Published in Nature on August 16, 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
Exome sequencing identifies the cause of a mendelian disorder. Nat Genet (2009) 32.06
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
Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci U S A (2013) 16.74
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res (2012) 15.90
Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med (2013) 15.85
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A (2009) 15.09
A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet (2014) 14.56
Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet (2011) 14.29
Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet (2010) 13.18
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
Clinical assessment incorporating a personal genome. Lancet (2010) 10.18
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
Somatic coding mutations in human induced pluripotent stem cells. Nature (2011) 9.50
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
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
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
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
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
Rare and common variants: twenty arguments. Nat Rev Genet (2012) 6.67
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
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med (2011) 5.82
De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet (2010) 5.72
Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N Engl J Med (2014) 5.47
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics (2011) 5.45
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
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
Modernizing reference genome assemblies. PLoS Biol (2011) 5.23
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol (2011) 5.11
Characterising and predicting haploinsufficiency in the human genome. PLoS Genet (2010) 4.85
Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol (2009) 4.80
Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat Methods (2010) 4.51
SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res (2012) 4.45
Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet (2010) 4.29
Whole exome capture in solution with 3 Gbp of data. Genome Biol (2010) 4.23
Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol (2011) 4.18
VPS35 mutations in Parkinson disease. Am J Hum Genet (2011) 4.16
Exome sequencing and the genetic basis of complex traits. Nat Genet (2012) 4.11
Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci Transl Med (2012) 4.05
Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet (2013) 4.03
Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med (2012) 4.02
Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet (2010) 3.99
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
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
The characterization of twenty sequenced human genomes. PLoS Genet (2010) 3.72
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
Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc Natl Acad Sci U S A (2011) 3.54
Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet (2010) 3.50
Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Am J Hum Genet (2010) 3.47
An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics (2012) 3.41
Preleukemic mutations in human acute myeloid leukemia affect epigenetic regulators and persist in remission. Proc Natl Acad Sci U S A (2014) 3.39
Evolutionary diagnosis method for variants in personal exomes. Nat Methods (2012) 3.32
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
Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A (2013) 3.25
Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries. Nucleic Acids Res (2010) 3.23
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
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol (2011) 3.09
The genetic landscape of mutations in Burkitt lymphoma. Nat Genet (2012) 3.03
Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res (2011) 3.00
Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet (2010) 2.98
Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics (2012) 2.92
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, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet (2011) 2.68
A yeast functional screen predicts new candidate ALS disease genes. Proc Natl Acad Sci U S A (2011) 2.68
CONTRA: copy number analysis for targeted resequencing. Bioinformatics (2012) 2.64
Unlocking Mendelian disease using exome sequencing. Genome Biol (2011) 2.62
Revisiting Mendelian disorders through exome sequencing. Hum Genet (2011) 2.57
The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet (2012) 2.57
A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nat Genet (2010) 2.57
Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. Cell (2012) 2.54
Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet (2011) 2.52
Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia. Nat Genet (2011) 2.48
Exome sequencing of a multigenerational human pedigree. PLoS One (2009) 2.48
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
Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome. Proc Natl Acad Sci U S A (2010) 2.45
The impact of next-generation sequencing on genomics. J Genet Genomics (2011) 2.41
Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet (2010) 2.39
Challenges of sequencing human genomes. Brief Bioinform (2010) 2.39
Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy. Am J Hum Genet (2011) 2.38
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol (2009) 2.32
Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol (2011) 2.32
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16
A haplotype map of the human genome. Nature (2005) 105.70
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
The consensus coding sequences of human breast and colorectal cancers. Science (2006) 60.02
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13
Next-generation DNA sequencing. Nat Biotechnol (2008) 34.95
Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 30.28
Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science (2004) 21.65
Prediction of deleterious human alleles. Hum Mol Genet (2001) 21.00
Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97
Direct selection of human genomic loci by microarray hybridization. Nat Methods (2007) 17.73
Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet (2005) 12.12
Human genetic variation and its contribution to complex traits. Nat Rev Genet (2009) 12.11
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science (2009) 7.39
Genetic variation in an individual human exome. PLoS Genet (2008) 6.68
Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods (2009) 6.36
1000 Genomes project. Nat Biotechnol (2008) 5.73
Power of deep, all-exon resequencing for discovery of human trait genes. Proc Natl Acad Sci U S A (2009) 5.61
When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet (1999) 5.32
Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Nat Genet (2006) 3.94
Enrichment of super-sized resequencing targets from the human genome. Nat Methods (2007) 2.68
A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs. Am J Hum Genet (2009) 2.62
Haplotype sorting using human fosmid clone end-sequence pairs. Genome Res (2008) 2.10
Finding the missing heritability of complex diseases. Nature (2009) 67.95
Exome sequencing identifies the cause of a mendelian disorder. Nat Genet (2009) 32.06
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods (2013) 31.15
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
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Fine-scale structural variation of the human genome. Nat Genet (2005) 24.31
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet (2003) 21.52
Recent segmental duplications in the human genome. Science (2002) 21.30
Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science (2008) 20.68
A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron (2011) 18.73
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
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
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
Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet (2010) 13.70
Segmental duplications and copy-number variation in the human genome. Am J Hum Genet (2005) 13.33
Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet (2010) 12.63
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet (2011) 11.94
Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet (2009) 11.73
Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med (2008) 10.88
Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet (2007) 10.38
Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet (2006) 10.36
A copy number variation morbidity map of developmental delay. Nat Genet (2011) 9.58
Complete Khoisan and Bantu genomes from southern Africa. Nature (2010) 9.06
Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet (2006) 9.04
Limitations of next-generation genome sequence assembly. Nat Methods (2010) 9.04
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature (2010) 8.99
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 comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet (2006) 8.61
A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat Genet (2008) 8.44
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Shotgun sequence assembly and recent segmental duplications within the human genome. Nature (2004) 7.91
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am J Hum Genet (2006) 7.70
De novo mutations in epileptic encephalopathies. Nature (2013) 7.42
Genome structural variation discovery and genotyping. Nat Rev Genet (2011) 7.34
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
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
A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet (2010) 6.62
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res (2009) 6.42
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
15q13.3 microdeletions increase risk of idiopathic generalized epilepsy. Nat Genet (2009) 6.21
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus. Mol Cell (2004) 6.08
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07
Challenges and standards in integrating surveys of structural variation. Nat Genet (2007) 6.05
Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat Genet (2009) 5.93
Complex SNP-related sequence variation in segmental genome duplications. Nat Genet (2004) 5.90
The genome of a songbird. Nature (2010) 5.90
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature (2005) 5.51
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