Next generation sequencing in cancer research and clinical application

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

(2012) Andrew Roth et al.   BIOINFORMATICS

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

(2012) K. Chen et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Intratumor Heterogeneity: Evolution through Space and Time

(2012) C. Swanton   CANCER RESEARCH

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

(2012) John S. Welch et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Next-generation sequencing: ready for the clinics?

(2012) AN Desai et al.   CLINICAL GENETICS

Next-generation sequencing-based testing for cancer mutational landscape diversity: clinical implications?

(2012) Christos Katsios et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders 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

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Recurrent R-spondin fusions in colon cancer

(2012) Somasekar Seshagiri 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

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Reading cancer's blueprint

(2012) Michael Eisenstein   NATURE BIOTECHNOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Detecting and annotating genetic variations using the HugeSeq pipeline

(2012) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Survival in BRAF V600–Mutant Advanced Melanoma Treated with Vemurafenib

(2012) Jeffrey A. Sosman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery

(2012) Rocco Piazza et al.   NUCLEIC ACIDS RESEARCH

Intra- and Inter-Tumor Heterogeneity of BRAFV600EMutations in Primary and Metastatic Melanoma

(2012) Molly Yancovitz et al.   PLoS One

A new branch on the tree: Next-generation sequencing in the study of cancer evolution

(2012) Jacqueline A. Brosnan et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Unraveling the Genetics of Cancer: Genome Sequencing and Beyond

(2011) Kit Man Wong et al.   Annual Review of Genomics and Human Genetics

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq

(2011) Yang Li et al.   BIOINFORMATICS

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Heterogeneity of breast cancer: etiology and clinical relevance

(2011) Vanessa Almendro et al.   Clinical & Translational Oncology

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene

(2011) John S. Welch   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Insight into the heterogeneity of breast cancer through next-generation sequencing

(2011) Hege G. Russnes et al.   JOURNAL OF CLINICAL INVESTIGATION

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

High-resolution characterization of a hepatocellular carcinoma genome

(2011) Yasushi Totoki et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

(2011) N. Agrawal et al.   SCIENCE

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

IntOGen: integration and data mining of multidimensional oncogenomic data

(2010) Gunes Gundem et al.   NATURE METHODS

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

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

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

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

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

(2009) Prateek Kumar et al.   Nature Protocols

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH