Published in Nat Genet on November 13, 2009
A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res (2010) 43.51
Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45
Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (2012) 17.12
Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet (2011) 14.29
Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med (2010) 13.57
Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet (2010) 12.63
Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet (2010) 10.15
Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet (2010) 9.53
Testing for an unusual distribution of rare variants. PLoS Genet (2011) 9.28
Dindel: accurate indel calls from short-read data. Genome Res (2010) 8.62
Predicting the functional effect of amino acid substitutions and indels. PLoS One (2012) 8.61
A de novo paradigm for mental retardation. Nat Genet (2010) 8.57
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet (2011) 8.53
Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34
Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med (2011) 8.20
Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron (2010) 7.87
Frequent mutation of BAP1 in metastasizing uveal melanomas. Science (2010) 7.47
Clinical interpretation and implications of whole-genome sequencing. JAMA (2014) 7.24
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat (2011) 6.97
Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med (2010) 6.84
Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet (2010) 6.79
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature (2010) 6.26
De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet (2010) 5.72
A decade's perspective on DNA sequencing technology. Nature (2011) 5.61
Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet (2011) 5.41
Low-coverage sequencing: implications for design of complex trait association studies. Genome Res (2011) 5.34
Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol (2010) 5.32
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol (2011) 5.11
Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am J Hum Genet (2010) 4.95
Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature (2011) 4.85
The predictive capacity of personal genome sequencing. Sci Transl Med (2012) 4.64
Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat Methods (2010) 4.51
Case definitions, diagnostic algorithms, and priorities in encephalitis: consensus statement of the international encephalitis consortium. Clin Infect Dis (2013) 4.51
Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Am J Hum Genet (2012) 4.45
Copy number variation detection and genotyping from exome sequence data. Genome Res (2012) 4.44
Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet (2010) 4.29
Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med (2012) 4.02
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med (2013) 3.90
Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci U S A (2010) 3.85
Progress and promise of genome-wide association studies for human complex trait genetics. Genetics (2010) 3.81
Human genome sequencing in health and disease. Annu Rev Med (2012) 3.76
Genomics, intellectual disability, and autism. N Engl J Med (2012) 3.74
A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A (2012) 3.72
The characterization of twenty sequenced human genomes. PLoS Genet (2010) 3.72
Using exome sequencing to reveal mutations in TREM2 presenting as a frontotemporal dementia-like syndrome without bone involvement. JAMA Neurol (2013) 3.70
Gain-of-function human STAT1 mutations impair IL-17 immunity and underlie chronic mucocutaneous candidiasis. J Exp Med (2011) 3.63
A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform (2013) 3.60
Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome. Nat Genet (2010) 3.60
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet (2011) 3.43
Rare-variant association analysis: study designs and statistical tests. Am J Hum Genet (2014) 3.42
An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics (2012) 3.41
The next-generation sequencing revolution and its impact on genomics. Cell (2013) 3.35
High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet (2010) 3.31
Massively parallel sequencing and rare disease. Hum Mol Genet (2010) 3.28
A probabilistic disease-gene finder for personal genomes. Genome Res (2011) 3.23
A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet (2011) 3.13
The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12
A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics (2012) 3.10
Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate. Am J Hum Genet (2010) 3.09
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol (2011) 3.09
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res (2010) 2.97
Genomics really gets personal: how exome and whole genome sequencing challenge the ethical framework of human genetics research. Am J Med Genet A (2011) 2.93
Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Cell (2011) 2.93
BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr Protoc Bioinformatics (2014) 2.90
Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res (2011) 2.89
Disease gene identification strategies for exome sequencing. Eur J Hum Genet (2012) 2.89
Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency. Nat Genet (2010) 2.81
Identification of PRRT2 as the causative gene of paroxysmal kinesigenic dyskinesias. Brain (2011) 2.80
Crop genomics: advances and applications. Nat Rev Genet (2011) 2.72
Exome sequencing can improve diagnosis and alter patient management. Sci Transl Med (2012) 2.70
Whole-exome sequencing-based discovery of STIM1 deficiency in a child with fatal classic Kaposi sarcoma. J Exp Med (2010) 2.70
A yeast functional screen predicts new candidate ALS disease genes. Proc Natl Acad Sci U S A (2011) 2.68
Unlocking Mendelian disease using exome sequencing. Genome Biol (2011) 2.62
Revisiting Mendelian disorders through exome sequencing. Hum Genet (2011) 2.57
Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet (2011) 2.52
TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Nat Genet (2012) 2.50
Exome sequencing makes medical genomics a reality. Nat Genet (2010) 2.47
Loss-of-function variants in the genomes of healthy humans. Hum Mol Genet (2010) 2.45
wANNOVAR: annotating genetic variants for personal genomes via the web. J Med Genet (2012) 2.43
The impact of next-generation sequencing on genomics. J Genet Genomics (2011) 2.41
The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet (2010) 2.38
Genetic mapping and exome sequencing identify variants associated with five novel diseases. PLoS One (2012) 2.33
Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol (2011) 2.32
Next-generation genetic testing for retinitis pigmentosa. Hum Mutat (2012) 2.30
Exome sequencing identifies FUS mutations as a cause of essential tremor. Am J Hum Genet (2012) 2.30
SLC25A22 is a novel gene for migrating partial seizures in infancy. Ann Neurol (2013) 2.28
Bioinformatics challenges for personalized medicine. Bioinformatics (2011) 2.28
Next-generation sequencing of a 40 Mb linkage interval reveals TSPAN12 mutations in patients with familial exudative vitreoretinopathy. Am J Hum Genet (2010) 2.26
The importance of phase information for human genomics. Nat Rev Genet (2011) 2.25
Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res (2013) 2.24
GEnomes Management Application (GEM.app): a new software tool for large-scale collaborative genome analysis. Hum Mutat (2013) 2.23
DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature (2011) 2.23
Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia. PLoS Genet (2011) 2.23
The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. Am J Hum Genet (2015) 2.22
Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet (2010) 2.19
Whole-exome-sequencing-based discovery of human FADD deficiency. Am J Hum Genet (2010) 2.17
Fine tuning of craniofacial morphology by distant-acting enhancers. Science (2013) 2.16
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Next-generation DNA sequencing. Nat Biotechnol (2008) 34.95
Targeted capture and massively parallel sequencing of 12 human exomes. Nature (2009) 33.96
Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A (2009) 15.09
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
The Human Gene Mutation Database: 2008 update. Genome Med (2009) 11.72
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet (2007) 10.92
Deletion of ultraconserved elements yields viable mice. PLoS Biol (2007) 4.81
SEX LIMITED INHERITANCE IN DROSOPHILA. Science (1910) 4.19
TGF alpha deficiency results in hair follicle and eye abnormalities in targeted and waved-1 mice. Cell (1993) 4.02
Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Nat Genet (2006) 3.94
Manifestation of the limb prepattern: limb development in the absence of sonic hedgehog function. Dev Biol (2001) 3.82
Postaxial acrofacial dysostosis syndrome. J Pediatr (1979) 2.93
Inhibition of NF-kappaB activity results in disruption of the apical ectodermal ridge and aberrant limb morphogenesis. Nature (1998) 2.89
Recurrence of the postaxial acrofacial dysostosis syndrome in a sibship: implications for genetic counseling. J Pediatr (1981) 2.69
Leflunomide: mode of action in the treatment of rheumatoid arthritis. Ann Rheum Dis (2000) 2.59
Functional diversity within the rudimentary locus of Drosophila melanogaster. Mol Gen Genet (1974) 2.55
[An extensive form of mandibulo-facial dysostosis]. J Genet Hum (1969) 2.42
The strength of selection on ultraconserved elements in the human genome. Am J Hum Genet (2007) 2.21
Postaxial acrofacial dysostosis (Miller) syndrome. J Med Genet (1987) 2.03
Teratogenicity study of the dihydroorotate-dehydrogenase inhibitor and protein tyrosine kinase inhibitor Leflunomide in mice. Reprod Toxicol (2007) 1.93
Orotic acid excretion and arginine metabolism. J Nutr (2007) 1.88
Miller syndrome (postaxial acrofacial dysostosis): further evidence for autosomal recessive inheritance and expansion of the phenotype. J Med Genet (1991) 1.85
Robin sequence and oligodactyly in mother and son. Am J Med Genet (1986) 1.82
Dihydroorotate dehydrogenase polymorphism influences the toxicity of leflunomide treatment in patients with rheumatoid arthritis. Ann Rheum Dis (2009) 1.78
Leflunomide protects from T-cell-mediated liver injury in mice through inhibition of nuclear factor kappaB. Hepatology (2004) 1.76
TCOF1 mutations excluded from a role in other first and second branchial arch-related disorders. Am J Med Genet (2002) 1.69
Analysis of the phenotypes exhibited by rudimentary-like mutants of Drosophila melanogaster. Biochem Genet (1982) 1.66
Postaxial acrofacial dysostosis: report on two patients. Am J Med Genet (1992) 1.62
Targeted capture and massively parallel sequencing of 12 human exomes. Nature (2009) 33.96
Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 30.28
Biological, clinical and population relevance of 95 loci for blood lipids. Nature (2010) 28.21
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet (2003) 21.52
Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45
Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (2012) 17.12
The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science (2005) 17.00
Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature (2012) 14.76
Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet (2011) 14.29
Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet (2010) 12.63
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet (2011) 11.94
Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet (2006) 9.04
Diversity of human copy number variation and multicopy genes. Science (2010) 8.97
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature (2012) 8.91
Target-enrichment strategies for next-generation sequencing. Nat Methods (2010) 8.78
Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N Engl J Med (2005) 8.77
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
Mapping complex disease loci in whole-genome association studies. Nature (2004) 7.31
Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One (2008) 7.16
Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol (2004) 7.11
Mobile elements create structural variation: analysis of a complete human genome. Genome Res (2009) 7.06
A three-dimensional model of the yeast genome. Nature (2010) 7.01
Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet (2004) 6.99
Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet (2009) 6.79
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods (2009) 6.36
Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science (2012) 6.21
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07
Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet (2012) 5.48
Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N Engl J Med (2014) 5.47
Genetic evidence for high-altitude adaptation in Tibet. Science (2010) 5.37
Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol (2010) 5.32
Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet (2003) 5.30
Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet (2012) 5.28
Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B. Nat Genet (2004) 5.19
Inactivating mutations in NPC1L1 and protection from coronary heart disease. N Engl J Med (2014) 4.94
NIPBL, encoding a homolog of fungal Scc2-type sister chromatid cohesion proteins and fly Nipped-B, is mutated in Cornelia de Lange syndrome. Nat Genet (2004) 4.90
Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res (2005) 4.81
Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet (2008) 4.53
Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol (2012) 4.51
Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat Methods (2010) 4.51
De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes. Nat Genet (2012) 4.51
Copy number variation detection and genotyping from exome sequence data. Genome Res (2012) 4.44
Completing the map of human genetic variation. Nature (2007) 4.38
The beginning of the end for microarrays? Nat Methods (2008) 4.19
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Actionable, pathogenic incidental findings in 1,000 participants' exomes. Am J Hum Genet (2013) 4.06
Ribosomal mutations cause p53-mediated dark skin and pleiotropic effects. Nat Genet (2008) 4.02
Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Nat Genet (2006) 3.94
Noninvasive whole-genome sequencing of a human fetus. Sci Transl Med (2012) 3.94
Pattern of sequence variation across 213 environmental response genes. Genome Res (2004) 3.93
Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet (2004) 3.91
A genomewide admixture mapping panel for Hispanic/Latino populations. Am J Hum Genet (2007) 3.85
Mutational and selective effects on copy-number variants in the human genome. Nat Genet (2007) 3.82
Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics (2005) 3.77
Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet (2004) 3.73
Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. Nat Genet (2013) 3.64
Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. Am J Hum Genet (2008) 3.61
High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol (2009) 3.58
Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc Natl Acad Sci U S A (2011) 3.54