A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci.

Alu Elements DNA Transposable Elements / genetics Genetic Predisposition to Disease Genetic Variation Genome, Human Genome-Wide Association Study Humans Polymorphism, Single Nucleotide Quantitative Trait Loci

Journal

Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021

Informations de publication

Date de publication:
04 2022
Historique:
received: 14 03 2021
accepted: 28 01 2022
pubmed: 26 3 2022
medline: 13 4 2022
entrez: 25 3 2022
Statut: ppublish

Résumé

Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-

Identifiants

DOI: 10.1101/gr.275515.121 PMID: 35332097 PMC: PMC8997352
pubmed: 35332097
pii: gr.275515.121
doi: 10.1101/gr.275515.121
pmc: PMC8997352
doi:

Substances chimiques

DNA Transposable Elements 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

656-670

Informations de copyright

© 2022 van Bree et al.; Published by Cold Spring Harbor Laboratory Press.

Références

Mob DNA. 2020 Mar 31;11:13
pubmed: 32266012
Nature. 2020 May;581(7809):444-451
pubmed: 32461652
PLoS Genet. 2013 Apr;9(4):e1003470
pubmed: 23637635
Nat Genet. 2013 Dec;45(12):1452-8
pubmed: 24162737
Aging Cell. 2013 Apr;12(2):247-56
pubmed: 23360310
Nat Commun. 2021 Jun 7;12(1):3417
pubmed: 34099642
Cell Rep. 2018 Jun 5;23(10):2874-2880
pubmed: 29874575
Nature. 1988 Mar 10;332(6160):164-6
pubmed: 2831458
PLoS Comput Biol. 2013;9(8):e1003118
pubmed: 23950696
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Cell Rep. 2014 Oct 23;9(2):767-79
pubmed: 25373911
Hum Mol Genet. 2016 Dec 1;25(23):5059-5068
pubmed: 27794540
Genome Biol. 2020 Sep 28;21(1):255
pubmed: 32988383
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Elife. 2018 Aug 02;7:
pubmed: 30070637
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Nat Genet. 2010 Sep;42(9):781-5
pubmed: 20711177
Nat Commun. 2018 Jan 15;9(1):189
pubmed: 29335486
Nat Neurosci. 2013 May;16(5):529-31
pubmed: 23563579
Gene. 2013 Jan 10;512(2):429-37
pubmed: 22960267
Science. 2009 Feb 27;323(5918):1208-1211
pubmed: 19251628
Mob DNA. 2016 May 06;7:9
pubmed: 27158268
Nat Commun. 2014 Sep 23;5:5011
pubmed: 25247314
Nat Biotechnol. 2011 Nov 13;30(1):99-104
pubmed: 22081020
PLoS One. 2014 Mar 07;9(6):e90833
pubmed: 24608899
Cell. 2019 Jan 24;176(3):663-675.e19
pubmed: 30661756
Bioinformatics. 2014 Apr 1;30(7):1008-9
pubmed: 24363377
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
Mol Neurobiol. 2015;51(3):1240-8
pubmed: 24981432
Mol Cell. 2020 Dec 3;80(5):915-928.e5
pubmed: 33186547
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genome Biol. 2014;15(12):550
pubmed: 25516281
Alzheimers Dement. 2014 Jan;10(1):45-52
pubmed: 23535033
Nucleic Acids Res. 1991 Jul 11;19(13):3619-23
pubmed: 1649453
Bioinformatics. 2012 Apr 15;28(8):1166-7
pubmed: 22368248
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Cell Res. 2018 Feb;28(2):187-203
pubmed: 29327725
Am J Hum Genet. 2007 Mar;80(3):393-406
pubmed: 17273961
Lancet Neurol. 2019 Dec;18(12):1091-1102
pubmed: 31701892
Genome Res. 2019 Oct;29(10):1567-1577
pubmed: 31575651
Nat Rev Genet. 2009 Oct;10(10):691-703
pubmed: 19763152
Nat Genet. 2009 Dec;41(12):1308-12
pubmed: 19915575
Am J Hum Genet. 2003 Dec;73(6):1444-51
pubmed: 14628287
NPJ Parkinsons Dis. 2021 May 25;7(1):44
pubmed: 34035310
Nature. 2021 Nov;599(7886):628-634
pubmed: 34662886
Mov Disord. 2020 Nov;35(11):2056-2067
pubmed: 32864809
Trends Neurosci. 2008 Jul;31(7):328-34
pubmed: 18550185
PLoS Genet. 2011 Feb;7(2):e1001308
pubmed: 21379329
Science. 2016 Mar 4;351(6277):1083-7
pubmed: 26941318
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
Neurobiol Aging. 2011 Apr;32(4):756.e11-5
pubmed: 21220176
Genome Biol. 2010;11(8):R86
pubmed: 20738864
Science. 2009 Feb 27;323(5918):1205-8
pubmed: 19251627
N Engl J Med. 2019 Jul 4;381(1):64-74
pubmed: 31269367
Genome Res. 2017 Oct;27(10):1623-1633
pubmed: 28855262
J Virol. 2005 Sep;79(17):10890-901
pubmed: 16103141
Neurology. 2013 Aug 6;81(6):541-4
pubmed: 23825177
Comput Appl Biosci. 1988 Mar;4(1):11-7
pubmed: 3382986
Genomics. 2013 May;101(5):273-81
pubmed: 23517681
Parkinsonism Relat Disord. 2017 Nov;44:79-84
pubmed: 28917824
Lancet Neurol. 2010 Oct;9(10):995-1007
pubmed: 20864052
BMC Evol Biol. 2013 May 21;13:101
pubmed: 23692647
Cell Stem Cell. 2019 May 2;24(5):724-735.e5
pubmed: 31006620
Am J Hum Genet. 2013 Nov 7;93(5):779-97
pubmed: 24210251
Nature. 2016 Feb 11;530(7589):177-83
pubmed: 26814963
Heredity (Edinb). 2021 Dec;127(6):485-497
pubmed: 34689168
Nat Genet. 2021 Mar;53(3):392-402
pubmed: 33589840
JAMA. 2010 May 12;303(18):1832-40
pubmed: 20460622
PLoS One. 2011 Feb 24;6(2):e16616
pubmed: 21390209
Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):629-631
pubmed: 28082723
Arch Neurol. 2011 Mar;68(3):320-8
pubmed: 21059989
PLoS Genet. 2014 Sep 04;10(9):e1004606
pubmed: 25188341
Nucleic Acids Res. 2017 Jan 4;45(D1):D896-D901
pubmed: 27899670
Nat Biotechnol. 2021 Mar;39(3):302-308
pubmed: 33288906
Transl Psychiatry. 2020 Nov 2;10(1):369
pubmed: 33139705
Prog Neurobiol. 2005 Sep-Oct;77(1-2):128-38
pubmed: 16243425
Nature. 2014 Dec 18;516(7531):405-9
pubmed: 25317556
Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E11020-E11028
pubmed: 29229810
Nat Genet. 2017 Oct;49(10):1511-1516
pubmed: 28892059
Nat Genet. 2014 Sep;46(9):989-93
pubmed: 25064009
Cell Stem Cell. 2008 Nov 6;3(5):519-32
pubmed: 18983967
Science. 2021 Apr 2;372(6537):
pubmed: 33632895
Nature. 2001 Feb 15;409(6822):860-921
pubmed: 11237011
Nat Genet. 2019 Mar;51(3):404-413
pubmed: 30617256
Nat Commun. 2019 Apr 16;10(1):1784
pubmed: 30992455
Bioinformatics. 2010 Sep 15;26(18):2336-7
pubmed: 20634204
J Alzheimers Dis. 2011;24(4):751-8
pubmed: 21321396
Nature. 2009 Feb 12;457(7231):854-8
pubmed: 19212405
Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23243-23253
pubmed: 31659027
BMC Genomics. 2018 Jun 18;19(1):468
pubmed: 29914366
Bioinformatics. 2015 Nov 1;31(21):3555-7
pubmed: 26139635
Nat Rev Neurol. 2014 Jun;10(6):337-48
pubmed: 24840975
Nature. 2014 Dec 11;516(7530):242-5
pubmed: 25274305
Bioinformatics. 2021 Apr 20;37(3):422-423
pubmed: 32745185
Curr Opin Genet Dev. 1999 Dec;9(6):657-63
pubmed: 10607616
Mol Psychiatry. 2013 Nov;18(11):1225-34
pubmed: 23399914
Bioinformatics. 2015 Apr 15;31(8):1334-6
pubmed: 25431330
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nat Rev Genet. 2019 Dec;20(12):760-772
pubmed: 31515540
Int J Mol Sci. 2019 Nov 27;20(23):
pubmed: 31783611
Neurosci Lett. 2016 Mar 11;616:189-96
pubmed: 26828303
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Stem Cell Reports. 2019 Feb 12;12(2):245-257
pubmed: 30639214
Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3984-E3992
pubmed: 28465436
Mol Neurobiol. 2018 Feb;55(2):1740-1749
pubmed: 28220356
Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5280-5
pubmed: 12682288
Genome Res. 2021 Apr;31(4):551-563
pubmed: 33722937
Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190347
pubmed: 32075564

Auteurs

Elisabeth J van Bree (EJ)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Rita L F P Guimarães (RLFP)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.
Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.

Mischa Lundberg (M)

Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia.

Elena R Blujdea (ER)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Jimi L Rosenkrantz (JL)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Fred T G White (FTG)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Josse Poppinga (J)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Paula Ferrer-Raventós (P)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Anne-Fleur E Schneider (AE)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Isabella Clayton (I)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

David Haussler (D)

UC Santa Cruz Genomics Institute, and Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, California 95064, USA.

Marcel J T Reinders (MJT)

Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands.

Henne Holstege (H)

Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.
Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.
Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands.
Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands.
ORCID: 0000-0002-7688-3087

Adam D Ewing (AD)

Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia.

Colette Moses (C)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Frank M J Jacobs (FMJ)

Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands.
ORCID: 0000-0003-4423-1479

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Effectiveness of Virtual Yoga for Chronic Low Back Pain: A Randomized Clinical Trial.

Hallie Tankha, Devyn Gaskins, Amanda Shallcross et al.
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées dispersées › Rétroéléments › Éléments SINE › Séquences Alu › A hidden layer of structural variation in...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées dispersées › Éléments transposables d'ADN › A hidden layer of structural variation in...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Prédisposition génétique à une maladie › A hidden layer of structural variation in...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › A hidden layer of structural variation in...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › A hidden layer of structural variation in...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › A hidden layer of structural variation in...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › A hidden layer of structural variation in...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › A hidden layer of structural variation in...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Locus génétiques › Locus de caractère quantitatif › A hidden layer of structural variation in...