Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics

GT-WGS: an efficient and economic tool for large-scale WGS analyses based on the AWS cloud service

(2018) Yiqi Wang et al.   BMC GENOMICS

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

The identification of growth, immune related genes and marker discovery through transcriptome in the yellow drum (Nibea albiflora)

(2018) Zhaofang Han et al.   Genes & Genomics

Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature

(2018) Katharina Schwarze et al.   GENETICS IN MEDICINE

Massively parallel sequencing analysis of mucinous ovarian carcinomas: genomic profiling and differential diagnoses

(2018) Jennifer J. Mueller et al.   GYNECOLOGIC ONCOLOGY

The Landscape of Somatic Genetic Alterations in Breast Cancers From ATM Germline Mutation Carriers

(2018) Britta Weigelt et al.   JNCI-Journal of the National Cancer Institute

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion

(2018) Shanrong Zhao et al.   Scientific Reports

The Landscape of Somatic Genetic Alterations in Breast Cancers From ATM Germline Mutation Carriers

(2018) Britta Weigelt et al.   JNCI-Journal of the National Cancer Institute

Exosomes in Cancer Liquid Biopsy: A Focus on Breast Cancer

(2018) Sina Halvaei et al.   Molecular Therapy-Nucleic Acids

Associations of Combined Genetic and Lifestyle Risks With Incident Cardiovascular Disease and Diabetes in the UK Biobank Study

(2018) M. Abdullah Said et al.   JAMA Cardiology

Viewpoint: When Will AI Exceed Human Performance? Evidence from AI Experts

(2018) Katja Grace et al.   JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations

(2018) Amit V. Khera et al.   NATURE GENETICS

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

(2018) Alexandre Coudray et al.   PeerJ

Whole exome sequencing: Uncovering causal genetic variants for ocular diseases

(2017) Shashank Gupta et al.   EXPERIMENTAL EYE RESEARCH

Racial/ethnic differences in multiple-gene sequencing results for hereditary cancer risk

(2017) Jennifer L Caswell-Jin et al.   GENETICS IN MEDICINE

A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology

(2017) Lisenka E.L.M. Vissers et al.   GENETICS IN MEDICINE

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis

(2017) Yan Guo et al.   GENOMICS

PERCH: A Unified Framework for Disease Gene Prioritization

(2017) Bing-Jian Feng   HUMAN MUTATION

Big Data Analytics for Genomic Medicine

(2017) Karen He et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Rare Variant, Gene-Based Association Study of Hereditary Melanoma Using Whole-Exome Sequencing

(2017) Mykyta Artomov et al.   JNCI-Journal of the National Cancer Institute

Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data

(2017) Bo-Young Kim et al.   PLoS One

CNNdel: Calling Structural Variations on Low Coverage Data Based on Convolutional Neural Networks

(2017) Jing Wang et al.   Biomed Research International

Rare Variant, Gene-Based Association Study of Hereditary Melanoma Using Whole-Exome Sequencing

(2017) Mykyta Artomov et al.   JNCI-Journal of the National Cancer Institute

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce

(2017) Dries Decap et al.   PLoS One

Whole Exome Sequencing to Identify Genetic Variants Associated with Raised Atherosclerotic Lesions in Young Persons

(2017) James E. Hixson et al.   Scientific Reports

Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity

(2017) Qingyu Wang et al.   Scientific Reports

Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium

(2016) Laura M. Amendola et al.   AMERICAN JOURNAL OF HUMAN GENETICS

UCSC Data Integrator and Variant Annotation Integrator

(2016) Angie S. Hinrichs et al.   BIOINFORMATICS

Whole-exome sequencing to identify genetic risk variants underlying inhibitor development in severe hemophilia A patients

(2016) M. M. Gorski et al.   BLOOD

Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data

(2016) Ítalo Faria do Valle et al.   BMC BIOINFORMATICS

VarElect: the phenotype-based variation prioritizer of the GeneCards Suite

(2016) Gil Stelzer et al.   BMC GENOMICS

Utilization of Whole Exome Sequencing to Identify Causative Mutations in Familial Congenital Heart Disease

(2016) Stephanie LaHaye et al.   Circulation-Cardiovascular Genetics

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Identification of Heterozygous Single- and Multi-exon Deletions in IL7R by Whole Exome Sequencing

(2016) Karin R. Engelhardt et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Clonal evolution of chemotherapy-resistant urothelial carcinoma

(2016) Bishoy M Faltas et al.   NATURE GENETICS

Quantification of private information leakage from phenotype-genotype data: linking attacks

(2016) Arif Harmanci et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort

(2016) Tomasz Gambin et al.   NUCLEIC ACIDS RESEARCH

The ExAC browser: displaying reference data information from over 60 000 exomes

(2016) Konrad J. Karczewski et al.   NUCLEIC ACIDS RESEARCH

Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2

(2016) Romina D'Aurizio et al.   NUCLEIC ACIDS RESEARCH

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data

(2016) Shani Ben-Ari Fuchs et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

(2016) Tonia C. Carter et al.   Journal of Healthcare Engineering

Utilization of Whole Exome Sequencing to Identify Causative Mutations in Familial Congenital Heart Disease

(2016) Stephanie LaHaye et al.   Circulation-Cardiovascular Genetics

VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

(2016) Ramesh Menon et al.   3 Biotech

VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

(2016) Ramesh Menon et al.   3 Biotech

Racial/Ethnic Disparities in Genomic Sequencing

(2016) Daniel E. Spratt et al.   JAMA Oncology

Privacy Risks from Genomic Data-Sharing Beacons

(2015) Suyash S. Shringarpure et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

(2015) Jessica X. Chong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ASEQ: fast allele-specific studies from next-generation sequencing data

(2015) Alessandro Romanel et al.   BMC Medical Genomics

From big data analysis to personalized medicine for all: challenges and opportunities

(2015) Akram Alyass et al.   BMC Medical Genomics

WGSA: an annotation pipeline for human genome sequencing studies

(2015) Xiaoming Liu et al.   JOURNAL OF MEDICAL GENETICS

Genome in a bottle—a human DNA standard

(2015)   NATURE BIOTECHNOLOGY

Next-generation diagnostics and disease-gene discovery with the Exomiser

(2015) Damian Smedley et al.   Nature Protocols

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

(2015) Xutao Deng et al.   NUCLEIC ACIDS RESEARCH

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

(2015) Aziz Belkadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A One-Page Summary Report of Genome Sequencing for the Healthy Adult

(2015) Jason L. Vassy et al.   Public Health Genomics

How to know when physicians are ready for genomic medicine

(2015) Jason L. Vassy et al.   Science Translational Medicine

De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries

(2015) Namjin Cho et al.   Nature Communications

Whole-exome tumor sequencing study in biliary cancer patients with a response to MEK inhibitors

(2015) Daniel H. Ahn et al.   Oncotarget

Performance comparison of four commercial human whole-exome capture platforms

(2015) Daichi Shigemizu et al.   Scientific Reports

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Complex nature of apparently balanced chromosomal rearrangements in patients with autism spectrum disorder

(2015) Anne-Claude Tabet et al.   Molecular Autism

Pembrolizumab

(2015) Leila Khoja et al.   Journal for ImmunoTherapy of Cancer

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Individualized Medicine from Prewomb to Tomb

(2014) Eric J. Topol   CELL

Summarizing polygenic risks for complex diseases in a clinical whole-genome report

(2014) Sek Won Kong et al.   GENETICS IN MEDICINE

Prioritization of neurodevelopmental disease genes by discovery of new mutations

(2014) Alexander Hoischen et al.   NATURE NEUROSCIENCE

Disentangling the heterogeneity of autism spectrum disorder through genetic findings

(2014) Shafali S. Jeste et al.   Nature Reviews Neurology

The personal genome browser: visualizing functions of genetic variants

(2014) Liran Juan et al.   NUCLEIC ACIDS RESEARCH

OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

(2014) Pengyuan Zhu et al.   PLoS One

Pharmacogenomics: Current State-of-the-Art

(2014) Daniel Carr et al.   Genes

The struggle to find reliable results in exome sequencing data: filtering out Mendelian errors

(2014) Zubin H. Patel et al.   Frontiers in Genetics

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies

(2013) Tim Beck et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The promise of whole-exome sequencing in medical genetics

(2013) Bahareh Rabbani et al.   JOURNAL OF HUMAN GENETICS

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The role of replicates for error mitigation in next-generation sequencing

(2013) Kimberly Robasky et al.   NATURE REVIEWS GENETICS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing

(2013) Chih-Ming Hung et al.   PLoS One

LIFE SCIENCE TECHNOLOGIES: Exome Sequencing: Toward an Interpretable Genome

(2013) J. M. Perkel   SCIENCE

Identifying Personal Genomes by Surname Inference

(2013) M. Gymrek et al.   SCIENCE

CAN I ACCESS MY PERSONAL GENOME? THE CURRENT LEGAL POSITION IN THE UK

(2013) Jane Kaye et al.   Medical Law Review

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Annual Report to the Nation on the status of cancer, 1975-2008, featuring cancers associated with excess weight and lack of sufficient physical activity

(2012) Christie Eheman et al.   CANCER

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

Global cancer statistics

(2011) Ahmedin Jemal et al.   CA-A CANCER JOURNAL FOR CLINICIANS

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21

(2011) Christopher A Haiman et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

(2011) J. Zhang et al.   Database-The Journal of Biological Databases and Curation

Whole-Exome Sequencing Identifies Homozygous AFG3L2 Mutations in a Spastic Ataxia-Neuropathy Syndrome Linked to Mitochondrial m-AAA Proteases

(2011) Tyler Mark Pierson et al.   PLoS Genetics

Pharmacogenetics of cytochrome P450 (CYP) in the elderly

(2010) Davide Seripa et al.   AGEING RESEARCH REVIEWS

BS Seeker: precise mapping for bisulfite sequencing

(2010) Pao-Yang Chen et al.   BMC BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Integrating genetic risk assessment for multi-factorial conditions into primary care

(2009) Alison Metcalfe et al.   Primary Health Care Research and Development

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The Genome Gets Personal—Almost

(2008) W. Gregory Feero   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Trends in Survival Over the Past Two Decades Among White and Black Patients With Newly Diagnosed Stage IV Breast Cancer

(2008) Shaheenah Dawood et al.   JOURNAL OF CLINICAL ONCOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

(2008) Nils Homer et al.   PLoS Genetics