Genome-wide association studies for common diseases and complex traits.

PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet (2007) 209.92

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95

Global variation in copy number in the human genome. Nature (2006) 57.50

The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80

KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60

Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet (2008) 26.79

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol (2010) 26.41

Population genomics of human gene expression. Nat Genet (2007) 24.49

A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet (2007) 22.96

The human disease network. Proc Natl Acad Sci U S A (2007) 19.58

Genotype imputation. Annu Rev Genomics Hum Genet (2009) 18.64

A HapMap harvest of insights into the genetics of common disease. J Clin Invest (2008) 18.31

Mapping determinants of human gene expression by regional and genome-wide association. Nature (2005) 17.24

Identification of ten loci associated with height highlights new biological pathways in human growth. Nat Genet (2008) 16.25

A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet (2006) 15.63

Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet (2007) 14.99

Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet (2007) 10.92

Family-based association tests for genomewide association scans. Am J Hum Genet (2007) 10.67

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature (2010) 10.66

A large-scale genetic association study confirms IL12B and leads to the identification of IL23R as psoriasis-risk genes. Am J Hum Genet (2006) 9.56

Prediction of individual genetic risk to disease from genome-wide association studies. Genome Res (2007) 8.48

High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet (2005) 6.86

Genetic variation in an individual human exome. PLoS Genet (2008) 6.68

Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet (2009) 6.61

Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Am J Hum Genet (2005) 6.61

LDL-cholesterol concentrations: a genome-wide association study. Lancet (2008) 6.44

Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet (2005) 6.12

African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet (2008) 6.06

Estimating local ancestry in admixed populations. Am J Hum Genet (2008) 5.90

Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet (2008) 5.78

Heterogeneity in meta-analyses of genome-wide association investigations. PLoS One (2007) 5.77

A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Nat Genet (2009) 5.75

A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. BMC Med Genet (2007) 5.64

Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53

Network-based global inference of human disease genes. Mol Syst Biol (2008) 5.01

Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS One (2008) 4.96

Genetic design and statistical power of nested association mapping in maize. Genetics (2008) 4.92

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84

A genome-wide linkage and association scan reveals novel loci for autism. Nature (2009) 4.76

Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. PLoS Genet (2009) 4.71

Bioinformatics challenges for genome-wide association studies. Bioinformatics (2010) 4.45

An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. PLoS One (2010) 4.42

Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39

A Bayesian measure of the probability of false discovery in genetic epidemiology studies. Am J Hum Genet (2007) 4.21

Methods for meta-analysis in genetic association studies: a review of their potential and pitfalls. Hum Genet (2007) 3.92

Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy. Nat Genet (2009) 3.83

Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet (2005) 3.76

Sequence features in regions of weak and strong linkage disequilibrium. Genome Res (2005) 3.74

Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A (2006) 3.68

Epistasis and its implications for personal genetics. Am J Hum Genet (2009) 3.52

The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat Rev Cancer (2008) 3.43

Accounting for ancestry: population substructure and genome-wide association studies. Hum Mol Genet (2008) 3.39

Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet (2007) 3.29

Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. Neuroimage (2010) 3.27

Genome-wide association scans identified CTNNBL1 as a novel gene for obesity. Hum Mol Genet (2008) 3.24

Addictions biology: haplotype-based analysis for 130 candidate genes on a single array. Alcohol Alcohol (2008) 3.13

A unified association analysis approach for family and unrelated samples correcting for stratification. Am J Hum Genet (2008) 3.00

IL23R variation determines susceptibility but not disease phenotype in inflammatory bowel disease. Gastroenterology (2007) 2.97

Validating therapeutic targets through human genetics. Nat Rev Drug Discov (2013) 2.94

Perspectives on human genetic variation from the HapMap Project. PLoS Genet (2005) 2.91

Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci U S A (2006) 2.90

Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. PLoS One (2009) 2.85

Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci U S A (2007) 2.81

Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One (2009) 2.72

Improved detection of common variants associated with schizophrenia and bipolar disorder using pleiotropy-informed conditional false discovery rate. PLoS Genet (2013) 2.68

Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet (2013) 2.67

Case-control association testing in the presence of unknown relationships. Genet Epidemiol (2009) 2.63

Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling. PLoS Genet (2008) 2.63

Machine learning for detecting gene-gene interactions: a review. Appl Bioinformatics (2006) 2.56

Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol (2010) 2.56

Chapter 11: Genome-wide association studies. PLoS Comput Biol (2012) 2.46

An international initiative to identify genetic modifiers of cancer risk in BRCA1 and BRCA2 mutation carriers: the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA). Breast Cancer Res (2007) 2.46

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol (2011) 2.45

Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol (2012) 2.42

Unraveling a multifactorial late-onset disease: from genetic susceptibility to disease mechanisms for age-related macular degeneration. Annu Rev Genomics Hum Genet (2009) 2.40

Genome-wide association scan of attention deficit hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet (2008) 2.40

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol (2008) 2.32

Genetics and genomics of pulmonary arterial hypertension. J Am Coll Cardiol (2009) 2.31

A decade of systems biology. Annu Rev Cell Dev Biol (2010) 2.30

Evolution in health and medicine Sackler colloquium: Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies. Proc Natl Acad Sci U S A (2010) 2.27

Biases and reconciliation in estimates of linkage disequilibrium in the human genome. Am J Hum Genet (2006) 2.26

Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study. BMC Med Genet (2007) 2.25

Insulin resistance and the polycystic ovary syndrome revisited: an update on mechanisms and implications. Endocr Rev (2012) 2.22

Common pathways in Crohn's disease and other inflammatory diseases revealed by genomics. Gut (2007) 2.20

Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci U S A (2009) 2.19

Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics (2008) 2.16

Current status of genome-wide association studies in cancer. Hum Genet (2011) 2.14

Genome wide association studies for milk production traits in Chinese Holstein population. PLoS One (2010) 2.13

GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res (2010) 2.09

All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. PLoS Genet (2013) 2.08

Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays. Genes Brain Behav (2008) 2.08

The advantages and limitations of trait analysis with GWAS: a review. Plant Methods (2013) 2.08

Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. Plant Cell (2009) 2.03

Improved detection of common variants associated with schizophrenia by leveraging pleiotropy with cardiovascular-disease risk factors. Am J Hum Genet (2013) 1.96

Lack of replication of thirteen single-nucleotide polymorphisms implicated in Parkinson's disease: a large-scale international study. Lancet Neurol (2006) 1.92

Identification of four gene variants associated with myocardial infarction. Am J Hum Genet (2005) 1.89

Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Circ Cardiovasc Genet (2008) 1.89

The Generation R Study Biobank: a resource for epidemiological studies in children and their parents. Eur J Epidemiol (2007) 1.89

Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell (2012) 1.88

Association genetics in Pinus taeda L. I. Wood property traits. Genetics (2006) 1.85

PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet (2007) 209.92

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science (2007) 51.70

The structure of haplotype blocks in the human genome. Science (2002) 50.88

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet (2008) 35.06

Integrating common and rare genetic variation in diverse human populations. Nature (2010) 32.30

The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet (2008) 30.20

A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science (2006) 27.49

Efficiency and power in genetic association studies. Nat Genet (2005) 25.56

Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04

Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med (2008) 19.71

Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet (2008) 19.55

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet (2007) 19.08

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet (2010) 17.38

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet (2008) 15.89

Common deletion polymorphisms in the human genome. Nat Genet (2006) 15.66

A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet (2006) 15.63

Genetic mapping in human disease. Science (2008) 15.12

Calibrating a coalescent simulation of human genome sequence variation. Genome Res (2005) 15.04

Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet (2006) 14.76

Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature (2011) 13.23

Efficient control of population structure in model organism association mapping. Genetics (2008) 12.32

Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet (2009) 12.19

Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study. Lancet (2012) 12.10

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet (2008) 12.07

Methods for high-density admixture mapping of disease genes. Am J Hum Genet (2004) 12.02

Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol (2008) 11.28

Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. Nat Genet (2008) 10.49

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet (2008) 9.52

Testing for an unusual distribution of rare variants. PLoS Genet (2011) 9.28

Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet (2007) 8.74

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet (2009) 8.39

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet (2011) 7.98

Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration. Nat Genet (2006) 7.49

Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat Genet (2009) 7.16

Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet (2008) 7.07

Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med (2010) 6.84

A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature (2007) 6.77

The mosaic structure of variation in the laboratory mouse genome. Nature (2002) 6.54

Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet (2008) 6.42

Parental phenotypes in family-based association analysis. Am J Hum Genet (2004) 6.35

Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet (2011) 6.20

Ascertainment through family history of disease often decreases the power of family-based association studies. Behav Genet (2007) 6.06

Genetic architectures of psychiatric disorders: the emerging picture and its implications. Nat Rev Genet (2012) 5.99

Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits. PLoS Genet (2010) 5.79

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet (2011) 5.58

Synaptic, transcriptional and chromatin genes disrupted in autism. Nature (2014) 5.30

Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet (2008) 5.08

Disruption of neurexin 1 associated with autism spectrum disorder. Am J Hum Genet (2008) 5.04

Transferability of tag SNPs in genetic association studies in multiple populations. Nat Genet (2006) 4.78

A genome-wide linkage and association scan reveals novel loci for autism. Nature (2009) 4.76

Whole population, genome-wide mapping of hidden relatedness. Genome Res (2008) 4.72

Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci U S A (2007) 4.71

Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet (2010) 4.65

Validating, augmenting and refining genome-wide association signals. Nat Rev Genet (2009) 4.56

Ipr1 gene mediates innate immunity to tuberculosis. Nature (2005) 4.53

Pervasive sharing of genetic effects in autoimmune disease. PLoS Genet (2011) 4.42

Common single nucleotide polymorphisms in TCF7L2 are reproducibly associated with type 2 diabetes and reduce the insulin response to glucose in nondiabetic individuals. Diabetes (2006) 4.36

Variation in complement factor 3 is associated with risk of age-related macular degeneration. Nat Genet (2007) 4.23

HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat Genet (2009) 4.11

Evaluation of common variants in the six known maturity-onset diabetes of the young (MODY) genes for association with type 2 diabetes. Diabetes (2007) 3.84

Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet (2009) 3.82

Seven new loci associated with age-related macular degeneration. Nat Genet (2013) 3.81

Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. Nat Genet (2009) 3.65

Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis. Proc Natl Acad Sci U S A (2008) 3.56

A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet (2011) 3.55

Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nat Genet (2009) 3.52

Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci U S A (2014) 3.47

Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant. PLoS One (2008) 3.36

WHAP: haplotype-based association analysis. Bioinformatics (2006) 3.36

Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). Proc Natl Acad Sci U S A (2010) 3.33

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet (2010) 3.31

Variation near complement factor I is associated with risk of advanced AMD. Eur J Hum Genet (2008) 3.29

Combined analysis from eleven linkage studies of bipolar disorder provides strong evidence of susceptibility loci on chromosomes 6q and 8q. Am J Hum Genet (2005) 3.24

Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet (2002) 3.24

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet (2012) 3.21

Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell (2012) 3.21

Common variants associated with plasma triglycerides and risk for coronary artery disease. Nat Genet (2013) 2.92

Prediction model for prevalence and incidence of advanced age-related macular degeneration based on genetic, demographic, and environmental variables. Invest Ophthalmol Vis Sci (2008) 2.91

The genome-wide patterns of variation expose significant substructure in a founder population. Am J Hum Genet (2008) 2.79

Myosin IXB variant increases the risk of celiac disease and points toward a primary intestinal barrier defect. Nat Genet (2005) 2.71

Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function. PLoS Genet (2010) 2.68

Comprehensive association testing of common mitochondrial DNA variation in metabolic disease. Am J Hum Genet (2006) 2.60

Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion. Nat Genet (2012) 2.55

Haplotype structure and genotype-phenotype correlations of the sulfonylurea receptor and the islet ATP-sensitive potassium channel gene region. Diabetes (2004) 2.52

A high-density screen for linkage in multiple sclerosis. Am J Hum Genet (2005) 2.50

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet (2012) 2.50

Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron (2013) 2.45