Sequencing studies in human genetics: design and interpretation

Genotype to phenotype: lessons from model organisms for human genetics

(2013) Ben Lehner   NATURE REVIEWS GENETICS

Multiple molecular mechanisms for a single GABAA mutation in epilepsy

(2013) C. A. Reid et al.   NEUROLOGY

Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

(2012) Mingfu Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome Sequencing Followed by Large-Scale Genotyping Suggests a Limited Role for Moderately Rare Risk Factors of Strong Effect in Schizophrenia

(2012) Anna C. Need et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome Sequencing Followed by Large-Scale Genotyping Fails to Identify Single Rare Variants of Large Effect in Idiopathic Generalized Epilepsy

(2012) Erin L. Heinzen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-Throughput Analysis of Protein–Protein Interactions in Picoliter-Volume Droplets Using Fluorescence Polarization

(2012) Jae-Won Choi et al.   ANALYTICAL CHEMISTRY

Genotype calling and haplotyping in parent-offspring trios

(2012) W. Chen et al.   GENOME RESEARCH

Clinical application of exome sequencing in undiagnosed genetic conditions

(2012) Anna C Need et al.   JOURNAL OF MEDICAL GENETICS

In Silico Cardiac Risk Assessment in Patients With Long QT Syndrome

(2012) Ryan Hoefen et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study

(2012) Anita Rauch et al.   LANCET

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

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

De novo mutations in ATP1A3 cause alternating hemiplegia of childhood

(2012) Erin L Heinzen et al.   NATURE GENETICS

Exome sequencing and the genetic basis of complex traits

(2012) Adam Kiezun et al.   NATURE GENETICS

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

(2012) Joep de Ligt et al.   NEW ENGLAND JOURNAL OF MEDICINE

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Epistatic interactions between Tgfb1 and genetic loci, Tgfbm2 and Tgfbm3, determine susceptibility to an asthmatic stimulus

(2012) J. Freimuth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

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

The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals

(2012) Martin Ladouceur et al.   PLoS Genetics

A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families

(2012) Bingshan Li et al.   PLoS Genetics

A Genome-wide Comparison of the Functional Properties of Rare and Common Genetic Variants in Humans

(2011) Qianqian Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A General Framework for Detecting Disease Associations with Rare Variants in Sequencing Studies

(2011) Dan-Yu Lin et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

(2011) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SVA: software for annotating and visualizing sequenced human genomes

(2011) Dongliang Ge et al.   BIOINFORMATICS

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Comparison of statistical tests for disease association with rare variants

(2011) Saonli Basu et al.   GENETIC EPIDEMIOLOGY

Accurate and comprehensive sequencing of personal genomes

(2011) S. S. Ajay et al.   GENOME RESEARCH

Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed

(2011) Stephanie Hicks et al.   HUMAN MUTATION

Variation in genome-wide mutation rates within and between human families

(2011) Donald F Conrad 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

Diseases in a dish: modeling human genetic disorders using induced pluripotent cells

(2011) Gustavo Tiscornia et al.   NATURE MEDICINE

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

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

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing

(2011) C. J. Bell et al.   Science Translational Medicine

Testing for an Unusual Distribution of Rare Variants

(2011) Benjamin M. Neale et al.   PLoS Genetics

Computational and statistical approaches to analyzing variants identified by exome sequencing

(2011) Nathan O Stitziel et al.   GENOME BIOLOGY

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

(2010) Alkes L. Price et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Human allelic variation: perspective from protein function, structure, and evolution

(2010) Daniel M Jordan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Analysis of next-generation genomic data in cancer: accomplishments and challenges

(2010) L. Ding et al.   HUMAN MOLECULAR GENETICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Diabetes Mellitus in Long-term Survivors of Childhood Cancer

(2009) Lillian R. Meacham et al.   ARCHIVES OF INTERNAL MEDICINE

The theory of discovering rare variants via DNA sequencing

(2009) Michael C Wendl et al.   BMC GENOMICS

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations

(2009) Heather A. Bruce et al.   PSYCHIATRIC GENETICS

A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic

(2009) Bo Eskerod Madsen et al.   PLoS Genetics

A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia

(2009) Anna C. Need et al.   PLoS Genetics

Methods for Detecting Associations with Rare Variants for Common Diseases: Application to Analysis of Sequence Data

(2008) Bingshan Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide significance for dense SNP and resequencing data

(2008) Clive J. Hoggart et al.   GENETIC EPIDEMIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS