Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

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

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis

(2012) L. J. M. Coin et al.   BIOINFORMATICS

CONTRA: copy number analysis for targeted resequencing

(2012) Jason Li et al.   BIOINFORMATICS

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

(2012) Vincent Plagnol et al.   BIOINFORMATICS

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

Copy number variation detection and genotyping from exome sequence data

(2012) N. Krumm 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

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

An integrative probabilistic model for identification of structural variation in sequencing data

(2012) Suzanne S Sindi et al.   GENOME BIOLOGY

Read count approach for DNA copy number variants detection

(2011) Alberto Magi et al.   BIOINFORMATICS

SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data

(2011) J. Zhang et al.   BIOINFORMATICS

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

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

(2011) Arief Gusnanto et al.   BIOINFORMATICS

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

(2011) Alexej Abyzov et al.   BIOINFORMATICS

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

(2011) Xutao Deng   BMC BIOINFORMATICS

Identification of genomic indels and structural variations using split reads

(2011) Zhengdong D Zhang et al.   BMC GENOMICS

Accurate and exact CNV identification from targeted high-throughput sequence data

(2011) Alex S Nord et al.   BMC GENOMICS

Simultaneous structural variation discovery among multiple paired-end sequenced genomes

(2011) F. Hormozdiari et al.   GENOME RESEARCH

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

(2011) Robert E Handsaker et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

(2011) Ji Qi et al.   NUCLEIC ACIDS RESEARCH

Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm

(2011) Alberto Magi et al.   NUCLEIC ACIDS RESEARCH

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

(2011) Christopher A. Miller et al.   PLoS One

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

(2010) Valentina Boeva et al.   BIOINFORMATICS

CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

(2010) Sergii Ivakhno 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

SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data

(2010) H. J. Abel et al.   BIOINFORMATICS

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data

(2010) Tae-Min Kim et al.   BMC BIOINFORMATICS

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

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

(2010) Lira Mamanova et al.   NATURE METHODS

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data

(2009) Qunyuan Zhang et al.   BIOINFORMATICS

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi 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

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Challenges for CNV interpretation in clinical molecular karyotyping: Lessons learned from a 1001 sample experience

(2009) Karen Buysse et al.   European Journal of Medical Genetics

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

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

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

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

(2009) Ken Chen et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

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

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS

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

(2008) Derek Y Chiang et al.   NATURE METHODS