Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants

GOLPH3 Links the Golgi, DNA Damage, and Cancer

(2015) M. D. Buschman et al.   CANCER RESEARCH

The emerging roles of ARID1A in tumor suppression

(2014) Ren-Chin Wu et al.   CANCER BIOLOGY & THERAPY

PLEKHA5 as a Biomarker and Potential Mediator of Melanoma Brain Metastasis

(2014) L. B. Jilaveanu et al.   CLINICAL CANCER RESEARCH

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

Structural Genomic Variation as Risk Factor for Idiopathic Recurrent Miscarriage

(2014) Liina Nagirnaja et al.   HUMAN MUTATION

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer

(2014) Serena Nik-Zainal et al.   NATURE GENETICS

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

(2014) Kai Wang et al.   NATURE GENETICS

GOLPH3 high expression predicts poor prognosis in patients with resected non-small cell lung cancer: an immunohistochemical analysis

(2014) Yu Zhang et al.   TUMOR BIOLOGY

Integrated analysis of germline and somatic variants in ovarian cancer

(2014) Krishna L. Kanchi et al.   Nature Communications

Exome sequencing identifies an MLL3 gene germ line mutation in a pedigree of colorectal cancer and acute myeloid leukemia

(2013) W.-D. Li et al.   BLOOD

Depletion of a Putatively Druggable Class of Phosphatidylinositol Kinases Inhibits Growth of p53-Null Tumors

(2013) Brooke M. Emerling et al.   CELL

Does germ-line deletion of the PIP gene constitute a widespread risk for cancer?

(2013) Amanda G Silva et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Expression of mammaglobin and gross cystic disease fluid protein-15 in breast carcinomas

(2013) Ming-Hua Luo et al.   HUMAN PATHOLOGY

Novel Germline Mutation in the Transmembrane Domain of HER2 in Familial Lung Adenocarcinomas

(2013) Hiromasa Yamamoto et al.   JNCI-Journal of the National Cancer Institute

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Prognosis of metastatic gastric and gastroesophageal junction cancer by HER2 status: a European and USA International collaborative analysis

(2012) Y. Y. Janjigian et al.   ANNALS OF ONCOLOGY

Overexpression of GOLPH3 Promotes Proliferation and Tumorigenicity in Breast Cancer via Suppression of the FOXO1 Transcription Factor

(2012) Z. Zeng et al.   CLINICAL CANCER RESEARCH

Altered LKB1/AMPK/TSC1/TSC2/mTOR signaling causes disruption of Sertoli cell polarity and spermatogenesis

(2012) Pradeep S. Tanwar et al.   HUMAN MOLECULAR GENETICS

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

(2012) Akihiro Fujimoto et al.   NATURE GENETICS

Exome sequencing of liver fluke–associated cholangiocarcinoma

(2012) Choon Kiat Ong et al.   NATURE GENETICS

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes

(2012) Zhi Jiang Zang et al.   NATURE GENETICS

Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation

(2012) Jin P. Szatkiewicz et al.   NUCLEIC ACIDS 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

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants

(2011) Dalila Pinto et al.   NATURE BIOTECHNOLOGY

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

(2011) Robert E Handsaker et al.   NATURE GENETICS

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

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

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

(2010) Valentina Boeva et al.   BIOINFORMATICS

Germline copy number variation and cancer risk

(2010) Roland P Kuiper et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Germline copy number variations in BRCA1-associated ovarian cancer patients

(2010) Kosuke Yoshihara et al.   GENES CHROMOSOMES & CANCER

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma

(2010) Siân Jones et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide screen of promoter methylation identifies novel markers in melanoma

(2009) Y. Koga et al.   GENOME RESEARCH

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

(2009) F. Hormozdiari et al.   GENOME RESEARCH

TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals

(2009) A. Chase et al.   HAEMATOLOGICA

GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer

(2009) Kenneth L. Scott et al.   NATURE

Copy number variation at 1q21.1 associated with neuroblastoma

(2009) Sharon J. Diskin et al.   NATURE

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

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

(2009) Ken Chen et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

Aberrant CpG island methylation in acute myeloid leukemia is accentuated at relapse

(2008) H. Kroeger et al.   BLOOD

Fast stable direct fitting and smoothness selection for generalized additive models

(2008) Simon N. Wood   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Large recurrent microdeletions associated with schizophrenia

(2008) Hreinn Stefansson et al.   NATURE

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

(2008) Derek Y Chiang et al.   NATURE METHODS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One

Excessive genomic DNA copy number variation in the Li-Fraumeni cancer predisposition syndrome

(2008) A. Shlien et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA