Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations

Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an...

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Published inNature communications Vol. 11; no. 1; pp. 255 - 9
Main Authors Li, Yun Rose, Glessner, Joseph T., Coe, Bradley P., Li, Jin, Mohebnasab, Maede, Chang, Xiao, Connolly, John, Kao, Charlly, Wei, Zhi, Bradfield, Jonathan, Kim, Cecilia, Hou, Cuiping, Khan, Munir, Mentch, Frank, Qiu, Haijun, Bakay, Marina, Cardinale, Christopher, Lemma, Maria, Abrams, Debra, Bridglall-Jhingoor, Andrew, Behr, Meckenzie, Harrison, Shanell, Otieno, George, Thomas, Alexandria, Wang, Fengxiang, Chiavacci, Rosetta, Wu, Lawrence, Hadley, Dexter, Goldmuntz, Elizabeth, Elia, Josephine, Maris, John, Grundmeier, Robert, Devoto, Marcella, Keating, Brendan, March, Michael, Pellagrino, Renata, Grant, Struan F. A., Sleiman, Patrick M. A., Li, Mingyao, Eichler, Evan E., Hakonarson, Hakon
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 14.01.2020
Nature Publishing Group
Nature Portfolio
Subjects
45/43
45/61
631/208/205/2138
631/208/726/649/2157
631/208/727/2000
692/699
Arrays
Bias
Binding sites
Child & adolescent psychiatry
Comparative Genomic Hybridization
Copy number
Databases, Genetic
Disease
DNA Copy Number Variations
European Continental Ancestry Group - genetics
Exons
Gene deletion
Genes
Genetic Loci
Genetic Predisposition to Disease - ethnology
Genetic Predisposition to Disease - genetics
Genome, Human - genetics
Genome-Wide Association Study
Genomes
Genomics
Hospitals
Humanities and Social Sciences
Humans
Hybridization
Medicine
Mental disorders
Metabolism
Molecular Sequence Annotation
multidisciplinary
Non-coding RNA
Phenotypes
Polymorphism, Single Nucleotide
Quality control
Science
Science (multidisciplinary)
Single-nucleotide polymorphism
Online AccessGet full text

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Abstract Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution ( P  < 1 × 10 −3 ). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease. Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array and array comparative genomic hybridization data of 100,028 individuals and report their associations with immune-related, cardiometabolic and neuropsychiatric diseases as well as cancer.
AbstractList Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution ( P  < 1 × 10 −3 ). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease. Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array and array comparative genomic hybridization data of 100,028 individuals and report their associations with immune-related, cardiometabolic and neuropsychiatric diseases as well as cancer.
Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array and array comparative genomic hybridization data of 100,028 individuals and report their associations with immune-related, cardiometabolic and neuropsychiatric diseases as well as cancer.
Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution (P < 1 × 10 ). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease.
Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution (P < 1 × 10-3). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease.Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution (P < 1 × 10-3). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease.
Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution ( P  < 1 × 10 −3 ). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease.
Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution (P < 1 × 10−3). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease.Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array and array comparative genomic hybridization data of 100,028 individuals and report their associations with immune-related, cardiometabolic and neuropsychiatric diseases as well as cancer.
ArticleNumber 255
Author Mentch, Frank
Wu, Lawrence
Sleiman, Patrick M. A.
Bradfield, Jonathan
Wei, Zhi
Bridglall-Jhingoor, Andrew
Kao, Charlly
Lemma, Maria
Abrams, Debra
Goldmuntz, Elizabeth
Hakonarson, Hakon
Elia, Josephine
Glessner, Joseph T.
Grundmeier, Robert
Khan, Munir
Hadley, Dexter
Devoto, Marcella
Hou, Cuiping
Chiavacci, Rosetta
Coe, Bradley P.
Otieno, George
Wang, Fengxiang
Maris, John
Keating, Brendan
Kim, Cecilia
Behr, Meckenzie
Pellagrino, Renata
Qiu, Haijun
March, Michael
Grant, Struan F. A.
Chang, Xiao
Eichler, Evan E.
Connolly, John
Bakay, Marina
Cardinale, Christopher
Thomas, Alexandria
Harrison, Shanell
Li, Yun Rose
Mohebnasab, Maede
Li, Mingyao
Li, Jin
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/31937769$$D View this record in MEDLINE/PubMed
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SSID ssj0000391844
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Snippet Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases,...
Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array...
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pubmed
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springer
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StartPage 255
SubjectTerms 45/43
45/61
631/208/205/2138
631/208/726/649/2157
631/208/727/2000
692/699
Arrays
Bias
Binding sites
Child & adolescent psychiatry
Comparative Genomic Hybridization
Copy number
Databases, Genetic
Disease
DNA Copy Number Variations
European Continental Ancestry Group - genetics
Exons
Gene deletion
Genes
Genetic Loci
Genetic Predisposition to Disease - ethnology
Genetic Predisposition to Disease - genetics
Genome, Human - genetics
Genome-Wide Association Study
Genomes
Genomics
Hospitals
Humanities and Social Sciences
Humans
Hybridization
Medicine
Mental disorders
Metabolism
Molecular Sequence Annotation
multidisciplinary
Non-coding RNA
Phenotypes
Polymorphism, Single Nucleotide
Quality control
Science
Science (multidisciplinary)
Single-nucleotide polymorphism
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Title Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations
URI https://link.springer.com/article/10.1038/s41467-019-13624-1
https://www.ncbi.nlm.nih.gov/pubmed/31937769
https://www.proquest.com/docview/2342502509
https://www.proquest.com/docview/2338994696
https://pubmed.ncbi.nlm.nih.gov/PMC6959272
https://doaj.org/article/bff05ccd6ca145f18966c6e073fcf8bb
Volume 11
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