CONTRA: copy number analysis for targeted resequencing.

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat Genet (2012) 7.00

A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform (2013) 3.60

Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diagn (2013) 2.20

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics (2013) 2.07

Colon and endometrial cancers with mismatch repair deficiency can arise from somatic, rather than germline, mutations. Gastroenterology (2014) 1.93

EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol (2013) 1.90

Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas. Clin Cancer Res (2014) 1.86

Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes. Eur J Hum Genet (2014) 1.67

Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control. Biomed Res Int (2013) 1.61

Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis. J Mol Diagn (2016) 1.49

Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions. PLoS One (2015) 1.41

Genomic landscape of cutaneous T cell lymphoma. Nat Genet (2015) 1.27

The genetics of microdeletion and microduplication syndromes: an update. Annu Rev Genomics Hum Genet (2014) 1.16

CoNVEX: copy number variation estimation in exome sequencing data using HMM. BMC Bioinformatics (2013) 1.09

Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet (2013) 1.06

A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders. Genome Res (2013) 1.06

Application of whole exome sequencing to identify disease-causing variants in inherited human diseases. Genomics Inform (2012) 1.05

Identification of copy number variants from exome sequence data. BMC Genomics (2014) 1.01

Inferring copy number and genotype in tumour exome data. BMC Genomics (2014) 1.01

Improved molecular diagnosis by the detection of exonic deletions with target gene capture and deep sequencing. Genet Med (2014) 1.01

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. Bioinformatics (2013) 1.00

Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma. Pigment Cell Melanoma Res (2014) 0.98

The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. Front Genet (2013) 0.96

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Comput Biol (2016) 0.95

Multiphasic analysis of whole exome sequencing data identifies a novel mutation of ACTG1 in a nonsyndromic hearing loss family. BMC Genomics (2013) 0.93

Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors. Exp Mol Pathol (2015) 0.92

Multiplex target capture with double-stranded DNA probes. Genome Med (2013) 0.91

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. Bioinformatics (2014) 0.90

Whole-Exome Sequencing in the Differential Diagnosis of Primary Adrenal Insufficiency in Children. Front Endocrinol (Lausanne) (2015) 0.90

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment. PLoS One (2014) 0.89

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data. Genet Med (2015) 0.89

Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma. Oncotarget (2015) 0.86

Molecular and genetic diversity in the metastatic process of melanoma. J Pathol (2014) 0.86

Frequent alterations in cytoskeleton remodelling genes in primary and metastatic lung adenocarcinomas. Nat Commun (2015) 0.85

Detection of gene rearrangements in targeted clinical next-generation sequencing. J Mol Diagn (2014) 0.85

High frequency of germline TP53 mutations in a prospective adult-onset sarcoma cohort. PLoS One (2013) 0.85

Outlier-based identification of copy number variations using targeted resequencing in a small cohort of patients with Tetralogy of Fallot. PLoS One (2014) 0.84

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice. Nat Genet (2016) 0.84

Application of targeted multi-gene panel testing for the diagnosis of inherited peripheral neuropathy provides a high diagnostic yield with unexpected phenotype-genotype variability. BMC Med Genet (2015) 0.83

Allele-specific copy-number discovery from whole-genome and whole-exome sequencing. Nucleic Acids Res (2015) 0.82

Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. Funct Integr Genomics (2013) 0.82

Multiplexed direct genomic selection (MDiGS): a pooled BAC capture approach for highly accurate CNV and SNP/INDEL detection. Nucleic Acids Res (2014) 0.81

Integrated genomic analyses identify frequent gene fusion events and VHL inactivation in gastrointestinal stromal tumors. Oncotarget (2016) 0.81

New challenges for BRCA testing: a view from the diagnostic laboratory. Eur J Hum Genet (2016) 0.80

Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN. Wellcome Open Res (2016) 0.80

Platform comparison of detecting copy number variants with microarrays and whole-exome sequencing. Genom Data (2014) 0.79

Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods. J Mol Diagn (2016) 0.79

Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls. BMC Bioinformatics (2015) 0.79

Co-existence of BRAF and NRAS driver mutations in the same melanoma cells results in heterogeneity of targeted therapy resistance. Oncotarget (2016) 0.78

Estimation of copy number alterations from exome sequencing data. PLoS One (2012) 0.78

Assessing the reproducibility of exome copy number variations predictions. Genome Med (2016) 0.77

A case report and genetic characterization of a massive acinic cell carcinoma of the parotid with delayed distant metastases. Case Rep Oncol Med (2013) 0.77

Application of Circulating Tumor DNA as a Non-Invasive Tool for Monitoring the Progression of Colorectal Cancer. PLoS One (2016) 0.77

Mutational profiling of familial male breast cancers reveals similarities with luminal A female breast cancer with rare TP53 mutations. Br J Cancer (2014) 0.77

Use of autocorrelation scanning in DNA copy number analysis. Bioinformatics (2013) 0.77

SMAC Mimetic Birinapant plus Radiation Eradicates Human Head and Neck Cancers with Genomic Amplifications of Cell Death Genes FADD and BIRC2. Cancer Res (2016) 0.76

GROM-RD: resolving genomic biases to improve read depth detection of copy number variants. PeerJ (2015) 0.76

Target capture and massive sequencing of genes transcribed in Mytilus galloprovincialis. Biomed Res Int (2014) 0.76

Cost effective assay choice for rare disease study designs. Orphanet J Rare Dis (2015) 0.76

Identifying the clonal origin of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platforms. Oncotarget (2017) 0.75

A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data. BMC Bioinformatics (2016) 0.75

Sacral agenesis: a pilot whole exome sequencing and copy number study. BMC Med Genet (2016) 0.75

RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing. Cancer Inform (2016) 0.75

A scientific treatment approach for acute mast cell leukemia: using a strategy based on next-generation sequencing data. Blood Res (2016) 0.75

Receptor tyrosine kinase amplification is predictive of distant metastasis in patients with oral squamous cell carcinoma. Cancer Sci (2016) 0.75

An improved understanding of cancer genomics through massively parallel sequencing. Transl Cancer Res (2014) 0.75

Molecular genetic heterogeneity in undifferentiated endometrial carcinomas. Mod Pathol (2016) 0.75

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. Int J Genomics (2016) 0.75

cnvCapSeq: detecting copy number variation in long-range targeted resequencing data. Nucleic Acids Res (2014) 0.75

The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells. BMC Genomics (2016) 0.75

Validation of copy number variation analysis for next-generation sequencing diagnostics. Eur J Hum Genet (2017) 0.75

Mutation Screening of 1,237 Cancer Genes across Six Model Cell Lines of Basal-Like Breast Cancer. PLoS One (2015) 0.75

MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance. Proc SIAM Int Conf Data Min (2016) 0.75

ExCNVSS: A Noise-Robust Method for Copy Number Variation Detection in Whole Exome Sequencing Data. Biomed Res Int (2017) 0.75

Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2009) 67.17

BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63

Targeted capture and massively parallel sequencing of 12 human exomes. Nature (2009) 33.96

High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18

Computational methods for discovering structural variation with next-generation sequencing. Nat Methods (2009) 7.20

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97

Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A (2010) 5.60

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics (2011) 5.45

Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate. Am J Hum Genet (2010) 3.09

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics (2010) 2.79

Detecting copy number variation with mated short reads. Genome Res (2010) 2.75

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One (2011) 2.34

Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics (2011) 2.20

CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics (2010) 1.74

Gender differences in publication output: towards an unbiased metric of research performance. PLoS One (2006) 4.44

No evidence of clonal somatic genetic alterations in cancer-associated fibroblasts from human breast and ovarian carcinomas. Nat Genet (2008) 3.32

Co-evolution of tumor cells and their microenvironment. Trends Genet (2008) 3.08

Options available--from start to finish--for obtaining data from DNA microarrays II. Nat Genet (2002) 2.62

Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov (2008) 2.58

Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev (2011) 2.31

SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA (2011) 2.03

Exome sequencing identifies rare deleterious mutations in DNA repair genes FANCC and BLM as potential breast cancer susceptibility alleles. PLoS Genet (2012) 1.84

High-resolution single nucleotide polymorphism array analysis of epithelial ovarian cancer reveals numerous microdeletions and amplifications. Clin Cancer Res (2007) 1.81

IL6-STAT3-HIF signaling and therapeutic response to the angiogenesis inhibitor sunitinib in ovarian clear cell cancer. Clin Cancer Res (2011) 1.79

An activating Pik3ca mutation coupled with Pten loss is sufficient to initiate ovarian tumorigenesis in mice. J Clin Invest (2012) 1.79

Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics (2008) 1.60

Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis. PLoS One (2010) 1.60

The maturational trajectories of NREM and REM sleep durations differ across adolescence on both school-night and extended sleep. Am J Physiol Regul Integr Comp Physiol (2011) 1.54

Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer. PLoS One (2010) 1.54

Differential hypermethylation of SOCS genes in ovarian and breast carcinomas. Oncogene (2004) 1.51

Copy number analysis identifies novel interactions between genomic loci in ovarian cancer. PLoS One (2010) 1.50

Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. PLoS Negl Trop Dis (2010) 1.39

Analysis of RAD51C germline mutations in high-risk breast and ovarian cancer families and ovarian cancer patients. Hum Mutat (2011) 1.38

Sleep EEG changes during adolescence: an index of a fundamental brain reorganization. Brain Cogn (2009) 1.38

The adolescent decline of NREM delta, an indicator of brain maturation, is linked to age and sex but not to pubertal stage. Am J Physiol Regul Integr Comp Physiol (2006) 1.36

Are there any more ovarian tumor suppressor genes? A new perspective using ultra high-resolution copy number and loss of heterozygosity analysis. Genes Chromosomes Cancer (2009) 1.31

Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. J Biomed Biotechnol (2008) 1.29

Common origins of MDA-MB-435 cells from various sources with those shown to have melanoma properties. Clin Exp Metastasis (2004) 1.29

A specific role for AKT3 in the genesis of ovarian cancer through modulation of G(2)-M phase transition. Cancer Res (2006) 1.26

Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays. Cancer Res (2007) 1.25

Mutation and methylation analysis of the chromodomain-helicase-DNA binding 5 gene in ovarian cancer. Neoplasia (2008) 1.23

EDD, the human orthologue of the hyperplastic discs tumour suppressor gene, is amplified and overexpressed in cancer. Oncogene (2003) 1.23

The DNMT3B C-->T promoter polymorphism and risk of breast cancer in a British population: a case-control study. Breast Cancer Res (2004) 1.22

Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells. Genome Res (2011) 1.22

RNF43 is a tumour suppressor gene mutated in mucinous tumours of the ovary. J Pathol (2013) 1.20

BRAF/NRAS wild-type melanomas have a high mutation load correlating with histologic and molecular signatures of UV damage. Clin Cancer Res (2013) 1.18

Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. Hum Mutat (2005) 1.15

Mutation analysis of EP300 in colon, breast and ovarian carcinomas. Int J Cancer (2002) 1.15

Mutation analysis of PIK3CA and PIK3CB in esophageal cancer and Barrett's esophagus. Int J Cancer (2006) 1.13

Massively parallel sequencing and analysis of the Necator americanus transcriptome. PLoS Negl Trop Dis (2010) 1.12

Large-scale genomic analysis of ovarian carcinomas. Mol Oncol (2008) 1.12

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition. Nucleic Acids Res (2011) 1.11

Breast-cancer stromal cells with TP53 mutations. N Engl J Med (2008) 1.10

CoNVEX: copy number variation estimation in exome sequencing data using HMM. BMC Bioinformatics (2013) 1.09

An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data. Bioinformatics (2003) 1.08

Transforming growth factor beta receptor 1 polyalanine polymorphism and exon 5 mutation analysis in breast and ovarian cancer. Cancer Epidemiol Biomarkers Prev (2002) 1.08

Inferring copy number and genotype in tumour exome data. BMC Genomics (2014) 1.01

The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments. BMC Genomics (2009) 1.00

Pre-invasive ovarian mucinous tumors are characterized by CDKN2A and RAS pathway aberrations. Clin Cancer Res (2012) 0.99

Genome-wide association study of subtype-specific epithelial ovarian cancer risk alleles using pooled DNA. Hum Genet (2013) 0.99

Topographic differences in the adolescent maturation of the slow wave EEG during NREM sleep. Sleep (2011) 0.97

A molecular model for sporadic human aneuploidy. Trends Genet (2006) 0.97

Frequent somatic mutations of GATA3 in non-BRCA1/BRCA2 familial breast tumors, but not in BRCA1-, BRCA2- or sporadic breast tumors. Breast Cancer Res Treat (2009) 0.96

Identification of copy number alterations associated with the progression of DCIS to invasive ductal carcinoma. Breast Cancer Res Treat (2011) 0.96

Genetic and epigenetic analysis of CHEK2 in sporadic breast, colon, and ovarian cancers. Clin Cancer Res (2006) 0.96

Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations. Bioinformatics (2010) 0.96

Functional analysis of genes in regions commonly amplified in high-grade serous and endometrioid ovarian cancer. Clin Cancer Res (2013) 0.95

FGFR2 mutations are rare across histologic subtypes of ovarian cancer. Gynecol Oncol (2010) 0.95

Kinetics of non-rapid eye movement delta production across sleep and waking in young and elderly normal subjects: theoretical implications. Sleep (2003) 0.94

Longitudinal sleep EEG trajectories indicate complex patterns of adolescent brain maturation. Am J Physiol Regul Integr Comp Physiol (2012) 0.94

Next-generation sequence analysis of cancer xenograft models. PLoS One (2013) 0.94

Rare variants in XRCC2 as breast cancer susceptibility alleles. J Med Genet (2012) 0.94

Genetic analysis of cancer-implicated MicroRNA in ovarian cancer. Clin Cancer Res (2008) 0.93

Oncolysis of human ovarian cancers by echovirus type 1. Int J Cancer (2005) 0.92

Effects of abdominal binding on cardiorespiratory function in cervical spinal cord injury. Respir Physiol Neurobiol (2011) 0.92

BRCA2 Polymorphic Stop Codon K3326X and the Risk of Breast, Prostate, and Ovarian Cancers. J Natl Cancer Inst (2015) 0.90

Kinetics of NREM delta EEG power density across NREM periods depend on age and on delta-band designation. Sleep (2007) 0.90

MIRAGAA--a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer. Bioinformatics (2009) 0.90

Human perforin mutations and susceptibility to multiple primary cancers. Oncoimmunology (2013) 0.90

Effects of spinal cord lesion level upon thermoregulation during exercise in the heat. Med Sci Sports Exerc (2003) 0.90

Central carbon metabolism of Leishmania parasites. Parasitology (2010) 0.90

Image-guided sampling reveals increased stroma and lower glandular complexity in mammographically dense breast tissue. Breast Cancer Res Treat (2011) 0.89

The HER2 I655V polymorphism and risk of breast cancer in women < age 40 years. Cancer Epidemiol Biomarkers Prev (2003) 0.88

Navigating the challenge of tumor heterogeneity in cancer therapy. Cancer Discov (2014) 0.87

Analysis of RAD51D in ovarian cancer patients and families with a history of ovarian or breast cancer. PLoS One (2013) 0.86

Analysis of the mitogen-activated protein kinase kinase 4 (MAP2K4) tumor suppressor gene in ovarian cancer. BMC Cancer (2011) 0.86

PIK3CA mutations in ovarian cancer. Clin Cancer Res (2005) 0.86