Application of second-generation sequencing to cancer genomics

Microindel detection in short-read sequence data

(2010) Peter Krawitz et al.   BIOINFORMATICS

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

(2010) Rodrigo Goya et al.   BIOINFORMATICS

Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing

(2010) Hane Lee et al.   BMC GENOMICS

Genome variation discovery with high-throughput sequencing data

(2010) A. V. Dalca et al.   BRIEFINGS IN BIOINFORMATICS

Digital transcriptome profiling from attomole-level RNA samples

(2010) F. Ozsolak et al.   GENOME RESEARCH

Integrative analysis of the melanoma transcriptome

(2010) M. F. Berger et al.   GENOME RESEARCH

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

(2010) Ryan D Morin et al.   NATURE GENETICS

FRT-seq: amplification-free, strand-specific transcriptome sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

(2010) Brian B. Tuch et al.   PLoS One

Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing

(2010) R. J. Leary et al.   Science Translational Medicine

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line

(2010) Michael James Clark et al.   PLoS Genetics

Methods for Genomic Partitioning

(2009) Emily H. Turner et al.   Annual Review of Genomics and Human Genetics

HI: haplotype improver using paired-end short reads

(2009) Q. Long et al.   BIOINFORMATICS

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

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

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

A transcriptional sketch of a primary human breast cancer by 454 deep sequencing

(2009) Alessandro Guffanti et al.   BMC GENOMICS

Digital PCR provides sensitive and absolute calibration for high throughput sequencing

(2009) Richard A White et al.   BMC GENOMICS

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction

(2009) Ji Luo et al.   CELL

The ethical use of existing samples for genome research

(2009) Oliver F Bathe et al.   GENETICS IN MEDICINE

Identification of rare cancer driver mutations by network reconstruction

(2009) A. Torkamani et al.   GENOME RESEARCH

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The SAAPdb web resource: A large-scale structural analysis of mutant proteins

(2009) Jacob M. Hurst et al.   HUMAN MUTATION

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer

(2009) Xiao-Song Wang et al.   NATURE BIOTECHNOLOGY

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Somatic and germline genetics at the JAK2 locus

(2009) Peter J Campbell   NATURE GENETICS

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

Quantification of rare allelic variants from pooled genomic DNA

(2009) Todd E Druley et al.   NATURE METHODS

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

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mutation ofFOXL2in Granulosa-Cell Tumors of the Ovary

(2009) Sohrab P. Shah et al.   NEW ENGLAND JOURNAL OF MEDICINE

ChimerDB 2.0—a knowledgebase for fusion genes updated

(2009) Pora Kim et al.   NUCLEIC ACIDS RESEARCH

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis

(2009) Michal R. Schweiger et al.   PLoS One

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Sequence and Structure Signatures of Cancer Mutation Hotspots in Protein Kinases

(2009) Anshuman Dixit et al.   PLoS One

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

(2009) Qi Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation patterns in cancer genomes

(2009) A. F. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer-associated mutations are preferentially distributed in protein kinase functional sites

(2009) Jose M. G. Izarzugaza et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Smoothened Mutation Confers Resistance to a Hedgehog Pathway Inhibitor in Medulloblastoma

(2009) R. L. Yauch et al.   SCIENCE

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

(2009) S. D. Boyd et al.   Science Translational Medicine

Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins

(2009) Hedi Hegyi 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

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

(2009) Joshua Z Levin et al.   GENOME BIOLOGY

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Predicting functional regulatory polymorphisms

(2008) Ali Torkamani et al.   BIOINFORMATICS

Probabilistic base calling of Solexa sequencing data

(2008) Jacques Rougemont et al.   BMC BIOINFORMATICS

Prediction of Cancer Driver Mutations in Protein Kinases

(2008) A. Torkamani et al.   CANCER RESEARCH

Cancers Exhibit a Mutator Phenotype: Clinical Implications

(2008) L. A. Loeb et al.   CANCER RESEARCH

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

(2008) O. A. Hampton et al.   GENOME RESEARCH

Computational prediction of the functional effects of amino acid substitutions in signal peptides using a model-based approach

(2008) Lawrence S. Hon et al.   HUMAN MUTATION

KLF6 and TP53 mutations are a rare event in prostate cancer: distinguishing between Taq polymerase artifacts and true mutations

(2008) Laia Agell et al.   MODERN PATHOLOGY

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

(2008) P. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome sequencing of malignant pleural mesothelioma tumors

(2008) D. J. Sugarbaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

(2008) Ali Bashir et al.   PLoS Computational Biology