4.4 Review

Computational and statistical approaches to analyzing variants identified by exome sequencing

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

Si Quang Le et al.

GENOME RESEARCH (2011)

Article Biochemistry & Molecular Biology

Association studies for next-generation sequencing

Li Luo et al.

GENOME RESEARCH (2011)

Article Genetics & Heredity

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

Mark A. DePristo et al.

NATURE GENETICS (2011)

Article Genetics & Heredity

Testing for an Unusual Distribution of Rare Variants

Benjamin M. Neale et al.

PLOS GENETICS (2011)

Article Genetics & Heredity

To Identify Associations with Rare Variants, Just WHaIT Weighted Haplotype and Imputation-Based Tests

Yun Li et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Genetics & Heredity

Extending Rare-Variant Testing Strategies Analysis of Noncoding Sequence and Imputed Genotypes

Matthew Zawistowski et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Genetics & Heredity

Exome Sequencing Identifies WDR35 Variants Involved in Sensenbrenner Syndrome

Christian Gilissen et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Genetics & Heredity

Mutations in the DBP-Deficiency Protein HSD17B4 Cause Ovarian Dysgenesis, Hearing Loss, and Ataxia of Perrault Syndrome

Sarah B. Pierce et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Genetics & Heredity

Replication Strategies for Rare Variant Complex Trait Association Studies via Next-Generation Sequencing

Dajiang J. Liu et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Genetics & Heredity

Whole-Exome-Sequencing-Based Discovery of Human FADD Deficiency

Alexandre Bolze et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Genetics & Heredity

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

Alkes L. Price et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Article Genetics & Heredity

Powerful SNP-Set Analysis for Case-Control Genome-wide Association Studies

Michael C. Wu et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Review Genetics & Heredity

Rare Variant Association Analysis Methods for Complex Traits

Jennifer Asimit et al.

ANNUAL REVIEW OF GENETICS, VOL 44 (2010)

Article Biochemical Research Methods

High quality SNP calling using Illumina data at shallow coverage

Nawar Malhis et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Fast and accurate long-read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Challenges of sequencing human genomes

Daniel C. Koboldt et al.

BRIEFINGS IN BIOINFORMATICS (2010)

Article Biochemical Research Methods

A survey of sequence alignment algorithms for next-generation sequencing

Heng Li et al.

BRIEFINGS IN BIOINFORMATICS (2010)

Article Genetics & Heredity

Detecting Rare Variants for Complex Traits Using Family and Unrelated Data

Xiaofeng Zhu et al.

GENETIC EPIDEMIOLOGY (2010)

Article Genetics & Heredity

An Evaluation of Statistical Approaches to Rare Variant Analysis in Genetic Association Studies

Andrew P. Morris et al.

GENETIC EPIDEMIOLOGY (2010)

Article Biochemistry & Molecular Biology

Detection of nonneutral substitution rates on mammalian phylogenies

Katherine S. Pollard et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

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

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

Massively parallel sequencing and rare disease

Sarah B. Ng et al.

HUMAN MOLECULAR GENETICS (2010)

Article Multidisciplinary Sciences

Integrating common and rare genetic variation in diverse human populations

David M. Altshuler et al.

NATURE (2010)

Article Multidisciplinary Sciences

A map of human genome variation from population-scale sequencing

David Altshuler et al.

NATURE (2010)

Article Genetics & Heredity

Exome sequencing identifies the cause of a mendelian disorder

Sarah B. Ng et al.

NATURE GENETICS (2010)

Article Genetics & Heredity

De novo mutations of SETBP1 cause Schinzel-Giedion syndrome

Alexander Hoischen et al.

NATURE GENETICS (2010)

Article Genetics & Heredity

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

Sarah B. Ng et al.

NATURE GENETICS (2010)

Letter Biochemical Research Methods

A method and server for predicting damaging missense mutations

Ivan A. Adzhubei et al.

NATURE METHODS (2010)

Letter Biochemical Research Methods

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

Gregory M. Cooper et al.

NATURE METHODS (2010)

Review Genetics & Heredity

APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation

Michael L. Metzker

NATURE REVIEWS GENETICS (2010)

Article Medicine, General & Internal

Exome Sequencing, ANGPTL3 Mutations, and Familial Combined Hypolipidemia

Kiran Musunuru et al.

NEW ENGLAND JOURNAL OF MEDICINE (2010)

Article Multidisciplinary Sciences

Comprehensive Approach to Analyzing Rare Genetic Variants

Thomas J. Hoffmann et al.

PLOS ONE (2010)

Article Biochemical Research Methods

A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes

Gaurav Bhatia et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Genetics & Heredity

An Evolutionary Framework for Association Testing in Resequencing Studies

C. Ryan King et al.

PLOS GENETICS (2010)

Article Genetics & Heredity

Rare, Evolutionarily Unlikely Missense Substitutions in ATM Confer Increased Risk of Breast Cancer

Sean V. Tavtigian et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2009)

Article Biochemical Research Methods

Genome-wide association analysis by lasso penalized logistic regression

Tong Tong Wu et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Identifying novel constrained elements by exploiting biased substitution patterns

Manuel Garber et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

SNP detection for massively parallel whole-genome resequencing

Ruiqiang Li et al.

GENOME RESEARCH (2009)

Article Multidisciplinary Sciences

Targeted capture and massively parallel sequencing of 12 human exomes

Sarah B. Ng et al.

NATURE (2009)

Article Biotechnology & Applied Microbiology

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

Andreas Gnirke et al.

NATURE BIOTECHNOLOGY (2009)

Article Multidisciplinary Sciences

Power of deep, all-exon resequencing for discovery of human trait genes

Gregory V. Kryukov et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

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

Lucia A. Hindorff et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Genetics & Heredity

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

Bo Eskerod Madsen et al.

PLOS GENETICS (2009)

Article Genetics & Heredity

Accommodating linkage disequilibrium in genetic-association analyses via ridge regression

Nathalie Malo et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2008)

Article Genetics & Heredity

Methods for detecting associations with rare variants for common diseases: Application to analysis of sequence data

Bingshan Li et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2008)

Article Biochemistry & Molecular Biology

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

Heng Li et al.

GENOME RESEARCH (2008)

Review Biotechnology & Applied Microbiology

Next-generation DNA sequencing

Jay Shendure et al.

NATURE BIOTECHNOLOGY (2008)

Article Biochemical Research Methods

Pyrobayes:: an improved base caller for SNP discovery in pyrosequences

Aaron R. Quinlan et al.

NATURE METHODS (2008)

Article Genetics & Heredity

Assessing the evolutionary impact of amino acid mutations in the human genome

Adam R. Boyko et al.

PLOS GENETICS (2008)

Article Biochemical Research Methods

Analysis of sequence conservation at nucleotide resolution

Saurabh Asthana et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Biochemical Research Methods

Microarray-based genomic selection for high-throughput resequencing

David T. Okou et al.

NATURE METHODS (2007)

Article Genetics & Heredity

PLINK: A tool set for whole-genome association and population-based linkage analyses

Shaun Purcell et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2007)

Article Biochemistry & Molecular Biology

SNAP: predict effect of non-synonymous polymorphisms on function

Yana Bromberg et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Genetics & Heredity

Most rare missense alleles are deleterious in humans: Implications for complex disease and association studies

Gregory V. Kryukov et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2007)

Article Biotechnology & Applied Microbiology

Determinants of protein function revealed by combinatorial entropy optimization

Boris Reva et al.

GENOME BIOLOGY (2007)

Review Genetics & Heredity

Medical sequencing at the extremes of human body mass

Nadav Ahituv et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2007)

Article Biochemistry & Molecular Biology

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

Paul D. Thomas et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

Lucia Conde et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Genetics & Heredity

A spectrum of PCSK9 Alleles contributes to plasma levels of low-density lipoprotein cholesterol

IK Kotowski et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2006)

Article Biochemistry & Molecular Biology

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

A Siepel et al.

GENOME RESEARCH (2005)

Article Biochemistry & Molecular Biology

Distribution and intensity of constraint in mammalian genomic sequence

GM Cooper et al.

GENOME RESEARCH (2005)

Article Multidisciplinary Sciences

Multiple rare Alleles contribute to low plasma levels of HDL cholesterol

JC Cohen et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

PANTHER: A library of protein families and subfamilies indexed by function

PD Thomas et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

SIFT: predicting amino acid changes that affect protein function

PC Ng et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Predicting deleterious amino acid substitutions

PC Ng et al.

GENOME RESEARCH (2001)

Article Biochemistry & Molecular Biology

Prediction of deleterious human alleles

S Sunyaev et al.

HUMAN MOLECULAR GENETICS (2001)

Article Biochemistry & Molecular Biology

dbSNP: the NCBI database of genetic variation

ST Sherry et al.

NUCLEIC ACIDS RESEARCH (2001)