Towards precision medicine

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

Integration of string and de Bruijn graphs for genome assembly

(2016) Yao-Ting Huang et al.   BIOINFORMATICS

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

(2016) Kevin E. Fisher et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

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

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

(2016) Julian R. Homburger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reclassification of genetic-based risk predictions as GWAS data accumulate

(2016) Joel Krier et al.   Genome Medicine

Medical implications of technical accuracy in genome sequencing

(2016) Rachel L. Goldfeder et al.   Genome Medicine

Taming the genome: towards better genetic test interpretation

(2016) Colleen Caleshu et al.   Genome Medicine

De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects

(2016) James R. Priest et al.   PLoS Genetics

Next-Generation Sequencing in Oncology in the Era of Precision Medicine

(2016) Gideon M. Blumenthal et al.   JAMA Oncology

The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States

(2015) Katarzyna Bryc et al.   AMERICAN JOURNAL OF HUMAN GENETICS

DNA Triplet Repeat Expansion and Mismatch Repair

(2015) Ravi R. Iyer et al.   Annual Review of Biochemistry

Preemptive Clinical Pharmacogenetics Implementation: Current Programs in Five US Medical Centers

(2015) Henry M. Dunnenberger et al.   Annual Review of Pharmacology and Toxicology

QVZ: lossy compression of quality values

(2015) Greg Malysa et al.   BIOINFORMATICS

Immune Checkpoint Targeting in Cancer Therapy: Toward Combination Strategies with Curative Potential

(2015) Padmanee Sharma et al.   CELL

Clinical application of whole-exome sequencing across clinical indications

(2015) Kyle Retterer et al.   GENETICS IN MEDICINE

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

The Undiagnosed Diseases Network of the National Institutes of Health

(2015) William A. Gahl et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The Precision Medicine Initiative

(2015) Euan A. Ashley   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Pooled Analysis of Long-Term Survival Data From Phase II and Phase III Trials of Ipilimumab in Unresectable or Metastatic Melanoma

(2015) Dirk Schadendorf et al.   JOURNAL OF CLINICAL ONCOLOGY

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

Quality score compression improves genotyping accuracy

(2015) Y William Yu et al.   NATURE BIOTECHNOLOGY

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Abundant contribution of short tandem repeats to gene expression variation in humans

(2015) Melissa Gymrek et al.   NATURE GENETICS

Systematic discovery of complex insertions and deletions in human cancers

(2015) Kai Ye et al.   NATURE MEDICINE

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Genetic variation and the de novo assembly of human genomes

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

Lumacaftor–Ivacaftor in Patients with Cystic Fibrosis Homozygous for Phe508del CFTR

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

ClinGen — The Clinical Genome Resource

(2015) Heidi L. Rehm et al.   NEW ENGLAND JOURNAL OF MEDICINE

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

Stevens–Johnson syndrome and toxic epidermal necrolysis: an update on pharmacogenetics studies in drug-induced severe skin reaction

(2015) Sara Rufini et al.   PHARMACOGENOMICS

Unmet needs: Research helps regulators do their jobs

(2015) Russ B. Altman et al.   Science Translational Medicine

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly

(2015) Rendong Yang et al.   Genome Medicine

Targeted therapies to improve CFTR function in cystic fibrosis

(2015) Malcolm Brodlie et al.   Genome Medicine

Achieving high-sensitivity for clinical applications using augmented exome sequencing

(2015) Anil Patwardhan et al.   Genome Medicine

Big Data: Astronomical or Genomical?

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

Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data

(2015) Frederick E. Dewey et al.   PLoS Genetics

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

Lumacaftor alone and combined with ivacaftor: preclinical and clinical trial experience of F508del CFTR correction

(2015) John J. Brewington et al.   Expert Review of Respiratory Medicine

Leading the way to genomic medicine

(2014) Teri A. Manolio et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

(2014) Reece K. Hart et al.   BIOINFORMATICS

Incorporation of Pharmacogenomics into Routine Clinical Practice: the Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline Development Process

(2014) Kelly Caudle et al.   CURRENT DRUG METABOLISM

The impact of chromosomal microarray on clinical management: a retrospective analysis

(2014) Lindsay B. Henderson et al.   GENETICS IN MEDICINE

Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort

(2014) Kyle Retterer et al.   GENETICS IN MEDICINE

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Molecular diagnosis of long QT syndrome at 10 days of life by rapid whole genome sequencing

(2014) James R. Priest et al.   HEART RHYTHM

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

(2014) Iakes Ezkurdia et al.   HUMAN MOLECULAR GENETICS

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur et al.   NATURE

Genome sequencing identifies major causes of severe intellectual disability

(2014) Christian Gilissen et al.   NATURE

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

(2014) Aaron M Newman et al.   NATURE MEDICINE

High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma

(2014) Carsten Linnemann et al.   NATURE MEDICINE

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine

(2014) Jason L Vassy et al.   Trials

Cost-Effectiveness of Using Pharmacogenetic Information in Warfarin Dosing for Patients With Nonvalvular Atrial Fibrillation

(2013) Mark H. Eckman   ANNALS OF INTERNAL MEDICINE

SW#–GPU-enabled exact alignments on genome scale

(2013) Matija Korpar et al.   BIOINFORMATICS

Molecular Testing Guideline for Selection of Lung Cancer Patients for EGFR and ALK Tyrosine Kinase Inhibitors: Guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology

(2013) Neal I. Lindeman et al.   Journal of Thoracic Oncology

A genomic view of mosaicism and human disease

(2013) Leslie G. Biesecker et al.   NATURE REVIEWS GENETICS

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Clopidogrel: A Case for Indication-Specific Pharmacogenetics

(2012) J A Johnson et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases

(2012) William A. Gahl et al.   GENETICS IN MEDICINE

Point-of-care genetic testing for personalisation of antiplatelet treatment (RAPID GENE): a prospective, randomised, proof-of-concept trial

(2012) Jason D Roberts et al.   LANCET

What makes UK Biobank special?

(2012) Rory Collins   LANCET

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

(2012)   NATURE

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

(2012) Zamin Iqbal et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Survival in BRAF V600–Mutant Advanced Melanoma Treated with Vemurafenib

(2012) Jeffrey A. Sosman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units

(2012) C. J. Saunders et al.   Science Translational Medicine

Novel method to estimate the phenotypic variation explained by genome-wide association studies reveals large fraction of the missing heritability

(2011) Zoltán Kutalik et al.   GENETIC EPIDEMIOLOGY

Efficient storage of high throughput DNA sequencing data using reference-based compression

(2011) M. Hsi-Yang Fritz et al.   GENOME RESEARCH

Charting a course for genomic medicine from base pairs to bedside

(2011) Eric D. Green et al.   NATURE

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

The importance of phase information for human genomics

(2011) Ryan Tewhey et al.   NATURE REVIEWS GENETICS

A CFTR Potentiator in Patients with Cystic Fibrosis and theG551DMutation

(2011) Bonnie W. Ramsey et al.   NEW ENGLAND JOURNAL OF MEDICINE

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Whole-Genome Sequencing for Optimized Patient Management

(2011) M. N. Bainbridge et al.   Science Translational Medicine

Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

(2011) Frederick E. Dewey et al.   PLoS Genetics

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

(2010) Elizabeth A Worthey et al.   GENETICS IN MEDICINE

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

Reduced-Function CYP2C19 Genotype and Risk of Adverse Clinical Outcomes Among Patients Treated With Clopidogrel Predominantly for PCI

(2010) Jessica L. Mega et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Warfarin Genotyping Reduces Hospitalization Rates

(2010) Robert S. Epstein et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Genetic variants in ABCB1 and CYP2C19 and cardiovascular outcomes after treatment with clopidogrel and prasugrel in the TRITON–TIMI 38 trial: a pharmacogenetic analysis

(2010) Jessica L Mega et al.   LANCET

Clinical assessment incorporating a personal genome

(2010) Euan A Ashley et al.   LANCET

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

Effects ofCYP2C19Genotype on Outcomes of Clopidogrel Treatment

(2010) Guillaume Paré et al.   NEW ENGLAND JOURNAL OF MEDICINE

Novel multi-nucleotide polymorphisms in the human genome characterized by whole genome and exome sequencing

(2010) Jeffrey A. Rosenfeld et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Estimation of the Warfarin Dose with Clinical and Pharmacogenetic Data

(2009)   NEW ENGLAND JOURNAL OF MEDICINE

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

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007

(2008) C Sue Richards et al.   GENETICS IN MEDICINE