A comprehensive analysis of common copy-number variations in the human genome.
paper
Cited
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- Authors
- Wong, Kendy K; deLeeuw, Ronald J; Dosanjh, Nirpjit S; Kimm, Lindsey R; Cheng, Ze; Horsman, Douglas E; MacAulay, Calum; Ng, Raymond T; Brown, Carolyn J; Eichler, Evan E; Lam, Wan L
- Year
- 2007
- Journal
- American journal of human genetics
- PMID
- 17160897
- DOI
- 10.1086/510560
- PMCID
- PMC1785303
Segmental copy-number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to diseases. More importantly, CNVs may represent a major genetic component of our phenotypic diversity. In this study, using a whole-genome array comparative genomic hybridization assay, we identified 3,654 autosomal segmental CNVs, 800 of which appeared at a frequency of at least 3%. Of these frequent CNVs, 77% are novel. In the 95 individuals analyzed, the two most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content. Approximately 68% of the 800 polymorphic regions overlap with genes, which may reflect human diversity in senses (smell, hearing, taste, and sight), rhesus phenotype, metabolism, and disease susceptibility. Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of the contribution of microRNAs to phenotypic diversity in humans. This in-depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics.
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| Gene copy number variations in Asian patients with congenital bilateral absence of the vas deferens. | Lee CH et al. | β | 2009 | β |
| Genetics of chronic obstructive pulmonary disease: a succinct review, future avenues and prospective clinical applications. | BossΓ© Y | β | 2009 | β |
| Genetics of ischemic stroke: inheritance of a sporadic disorder. | Ross OA et al. | β | 2009 | β |
| Genome-wide association study suggested copy number variation may be associated with body mass index in the Chinese population. | Sha BY et al. | β | 2009 | β |
| Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances. | Cheung KJ et al. | β | 2009 | β |
| Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies. | Iqbal J et al. | β | 2009 | β |
| Genomic drift and evolution of microsatellite DNAs in human populations. | Takezaki N et al. | β | 2009 | β |
| Genomic imbalances in precancerous tissues signal oral cancer risk. | Garnis C et al. | β | 2009 | β |
| Genomic landscape of a three-generation pedigree segregating affective disorder. | Yang S et al. | β | 2009 | β |
| High frequency of common DNA copy number abnormalities detected by bacterial artificial chromosome array comparative genomic hybridization in 24 breast cancer cell lines. | Saito S et al. | β | 2009 | β |
| High-resolution array genomic hybridization in prenatal diagnosis. | Friedman JM | β | 2009 | β |
| High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians. | Matsuzaki H et al. | β | 2009 | β |
| High resolution genomic analysis of 18q- using oligo-microarray comparative genomic hybridization (aCGH). | Heard PL et al. | β | 2009 | β |
| High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. | Shaikh TH et al. | β | 2009 | β |
| Identification of candidate genes for sporadic amyotrophic lateral sclerosis by array comparative genomic hybridization. | Shoichet SA et al. | β | 2009 | β |
| Inter-individual variation in expression: a missing link in biomarker biology? | Little PF et al. | β | 2009 | β |
| Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genes. | Zhao Y et al. | β | 2009 | β |
| Mapping DNA structural variation in dogs. | Chen WK et al. | β | 2009 | β |
| Mapping of partially overlapping de novo deletions across an autism susceptibility region (AUTS5) in two unrelated individuals affected by developmental delays with communication impairment. | Newbury DF et al. | β | 2009 | β |
| Mechanisms of change in gene copy number. | Hastings PJ et al. | β | 2009 | β |
| Minimum altered regions in early prostate cancer progression identified by high resolution whole genome tiling path BAC array comparative hybridization. | Watson SK et al. | β | 2009 | β |
| Mobile elements create structural variation: analysis of a complete human genome. | Xing J et al. | β | 2009 | β |
| Molecular spectrum of spontaneous de novo mutations in male and female germline cells of Drosophila melanogaster. | Watanabe Y et al. | β | 2009 | β |
| Multiple pathways in the FGF signaling network are frequently deregulated by gene amplification in oral dysplasias. | Tsui IF et al. | β | 2009 | β |
| Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution. | Pace JK et al. | β | 2009 | β |
| Searching genetic risk factors for schizophrenia and bipolar disorder: learn from the past and back to the future. | Alaerts M et al. | β | 2009 | β |
| Tandem repeats modify the structure of human genes hosted in segmental duplications. | De Grassi A et al. | β | 2009 | β |
| The future of genetics in psychology and psychiatry: microarrays, genome-wide association, and non-coding RNA. | Plomin R et al. | β | 2009 | β |
| The HLA genomic loci map: expression, interaction, diversity and disease. | Shiina T et al. | β | 2009 | β |
| The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation. | ten Tusscher KH et al. | β | 2009 | β |
| Use of cell lines in the investigation of pharmacogenetic loci. | Zhang W et al. | β | 2009 | β |
| Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations. | Li J et al. | β | 2009 | β |
| A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan. | Lin CH et al. | β | 2008 | β |
| Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. | Lee AS et al. | β | 2008 | β |
| Applying rapid genome sequencing technologies to characterize pathogen genomes. | Steinberg KM et al. | β | 2008 | β |
| A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. | Sharp AJ et al. | β | 2008 | β |
| A snapshot of CNVs in the pig genome. | Fadista J et al. | β | 2008 | β |
| Association between the catechol-O-methyltransferase Val158Met polymorphism and cocaine dependence. | Lohoff FW et al. | β | 2008 | β |
| Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome. | Camps J et al. | β | 2008 | β |
| Clinical features of maternal uniparental disomy 14 in patients with an epimutation and a deletion of the imprinted DLK1/GTL2 gene cluster. | Buiting K et al. | β | 2008 | β |
| Clinical utility of contemporary molecular cytogenetics. | Bejjani BA et al. | β | 2008 | β |
| CNTNAP2 gene dosage variation is associated with schizophrenia and epilepsy. | Friedman JI et al. | β | 2008 | β |
| Copy number variation at the 7q11.23 segmental duplications is a susceptibility factor for the Williams-Beuren syndrome deletion. | CuscΓ³ I et al. | β | 2008 | β |
| Copy number variation in the autism genome. | Feuk L | β | 2008 | β |
| Copy number variations (CNVs) identified in Korean individuals. | Kang TW et al. | β | 2008 | β |
| Copy number variations in the NF1 gene region are infrequent and do not predispose to recurrent type-1 deletions. | Steinmann K et al. | β | 2008 | β |
| Detailed analysis of 22q11.2 with a high density MLPA probe set. | Jalali GR et al. | β | 2008 | β |
| Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. | Franke L et al. | β | 2008 | β |
| Detection of known and novel genomic rearrangements by array based comparative genomic hybridisation: deletion of ZNF533 and duplication of CHARGE syndrome genes. | Monfort S et al. | β | 2008 | β |
| Development of therapeutic siRNAs for pachyonychia congenita. | Smith FJ et al. | β | 2008 | β |
| Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. | Baldwin EL et al. | β | 2008 | β |
| Fine-mapping subtelomeric deletions and duplications by comparative genomic hybridization in 42 individuals. | DeScipio C et al. | β | 2008 | β |
| FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. | Chen R et al. | β | 2008 | β |
| From human genetics and genomics to pharmacogenetics and pharmacogenomics: past lessons, future directions. | Nebert DW et al. | β | 2008 | β |
| Functional genetic variation of human miRNAs and phenotypic consequences. | Borel C et al. | β | 2008 | β |
| Gene copy number variation in schizophrenia. | Sutrala SR et al. | β | 2008 | β |
| Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility. | SolΓ© X et al. | β | 2008 | β |
| Genetic modifiers of the beta-haemoglobinopathies. | Thein SL | β | 2008 | β |
| Genetics of infantile seizures with paroxysmal dyskinesia: the infantile convulsions and choreoathetosis (ICCA) and ICCA-related syndromes. | Rochette J et al. | β | 2008 | β |
| Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling. | Lin CH et al. | β | 2008 | β |
| Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays. | Butcher LM et al. | β | 2008 | β |
| Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines. | Arriola E et al. | β | 2008 | β |
| Genomic investigation of alpha-synuclein multiplication and parkinsonism. | Ross OA et al. | β | 2008 | β |
| Genomics: the next step to elucidate the etiology of calcific aortic valve stenosis. | BossΓ© Y et al. | β | 2008 | β |
| Genotype, haplotype and copy-number variation in worldwide human populations. | Jakobsson M et al. | β | 2008 | β |
| High-resolution whole genome tiling path array CGH analysis of CD34+ cells from patients with low-risk myelodysplastic syndromes reveals cryptic copy number alterations and predicts overall and leukemia-free survival. | Starczynowski DT et al. | β | 2008 | β |
| How segmental duplications shape our genome: recent evolution of ABCC6 and PKD1 Mendelian disease genes. | Symmons O et al. | β | 2008 | β |
| Human copy number polymorphic genes. | Bailey JA et al. | β | 2008 | β |
| Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease. | de Smith AJ et al. | β | 2008 | β |
| Human MHC architecture and evolution: implications for disease association studies. | Traherne JA | β | 2008 | β |
| Identification of a 2244 base pair interstitial deletion within the human ESR1 gene in the Spanish population. | Galan JJ et al. | β | 2008 | β |
| Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes. | Shen F et al. | β | 2008 | β |
| Long interspersed nuclear element-1 (LINE1)-mediated deletion of EVC, EVC2, C4orf6, and STK32B in Ellis-van Creveld syndrome with borderline intelligence. | Temtamy SA et al. | β | 2008 | β |
| [Management of the CNVs in constitutional human genetics using array CGH]. | Nemos C et al. | β | 2008 | β |
| Mapping and sequencing of structural variation from eight human genomes. | Kidd JM et al. | β | 2008 | β |
| Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device. | Dube S et al. | β | 2008 | β |
| MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. | Chi B et al. | β | 2008 | β |
| Molecular mechanisms and diagnosis of chromosome 22q11.2 rearrangements. | Emanuel BS | β | 2008 | β |
| Multiple aberrations of chromosome 3p detected in oral premalignant lesions. | Tsui IF et al. | β | 2008 | β |
| p73 regulates neurodegeneration and phospho-tau accumulation during aging and Alzheimer's disease. | Wetzel MK et al. | β | 2008 | β |
| Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. | BrockmΓΆller J et al. | β | 2008 | β |
| Phenotypes, genotypes and disease susceptibility associated with gene copy number variations: complement C4 CNVs in European American healthy subjects and those with systemic lupus erythematosus. | Wu YL et al. | β | 2008 | β |
| Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. | Bruder CE et al. | β | 2008 | β |
| Population structure in copy number variation and SNPs in the CCL4L chemokine gene. | Colobran R et al. | β | 2008 | β |
| Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA). | GonzΓ‘lez JR et al. | β | 2008 | β |
| Progranulin locus deletion in frontotemporal dementia. | Gijselinck I et al. | β | 2008 | β |
| Quantitative analysis of single nucleotide polymorphisms within copy number variation. | Lee S et al. | β | 2008 | β |
| Quantitative trait locus association scan of early reading disability and ability using pooled DNA and 100K SNP microarrays in a sample of 5760 children. | Meaburn EL et al. | β | 2008 | β |
| Reduced purifying selection prevails over positive selection in human copy number variant evolution. | Nguyen DQ et al. | β | 2008 | β |
| Segmental copy-number variation observed in Japanese by array-CGH. | Takahashi N et al. | β | 2008 | β |
| Small deletion variants have stable breakpoints commonly associated with alu elements. | de Smith AJ et al. | β | 2008 | β |
| Somatic mosaicism for copy number variation in differentiated human tissues. | Piotrowski A et al. | β | 2008 | β |
| Studying copy number variations using a nanofluidic platform. | Qin J et al. | β | 2008 | β |
| Sub-megabase resolution tiling (SMRT) array-based comparative genomic hybridization profiling reveals novel gains and losses of chromosomal regions in Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma cell lines. | Fadlelmola FM et al. | β | 2008 | β |
| The common inversion of the Williams-Beuren syndrome region at 7q11.23 does not cause clinical symptoms. | Tam E et al. | β | 2008 | β |
| The current excitement about copy-number variation: how it relates to gene duplications and protein families. | Korbel JO et al. | β | 2008 | β |
| The effect of pedigree structure on detection of deletions and other null alleles. | Johansson AM et al. | β | 2008 | β |
| The fine-scale and complex architecture of human copy-number variation. | Perry GH et al. | β | 2008 | β |
| The positives, protocols, and perils of genome-wide association. | Neale BM et al. | β | 2008 | β |
| Therapeutic interference: a step closer for pachyonychia congenita? | Rugg EL | β | 2008 | β |
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| Three tiers of genome evolution in reptiles. | Organ CL et al. | β | 2008 | β |
| Trypsinogen copy number mutations in patients with idiopathic chronic pancreatitis. | Masson E et al. | β | 2008 | β |
| Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. | Chiang CW et al. | β | 2008 | β |
| Understanding incidental findings in the context of genetics and genomics. | Cho MK | β | 2008 | β |
| Where do we go for atherothrombotic disease genetics? | Brand-Herrmann SM | β | 2008 | β |
| Whole-genome amplification enables accurate genotyping for microarray-based high-density single nucleotide polymorphism array. | Jasmine F et al. | β | 2008 | β |
| wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data. | Cahan P et al. | β | 2008 | β |
| A Bayesian approach to copy-number-polymorphism analysis in nuclear pedigrees. | Kosta K et al. | β | 2007 | β |
| An innocuous duplication of 11.2 Mb at 13q21 is gene poor: sub-bands of gene paucity and pervasive CNV characterize the chromosome anomalies. | Daniel A et al. | β | 2007 | β |
| Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs. | Aradhya S et al. | β | 2007 | β |
| Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. | de Smith AJ et al. | β | 2007 | β |
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| Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. | Marioni JC et al. | β | 2007 | β |
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| Chromogenic and fluorescent in situ hybridization in breast cancer. | Lambros MB et al. | β | 2007 | β |
| Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. | Estivill X et al. | β | 2007 | β |
| Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. | Beckmann JS et al. | β | 2007 | β |
| Copy number variation in the human genome and its implications for cardiovascular disease. | Pollex RL et al. | β | 2007 | β |
| Copy-number variations and human disease. | Hegele RA | β | 2007 | β |
| Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. | Shen Y et al. | β | 2007 | β |
| Estimating prevalence, false-positive rate, and false-negative rate with use of repeated testing when true responses are unknown. | Jakobsdottir J et al. | β | 2007 | β |
| Evaluation of a commercially available focused aCGH platform for the detection of constitutional chromosome anomalies. | Shearer BM et al. | β | 2007 | β |
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| Functional constraint and small insertions and deletions in the ENCODE regions of the human genome. | Clark TG et al. | β | 2007 | β |
| Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. | Yang Y et al. | β | 2007 | β |
| Genomic drift and copy number variation of sensory receptor genes in humans. | Nozawa M et al. | β | 2007 | β |
| Genomic rearrangements and sporadic disease. | Lupski JR | β | 2007 | β |
| Germ-line DNA copy number variation frequencies in a large North American population. | Zogopoulos G et al. | β | 2007 | β |
| Interstitial deletion of chromosome 4p associated with mild mental retardation, epilepsy and polymicrogyria of the left temporal lobe. | MΓΈller RS et al. | β | 2007 | β |
| Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis. | Qiao Y et al. | β | 2007 | β |
| Methods and strategies for analyzing copy number variation using DNA microarrays. | Carter NP | β | 2007 | β |
| MLPA screening reveals novel subtelomeric rearrangements in holoprosencephaly. | Bendavid C et al. | β | 2007 | β |
| Modeling recurrent DNA copy number alterations in array CGH data. | Shah SP et al. | β | 2007 | β |
| Molecular karyotyping in patients with mental retardation using 100K single-nucleotide polymorphism arrays. | Hoyer J et al. | β | 2007 | β |
| Multiple prostate cancer risk variants on 8q24. | Witte JS | β | 2007 | β |
| Mutational and selective effects on copy-number variants in the human genome. | Cooper GM et al. | β | 2007 | β |
| Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments. | Lynch AG et al. | β | 2007 | β |
| Ohno's dilemma: evolution of new genes under continuous selection. | Bergthorsson U et al. | β | 2007 | β |
| PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. | Wang K et al. | β | 2007 | β |
| Polymorphic miRNA-mediated gene regulation: contribution to phenotypic variation and disease. | Georges M et al. | β | 2007 | β |
| QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. | Colella S et al. | β | 2007 | β |
| Reading and Generalist Genes. | Haworth CM et al. | β | 2007 | β |
| Recurrent DNA inversion rearrangements in the human genome. | Flores M et al. | β | 2007 | β |
| Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy. | Mefford HC et al. | β | 2007 | β |
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| Significant gene content variation characterizes the genomes of inbred mouse strains. | Cutler G et al. | β | 2007 | β |
| Simultaneous discovery and testing of deletions for disease association in SNP genotyping studies. | Kohler JR et al. | β | 2007 | β |
| Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. | Duan R et al. | β | 2007 | β |
| Skewed X-chromosome inactivation is associated with primary but not secondary ovarian failure. | Bretherick KL et al. | β | 2007 | β |
| The impact of array genomic hybridization on mental retardation research: a review of current technologies and their clinical utility. | Zahir F et al. | β | 2007 | β |
| Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio. | Ting JC et al. | β | 2007 | β |
| What a difference copy number variation makes. | Kehrer-Sawatzki H | β | 2007 | β |
| Whole-genome analysis and HLA genotyping of enteropathy-type T-cell lymphoma reveals 2 distinct lymphoma subtypes. | Deleeuw RJ et al. | β | 2007 | β |
| X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation. | Madrigal I et al. | β | 2007 | β |