RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

DeTiN: overcoming tumor-in-normal contamination

(2018) Amaro Taylor-Weiner et al.   NATURE METHODS

The tumour microenvironment creates a niche for the self-renewal of tumour-promoting macrophages in colon adenoma

(2018) Irene Soncin et al.   Nature Communications

Role of tumor microenvironment in ovarian cancer pathobiology

(2018) Alia Ghoneum et al.   Oncotarget

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

(2018) Theo A. Knijnenburg et al.   Cell Reports

Integrated Molecular Characterization of Testicular Germ Cell Tumors

(2018) Hui Shen et al.   Cell Reports

Aging and the rise of somatic cancer-associated mutations in normal tissues

(2018) Rosa Ana Risques et al.   PLoS Genetics

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

(2018) Kyle Ellrott et al.   Cell Systems

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer

(2017) Giannicola Genovese et al.   NATURE

Integrated genomic characterization of oesophageal carcinoma

(2017)   NATURE

Integrated genomic and molecular characterization of cervical cancer

(2017)   NATURE

Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations

(2017) Florian T. Merkle et al.   NATURE

Inflammatory microenvironment in the initiation and progression of bladder cancer

(2017) Xinbing Sui et al.   Oncotarget

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

(2016) Siyuan Zheng et al.   CANCER CELL

The Case for a Pre-Cancer Genome Atlas (PCGA)

(2016) J. D. Campbell et al.   Cancer Prevention Research

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair

(2016) Nicholas J. Haradhvala et al.   CELL

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

The tumor microenvironment in esophageal cancer

(2016) E W Lin et al.   ONCOGENE

Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somaticTP53mutations in noncancerous tissues

(2016) Jeffrey D. Krimmel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

(2016) Uri Weissbein et al.   Nature Communications

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts

(2016) Natalie Saini et al.   PLoS Genetics

Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study

(2016) Navya Nair et al.   PLOS MEDICINE

Consumption of hot beverages and foods and the risk of esophageal cancer: a meta-analysis of observational studies

(2015) Yawen Chen et al.   BMC CANCER

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Variation in cancer risk among tissues can be explained by the number of stem cell divisions

(2015) C. Tomasetti et al.   SCIENCE

Mutant p53 in Cancer: New Functions and Therapeutic Opportunities

(2014) Patricia A.J. Muller et al.   CANCER CELL

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Genomic and molecular characterization of esophageal squamous cell carcinoma

(2014) De-Chen Lin et al.   NATURE GENETICS

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes

(2014) Siddhartha Jaiswal et al.   NEW ENGLAND JOURNAL OF MEDICINE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

(2014) Amie J. Radenbaugh et al.   PLoS One

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

(2014) Xuyu Cai et al.   Cell Reports

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

Two hot spot mutant p53 mouse models display differential gain of function in tumorigenesis

(2013) W Hanel et al.   CELL DEATH AND DIFFERENTIATION

Consistent and Differential Genetic Aberrations between Esophageal Dysplasia and Squamous Cell Carcinoma Detected By Array Comparative Genomic Hybridization

(2013) Z.-Z. Shi et al.   CLINICAL CANCER RESEARCH

Air pollution and lung cancer incidence in 17 European cohorts: prospective analyses from the European Study of Cohorts for Air Pollution Effects (ESCAPE)

(2013) Ole Raaschou-Nielsen et al.   LANCET ONCOLOGY

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

Impact of deleterious passenger mutations on cancer progression

(2013) C. D. McFarland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation

(2013) C. Tomasetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic Mutation, Genomic Variation, and Neurological Disease

(2013) A. Poduri et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

(2011) Juan R González et al.   BMC BIOINFORMATICS

Cigarette smoking and lung cancer-relative risk estimates for the major histological types from a pooled analysis of case-control studies

(2011) Beate Pesch et al.   INTERNATIONAL JOURNAL OF CANCER

Wnt/β-Catenin Pathway Deregulation in Childhood Adrenocortical Tumors

(2011) Letícia F. Leal et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

DARNED: a DAtabase of RNa EDiting in humans

(2010) A. Kiran et al.   BIOINFORMATICS

Wnt/β-Catenin Pathway Activation in Adrenocortical Adenomas Is Frequently due to Somatic CTNNB1-Activating Mutations, Which Are Associated with Larger and Nonsecreting Tumors: A Study in Cortisol-Secreting and -Nonsecreting Tumors

(2010) Stéphane Bonnet et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Mutant p53 Drives Invasion by Promoting Integrin Recycling

(2009) Patricia A.J. Muller et al.   CELL

Environmental Causes of Esophageal Cancer

(2009) Farin Kamangar et al.   GASTROENTEROLOGY CLINICS OF NORTH AMERICA

High-temperature beverages and foods and esophageal cancer risk-A systematic review

(2009) Farhad Islami et al.   INTERNATIONAL JOURNAL OF CANCER

Identification of GRO1 as a Critical Determinant for Mutant p53 Gain of Function

(2009) Wensheng Yan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

DNA deletions and clonal mutations drive premature aging in mitochondrial mutator mice

(2008) Marc Vermulst et al.   NATURE GENETICS

Melanoma and the tumor microenvironment

(2008) Jessie Villanueva et al.   Current Oncology Reports