Identification of Single Nucleotide Non-coding Driver Mutations in Cancer

APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL

(2017) Z Li et al.   LEUKEMIA

Recurrent and functional regulatory mutations in breast cancer

(2017) Esther Rheinbay et al.   NATURE

Characterization of noncoding regulatory DNA in the human genome

(2017) Ran Elkon et al.   NATURE BIOTECHNOLOGY

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer

(2017) Yongsheng Li et al.   Cell Reports

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

(2017) Zeynep Kalender Atak et al.   Genome Medicine

Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma

(2017) Kirill Batmanov et al.   Scientific Reports

Detection of Somatic Mutations in Exome Sequencing of Tumor-only Samples

(2017) Yu-Chin Hsu et al.   Scientific Reports

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

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

(2016) Serena Nik-Zainal et al.   NATURE

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites: Fig. 1.

(2015) Simon G. Coetzee et al.   BIOINFORMATICS

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing

(2015) Lucia Cavelier et al.   BMC CANCER

Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants

(2015) Juan I. Fuxman Bass et al.   CELL

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

(2015) Carlos L Araya et al.   NATURE GENETICS

Intron retention is a widespread mechanism of tumor-suppressor inactivation

(2015) Hyunchul Jung 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

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2015) Lucas Lochovsky et al.   NUCLEIC ACIDS RESEARCH

Multiple conformations are a conserved and regulatory feature of theRB15′ UTR

(2015) Katrina M. Kutchko et al.   RNA

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

(2015) R. J. A. Bell et al.   SCIENCE

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

(2015) Tyler S. Alioto et al.   Nature Communications

Inhibition of vemurafenib-resistant melanoma by interference with pre-mRNA splicing

(2015) Maayan Salton et al.   Nature Communications

Frequent DPH3 promoter mutations in skin cancers

(2015) Evgeniya Denisova et al.   Oncotarget

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

Massively parallel functional annotation of 3′ untranslated regions

(2014) Wenxue Zhao et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold 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

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

High Incidence of ActivatingTERTPromoter Mutations in Meningiomas Undergoing Malignant Progression

(2013) Stéphane Goutagny et al.   BRAIN PATHOLOGY

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

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

(2013) Ilaria Mogno et al.   GENOME RESEARCH

Frequent somatic mutations of the telomerase reverse transcriptase promoter in ovarian clear cell carcinoma but not in other major types of gynaecological malignancy

(2013) Ren-Chin Wu et al.   JOURNAL OF PATHOLOGY

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

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data

(2013) Yuichi Shiraishi et al.   NUCLEIC ACIDS RESEARCH

The age- and shorter telomere-dependent TERT promoter mutation in follicular thyroid cell-derived carcinomas

(2013) T Liu et al.   ONCOGENE

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

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

MotifSuite: workflow for probabilistic motif detection and assessment

(2012) M. Claeys et al.   BIOINFORMATICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Towards a theoretical understanding of false positives in DNA motif finding

(2012) Amin Zia et al.   BMC BIOINFORMATICS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Annotation of functional variation in personal genomes using RegulomeDB

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

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Identification of fifteen novel germline variants in theBRCA13′UTR reveals a variant in a breast cancer case that introduces a functionalmiR-103target site

(2012) Brooke L. Brewster et al.   HUMAN MUTATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The Human Gene Mutation Database: 2008 update

(2009) Peter D Stenson et al.   Genome Medicine

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE