CopywriteR: DNA copy number detection from off-target sequence data

Detailed imaging and genetic analysis reveal a secondaryBRAFL505Hresistance mutation and extensive intrapatient heterogeneity in metastaticBRAFmutant melanoma patients treated with vemurafenib

(2015) Marlous Hoogstraat et al.   Pigment Cell & Melanoma Research

Detection of Somatic Copy Number Alterations in Cancer Using Targeted Exome Capture Sequencing

(2015) Robert J. Lonigro et al.   NEOPLASIA

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

(2014) Ilari Scheinin et al.   GENOME RESEARCH

An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data

(2014) Renjie Tan et al.   HUMAN MUTATION

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing

(2013) Carson Holt et al.   BIOINFORMATICS

Detection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing

(2013) Joep de Ligt et al.   HUMAN MUTATION

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Finding the lost treasures in exome sequencing data

(2013) David C. Samuels et al.   TRENDS IN GENETICS

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A regression model for estimating DNA copy number applied to capture sequencing data

(2012) Guillem J. Rigaill et al.   BIOINFORMATICS

Focal aberrations indicateEYA2andhsa-miR-375as oncogene and tumor suppressor in cervical carcinogenesis

(2012) Mariska Bierkens et al.   GENES CHROMOSOMES & CANCER

Copy number variation detection and genotyping from exome sequence data

(2012) N. Krumm et al.   GENOME RESEARCH

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Read count approach for DNA copy number variants detection

(2011) Alberto Magi et al.   BIOINFORMATICS

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Primary Colorectal Cancers and Their Subsequent Hepatic Metastases Are Genetically Different: Implications for Selection of Patients for Targeted Treatment

(2011) J. S. Vermaat et al.   CLINICAL CANCER RESEARCH

CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material

(2011) Oscar Krijgsman et al.   GENES CHROMOSOMES & CANCER

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) Laura Poliseno et al.   NATURE

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

(2010) Henry M. Wood et al.   NUCLEIC ACIDS RESEARCH

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

The pitfalls of platform comparison: DNA copy number array technologies assessed

(2009) Christina Curtis et al.   BMC GENOMICS

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Genomic Loss of microRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer

(2008) S. Varambally et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY