Role of non-coding sequence variants in cancer

The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo

(2015) Florian A. Karreth et al.   CELL

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

Organoid Models of Human and Mouse Ductal Pancreatic Cancer

(2015) Sylvia F. Boj et al.   CELL

Systematic Screening of Promoter Regions Pinpoints Functional Cis-Regulatory Mutations in a Cutaneous Melanoma Genome

(2015) R. C. Poulos et al.   MOLECULAR CANCER RESEARCH

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

(2015) Derek A. Oldridge et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations

(2015) Lucas Lochovsky et al.   NUCLEIC ACIDS RESEARCH

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types

(2015) K. S. Smith et al.   NUCLEIC ACIDS RESEARCH

Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR–Cas9-mediated mutagenesis

(2015) Davide Seruggia et al.   NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

In-silico identification and functional validation of allele-dependent AR enhancers

(2015) Sonia Garritano et al.   Oncotarget

Precision cancer mouse models through genome editing with CRISPR-Cas9

(2015) Haiwei Mou et al.   Genome Medicine

Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

(2015) Ophir Shalem et al.   PLoS Genetics

On the identification of potential regulatory variants within genome wide association candidate SNP sets

(2014) Chih-yu Chen et al.   BMC Medical Genomics

Organoid Cultures Derived from Patients with Advanced Prostate Cancer

(2014) Dong Gao et al.   CELL

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

A Novel Splice Site Mutation in the Noncoding Region ofBRCA2: Implications for Fanconi Anemia and Familial Breast Cancer Diagnostics

(2014) Janine L. Bakker et al.   HUMAN MUTATION

Effects of a Novel Long Noncoding RNA, lncUSMycN, on N-Myc Expression and Neuroblastoma Progression

(2014) Pei Y. Liu et al.   JNCI-Journal of the National Cancer Institute

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding

(2014) Qilai Huang et al.   NATURE GENETICS

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

(2014) Kai Wang et al.   NATURE GENETICS

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

A molecular basis for classic blond hair color in Europeans

(2014) Catherine A Guenther et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Targeted resequencing of the microRNAome and 3′UTRome reveals functional germline DNA variants with altered prevalence in epithelial ovarian cancer

(2014) X Chen et al.   ONCOGENE

Transcribed ultraconserved region in human cancers

(2014) Jiang Chen Peng et al.   RNA Biology

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Enhancer alterations in cancer: a source for a cell identity crisis

(2014) Ken J Kron et al.   Genome Medicine

Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer

(2013) Joachim Weischenfeldt et al.   CANCER CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

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

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

TERT promoter mutations in cancer development

(2013) Barbara Heidenreich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Variants at IRX4 as prostate cancer expression quantitative trait loci

(2013) Xing Xu et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

(2013) Ilaria Mogno et al.   GENOME RESEARCH

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

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

iCOGS collection provides a collaborative model

(2013) Orli G Bahcall   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

LncRNA loc285194 is a p53-regulated tumor suppressor

(2013) Qian Liu et al.   NUCLEIC ACIDS RESEARCH

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications

(2013) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

TERT promoter mutations in bladder cancer affect patient survival and disease recurrence through modification by a common polymorphism

(2013) P. S. Rachakonda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal

(2013) P. J. Killela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast

(2013) S. Dvir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Mining cancer methylomes: prospects and challenges

(2013) Clare Stirzaker et al.   TRENDS IN GENETICS

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-Control Whole-Exome Sequencing Studies

(2012) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Epigenetic Repression of miR-31 Disrupts Androgen Receptor Homeostasis and Contributes to Prostate Cancer Progression

(2012) P.-C. Lin et al.   CANCER RESEARCH

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

After GWAS: mice to the rescue?

(2012) Joerg Ermann et al.   CURRENT OPINION IN IMMUNOLOGY

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

3C-based technologies to study the shape of the genome

(2012) Wouter de Laat et al.   METHODS

N-myc and Noncoding RNAs in Neuroblastoma

(2012) J. Buechner et al.   MOLECULAR CANCER RESEARCH

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

(2012) Alexej Abyzov et al.   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

A powerful test for multiple rare variants association studies that incorporates sequencing qualities

(2012) Z. John Daye et al.   NUCLEIC ACIDS RESEARCH

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs

(2012) Simon G. Coetzee et al.   NUCLEIC ACIDS RESEARCH

Exploring functional variant discovery in non-coding regions with SInBaD

(2012) Kjong-Van Lehmann et al.   NUCLEIC ACIDS RESEARCH

SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update)

(2012) A. Z. Dayem Ullah et al.   NUCLEIC ACIDS RESEARCH

Genetic variations in miR-27a gene decrease mature miR-27a level and reduce gastric cancer susceptibility

(2012) Q Yang et al.   ONCOGENE

A Streamlined Method for Detecting Structural Variants in Cancer Genomes by Short Read Paired-End Sequencing

(2012) Martina Mijušković et al.   PLoS One

Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk

(2012) F. Demichelis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions

(2012) W. Xue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The hallmarks of cancer

(2012) Tony Gutschner et al.   RNA Biology

Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Inducing Cell Proliferation Inhibition, Apoptosis, and Motility Reduction by Silencing Long Noncoding Ribonucleic Acid Metastasis-associated Lung Adenocarcinoma Transcript 1 in Urothelial Carcinoma of the Bladder

(2012) Yonghua Han et al.   UROLOGY

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Somatic mosaicism in healthy human tissues

(2011) Subhajyoti De   TRENDS IN GENETICS

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

is-rSNP: a novel technique for in silico regulatory SNP detection

(2010) Geoff Macintyre et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression

(2010) Jindan Yu et al.   CANCER CELL

Recurrent Focal Copy-Number Changes and Loss of Heterozygosity Implicate Two Noncoding RNAs and One Tumor Suppressor Gene at Chromosome 3q13.31 in Osteosarcoma

(2010) I. Pasic et al.   CANCER RESEARCH

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Segmental duplications in the human genome reveal details of pseudogene formation

(2010) Ekta Khurana et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Boveri revisited: chromosomal instability, aneuploidy and tumorigenesis

(2009) Andrew J. Holland et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms

(2008) C. Chelala et al.   BIOINFORMATICS

Genome-wide association studies in cancer

(2008) D. F. Easton et al.   HUMAN MOLECULAR GENETICS

Genomics: Protein fossils live on as RNA

(2008) Rajkumar Sasidharan et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE