Genome-wide detection of tandem DNA repeats that are expanded in autism

Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders 1 . Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we inve...

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Published inNature (London) Vol. 586; no. 7827; pp. 80 - 86
Main Authors Trost, Brett, Engchuan, Worrawat, Nguyen, Charlotte M., Thiruvahindrapuram, Bhooma, Dolzhenko, Egor, Backstrom, Ian, Mirceta, Mila, Mojarad, Bahareh A., Yin, Yue, Dov, Alona, Chandrakumar, Induja, Prasolava, Tanya, Shum, Natalie, Hamdan, Omar, Pellecchia, Giovanna, Howe, Jennifer L., Whitney, Joseph, Klee, Eric W., Baheti, Saurabh, Amaral, David G., Anagnostou, Evdokia, Elsabbagh, Mayada, Fernandez, Bridget A., Hoang, Ny, Lewis, M. E. Suzanne, Liu, Xudong, Sjaarda, Calvin, Smith, Isabel M., Szatmari, Peter, Zwaigenbaum, Lonnie, Glazer, David, Hartley, Dean, Stewart, A. Keith, Eberle, Michael A., Sato, Nozomu, Pearson, Christopher E., Scherer, Stephen W., Yuen, Ryan K. C.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.10.2020
Nature Publishing Group
Subjects
45/22
45/23
45/29
45/77
631/208/212/2301
631/208/457/649
631/378/2583
692/699/375/366/1373
Autism
Autism Spectrum Disorder - genetics
Cardiovascular system
Complexity
Cytogenetics
Deoxyribonucleic acid
DNA
DNA Repeat Expansion - genetics
Etiology
Exons
Female
Fibroblast Growth Factors - genetics
Fragile sites
Frataxin
Genes
Genetic Predisposition to Disease
Genetics
Genome, Human - genetics
Genomes
Genomics
Heterogeneity
Humanities and Social Sciences
Humans
Intelligence - genetics
Iron-Binding Proteins - genetics
Male
multidisciplinary
Muscles
Myotonin-Protein Kinase - genetics
Nervous system
Nucleotide Motifs
Nucleotide sequence
Polymorphism
Polymorphism, Genetic
Population control
Science
Science (multidisciplinary)
Splice junctions
Tandem Repeat Sequences - genetics
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Abstract Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders 1 . Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2–20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD) 2 , 3 and population control individuals 4 . We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN , which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1 . Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD. Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.
AbstractList Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.
Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders . Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD) and population control individuals . We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.
Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics oftandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions oftandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.
Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders 1 . Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2–20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD) 2 , 3 and population control individuals 4 . We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN , which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1 . Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD. Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.
Author Smith, Isabel M.
Amaral, David G.
Mojarad, Bahareh A.
Sato, Nozomu
Thiruvahindrapuram, Bhooma
Chandrakumar, Induja
Howe, Jennifer L.
Trost, Brett
Yuen, Ryan K. C.
Stewart, A. Keith
Yin, Yue
Dov, Alona
Szatmari, Peter
Eberle, Michael A.
Anagnostou, Evdokia
Scherer, Stephen W.
Engchuan, Worrawat
Glazer, David
Hamdan, Omar
Liu, Xudong
Nguyen, Charlotte M.
Fernandez, Bridget A.
Hoang, Ny
Zwaigenbaum, Lonnie
Dolzhenko, Egor
Sjaarda, Calvin
Klee, Eric W.
Prasolava, Tanya
Lewis, M. E. Suzanne
Backstrom, Ian
Pearson, Christopher E.
Mirceta, Mila
Hartley, Dean
Shum, Natalie
Baheti, Saurabh
Whitney, Joseph
Pellecchia, Giovanna
Elsabbagh, Mayada
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Snippet Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic...
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SubjectTerms 45/22
45/23
45/29
45/77
631/208/212/2301
631/208/457/649
631/378/2583
692/699/375/366/1373
Autism
Autism Spectrum Disorder - genetics
Cardiovascular system
Complexity
Cytogenetics
Deoxyribonucleic acid
DNA
DNA Repeat Expansion - genetics
Etiology
Exons
Female
Fibroblast Growth Factors - genetics
Fragile sites
Frataxin
Genes
Genetic Predisposition to Disease
Genetics
Genome, Human - genetics
Genomes
Genomics
Heterogeneity
Humanities and Social Sciences
Humans
Intelligence - genetics
Iron-Binding Proteins - genetics
Male
multidisciplinary
Muscles
Myotonin-Protein Kinase - genetics
Nervous system
Nucleotide Motifs
Nucleotide sequence
Polymorphism
Polymorphism, Genetic
Population control
Science
Science (multidisciplinary)
Splice junctions
Tandem Repeat Sequences - genetics
Title Genome-wide detection of tandem DNA repeats that are expanded in autism
URI https://link.springer.com/article/10.1038/s41586-020-2579-z
https://www.ncbi.nlm.nih.gov/pubmed/32717741
https://www.proquest.com/docview/2755620764
https://www.proquest.com/docview/2428064396
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