

Whole genomes redefine the mutational landscape of pancreatic cancer

(2015) Nicola Waddell et al.   NATURE

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

(2015) Aziz Belkadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

Exome sequence read depth methods for identifying copy number changes

(2014) L. Kadalayil et al.   BRIEFINGS IN BIOINFORMATICS

Prioritization of neurodevelopmental disease genes by discovery of new mutations

(2014) Alexander Hoischen et al.   NATURE NEUROSCIENCE

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

(2014) Katia Nones et al.   Nature Communications

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes

(2013) Seung Chul Shin et al.   PLoS One

Somatic Point Mutation Calling in Low Cellularity Tumors

(2013) Karin S. Kassahn et al.   PLoS One

Clinical and molecular characterization of HER2 amplified-pancreatic cancer

(2013) Angela Chou et al.   Genome Medicine

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multicentre phase II trial of trastuzumab and capecitabine in patients with HER2 overexpressing metastatic pancreatic cancer

(2012) J Harder et al.   BRITISH JOURNAL OF CANCER

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Safety and Activity of Anti–PD-L1 Antibody in Patients with Advanced Cancer

(2012) Julie R. Brahmer et al.   NEW ENGLAND JOURNAL OF MEDICINE

HER2-amplified breast cancer: mechanisms of trastuzumab resistance and novel targeted therapies

(2011) Devika Gajria et al.   Expert Review of Anticancer Therapy

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial

(2010) Yung-Jue Bang et al.   LANCET

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE