Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes

Comprehensive Characterization of Cancer Driver Genes and Mutations

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The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Integrative detection and analysis of structural variation in cancer genomes

(2018) Jesse R. Dixon et al.   NATURE GENETICS

AWESOME: a database of SNPs that affect protein post-translational modifications

(2018) Yang Yang et al.   NUCLEIC ACIDS RESEARCH

Association analysis identifies 65 new breast cancer risk loci

(2017) Kyriaki Michailidou et al.   NATURE

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

(2017) Roger L Milne et al.   NATURE GENETICS

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

(2017) Jeanne Chèneby et al.   NUCLEIC ACIDS RESEARCH

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue

(2017) Alejandro Quiroz-Zárate et al.   PLoS One

DNA methylation at enhancers identifies distinct breast cancer lineages

(2017) Thomas Fleischer et al.   Nature Communications

Evidence that the 5p12 Variant rs10941679 Confers Susceptibility to Estrogen-Receptor-Positive Breast Cancer through FGF10 and MRPS30 Regulation

(2016) Maya Ghoussaini et al.   AMERICAN JOURNAL OF HUMAN GENETICS

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

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Improved methods for multi-trait fine mapping of pleiotropic risk loci

(2016) Gleb Kichaev et al.   BIOINFORMATICS

The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

(2016) Christopher I. Amos et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

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An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression

(2016) Asaf Wyszynski et al.   HUMAN MOLECULAR GENETICS

Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

(2016) Jiajun Shi et al.   INTERNATIONAL JOURNAL OF CANCER

Unusual roles of caspase-8 in triple-negative breast cancer cell line MDA-MB-231

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Age- and Tumor Subtype–Specific Breast Cancer Risk Estimates for CHEK2*1100delC Carriers

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Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170

(2016) Alison M Dunning et al.   NATURE GENETICS

Fine-Mapping of the 1p11.2 Breast Cancer Susceptibility Locus

(2016) Hisani N. Horne et al.   PLoS One

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus

(2016) Kate Lawrenson et al.   Nature Communications

Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)

(2016) Hatef Darabi et al.   Scientific Reports

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks

(2016) Davide Pellacani et al.   Cell Reports

The Immune System in Cancer Pathogenesis: Potential Therapeutic Approaches

(2016) Pankita H. Pandya et al.   Journal of Immunology Research

Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1

(2015) Dylan M. Glubb et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Polymorphisms in a Putative Enhancer at the 10q21.2 Breast Cancer Risk Locus Regulate NRBF2 Expression

(2015) Hatef Darabi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Disruption of the ribosomal P complex leads to stress-induced autophagy

(2015) Ana Artero-Castro et al.   Autophagy

Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk

(2015) X. Guo et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

(2015) N. Orr et al.   HUMAN MOLECULAR GENETICS

BRCA2 Polymorphic Stop Codon K3326X and the Risk of Breast, Prostate, and Ovarian Cancers

(2015) Huong D. Meeks et al.   JNCI-Journal of the National Cancer Institute

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

(2015) Kyriaki Michailidou et al.   NATURE GENETICS

Targeting Notch, Hedgehog and Wnt pathways in cancer stem cells: clinical update

(2015) Naoko Takebe et al.   Nature Reviews Clinical Oncology

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Targeting Mdmx to treat breast cancers with wild-type p53

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A Common Cancer Risk-Associated Allele in the hTERT Locus Encodes a Dominant Negative Inhibitor of Telomerase

(2015) Anagha Killedar et al.   PLoS Genetics

BRCA2 Polymorphic Stop Codon K3326X and the Risk of Breast, Prostate, and Ovarian Cancers

(2015) Huong D. Meeks et al.   JNCI-Journal of the National Cancer Institute

Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk

(2014) Wei-Yu Lin et al.   HUMAN MOLECULAR GENETICS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

Functional Variants at the 11q13 Risk Locus for Breast Cancer Regulate Cyclin D1 Expression through Long-Range Enhancers

(2013) Juliet D. French et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fine-Scale Mapping of the FGFR2 Breast Cancer Risk Locus: Putative Functional Variants Differentially Bind FOXA1 and E2F1

(2013) Kerstin B. Meyer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci

(2013) Qiyuan Li et al.   CELL

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer

(2013) Stig E Bojesen et al.   NATURE GENETICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Large-scale genotyping identifies 41 new loci associated with breast cancer risk

(2013) Kyriaki Michailidou et al.   NATURE GENETICS

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

(2013) Fergus J. Couch et al.   PLoS Genetics

Identification of a BRCA2-Specific Modifier Locus at 6p24 Related to Breast Cancer Risk

(2013) Mia M. Gaudet et al.   PLoS Genetics

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Fast and accurate inference of local ancestry in Latino populations

(2012) Yael Baran et al.   BIOINFORMATICS

Evaluation of Association Methods for Analysing Modifiers of Disease Risk in Carriers of High-Risk Mutations

(2012) Daniel R. Barnes et al.   GENETIC EPIDEMIOLOGY

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

TGFβ signalling in context

(2012) Joan Massagué   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

METAL: fast and efficient meta-analysis of genomewide association scans

(2010) C. J. Willer et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Evaluating the power to discriminate between highly correlated SNPs in genetic association studies

(2010) Miriam S. Udler et al.   GENETIC EPIDEMIOLOGY

Genetic susceptibility to breast cancer

(2010) Nasim Mavaddat et al.   Molecular Oncology

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

NF-κB and estrogen receptor α interactions: Differential function in estrogen receptor-negative and -positive hormone-independent breast cancer cells

(2009) Nathalie Gionet et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood 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

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

(2009) François-Olivier Desmet et al.   NUCLEIC ACIDS RESEARCH

Bias-reduced estimators and confidence intervals for odds ratios in genome-wide association studies

(2008) H. Zhong et al.   BIOSTATISTICS

Musashi1 Modulates Mammary Progenitor Cell Expansion through Proliferin-Mediated Activation of the Wnt and Notch Pathways

(2008) X.-Y. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH