Next generation sequencing: implications in personalized medicine and pharmacogenomics

Comparison of Next-Generation Sequencing and Mutation-Specific Platforms in Clinical Practice

(2015) John W. J. Hinrichs et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Cypiripi: exact genotyping ofCYP2D6using high-throughput sequencing data

(2015) Ibrahim Numanagić et al.   BIOINFORMATICS

Comparison of Custom Capture for Targeted Next-Generation DNA Sequencing

(2015) Eric Samorodnitsky et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure

(2014) Sofiane Mohamed et al.   AIDS

High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

(2014) Guillaume Girault et al.   BMC GENOMICS

Integrated Next-Generation Sequencing and Avatar Mouse Models for Personalized Cancer Treatment

(2014) E. Garralda et al.   CLINICAL CANCER RESEARCH

Identification of Immunity-Related Genes in Ostrinia furnacalis against Entomopathogenic Fungi by RNA-Seq Analysis

(2014) Yang Liu et al.   PLoS One

Challenges in pharmacogenetics

(2013) Ingolf Cascorbi et al.   EUROPEAN JOURNAL OF CLINICAL PHARMACOLOGY

Meeting summary: ethical aspects of whole exome and whole genome sequencing studies (WES/WGS) in rare diseases, Tel Aviv, Israel, January 2013

(2013) LUBA FARBEROV et al.   Genetics Research

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

(2013) P. Jia et al.   GENOME RESEARCH

Multiplexed deep sequencing analysis of ALK kinase domain identifies resistance mutations in relapsed patients following crizotinib treatment

(2013) Donghui Huang et al.   GENOMICS

Pharmacogenetics: Implications of race and ethnicity on defining genetic profiles for personalized medicine

(2013) Victor E. Ortega et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The promise of whole-exome sequencing in medical genetics

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

The Database of Genomic Variants: a curated collection of structural variation in the human genome

(2013) Jeffrey R. MacDonald et al.   NUCLEIC ACIDS RESEARCH

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing

(2013) Marisa P. Dolled-Filhart et al.   TheScientificWorldJOURNAL

Whole-Genome Sequencing of Trypanosoma brucei Reveals Introgression between Subspecies That Is Associated with Virulence

(2013) I. Goodhead et al.   mBio

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes

(2012) A. Albrechtsen et al.   DIABETOLOGIA

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes

(2012) A. Gall et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders

(2012) Bahareh Rabbani et al.   JOURNAL OF HUMAN GENETICS

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

(2012)   NATURE

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Whole-Exome Sequencing Efficiently Detects Rare Mutations in Autosomal Recessive Nonsyndromic Hearing Loss

(2012) Oscar Diaz-Horta et al.   PLoS One

Bisphenol A alters the development of the rhesus monkey mammary gland

(2012) A. P. Tharp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-generation sequencing of dried blood spot specimens: a novel approach to HIV drug-resistance surveillance

(2011) Hezhao Ji et al.   ANTIVIRAL THERAPY

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

Trastuzumab combined to neoadjuvant chemotherapy in patients with HER2-positive breast cancer: A systematic review and meta-analysis

(2011) Antonis Valachis et al.   BREAST

CPIC: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network

(2011) M V Relling et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Rep-Seq: uncovering the immunological repertoire through next-generation sequencing

(2011) Jennifer Benichou et al.   IMMUNOLOGY

Gain-of-function humanSTAT1mutations impair IL-17 immunity and underlie chronic mucocutaneous candidiasis

(2011) Luyan Liu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

One genome, two haplotypes

(2011) Nicole Rusk   NATURE METHODS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Deep Sequencing of Patient Genomes for Disease Diagnosis: When Will It Become Routine?

(2011) S. F. Kingsmore et al.   Science Translational Medicine

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

(2011) J. T. Dudley et al.   Science Translational Medicine

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

Molecular biomarkers: a US FDA effort

(2010) Huixiao Hong et al.   Biomarkers in Medicine

Challenges of sequencing human genomes

(2010) D. C. Koboldt et al.   BRIEFINGS IN BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

A window into third-generation sequencing

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

Clinical assessment incorporating a personal genome

(2010) Euan A Ashley et al.   LANCET

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis

(2010) Sergio E. Baranzini et al.   NATURE

Graphene as a subnanometre trans-electrode membrane

(2010) S. Garaj et al.   NATURE

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Nanotechnology: Holes with an edge

(2010) Hagan Bayley   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Genome-wide association studies in pharmacogenomics

(2010) Ann K. Daly   NATURE REVIEWS GENETICS

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

(2010) A. M. Smith et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. elegans

(2010) Katherine P. Weber et al.   PLoS One

Semiconductors Inspire New Sequencing Technologies

(2010) E. Pennisi   SCIENCE

Pharmacogenetics of Warfarin

(2009) Farhad Kamali et al.   Annual Review of Medicine

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

A Branched-Chain Amino Acid-Related Metabolic Signature that Differentiates Obese and Lean Humans and Contributes to Insulin Resistance

(2009) Christopher B. Newgard et al.   Cell Metabolism

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlates of Metabolic Abnormalities in Bipolar I Disorder at Initiation of Acute Phase Treatment

(2009) Byungsu Kim et al.   Psychiatry Investigation

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Human metabolic phenotype diversity and its association with diet and blood pressure

(2008) Elaine Holmes et al.   NATURE

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

Common variants in the GDF5-UQCC region are associated with variation in human height

(2008) Serena Sanna et al.   NATURE GENETICS

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

(2008) Anton Valouev et al.   NATURE METHODS

Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures

(2008) J. Korlach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Therapy and epidemiology of autism–clostridial spores as key elements

(2007) Sydney M. Finegold   MEDICAL HYPOTHESES