Genome-Wide Gene-Set Analysis Approaches in Amyotrophic Lateral Sclerosis.
ALS pathology
amyotrophic lateral sclerosis
functional genomics
gene-set analysis
genome-wide association studies
Journal
Journal of personalized medicine
ISSN: 2075-4426
Titre abrégé: J Pers Med
Pays: Switzerland
ID NLM: 101602269
Informations de publication
Date de publication:
20 Nov 2022
20 Nov 2022
Historique:
received:
30
09
2022
revised:
11
11
2022
accepted:
12
11
2022
entrez:
24
11
2022
pubmed:
25
11
2022
medline:
25
11
2022
Statut:
epublish
Résumé
The rapid increase in the number of genetic variants identified to be associated with Amyotrophic Lateral Sclerosis (ALS) through genome-wide association studies (GWAS) has created an emerging need to understand the functional pathways that are implicated in the pathology of ALS. Gene-set analysis (GSA) is a powerful method that can provide insight into the associated biological pathways, determining the joint effect of multiple genetic markers. The main contribution of this review is the collection of ALS GSA studies that employ GWAS or individual-based genotype data, investigating their methodology and results related to ALS-associated molecular pathways. Furthermore, the limitations in standard single-gene analyses are summarized, highlighting the power of gene-set analysis, and a brief overview of the statistical properties of gene-set analysis and related concepts is provided. The main aims of this review are to investigate the reproducibility of the collected studies and identify their strengths and limitations, in order to enhance the experimental design and therefore the quality of the results of future studies, deepening our understanding of this devastating disease.
Identifiants
pubmed: 36422108
pii: jpm12111932
doi: 10.3390/jpm12111932
pmc: PMC9699154
pii:
doi:
Types de publication
Journal Article
Review
Langues
eng
Subventions
Organisme : Department for the Economy
ID : No number
Références
PLoS Comput Biol. 2015 Apr 17;11(4):e1004219
pubmed: 25885710
Brain Commun. 2020 Aug 14;2(2):fcaa119
pubmed: 33005893
Nature. 1993 Mar 4;362(6415):59-62
pubmed: 8446170
Mol Biol Cell. 2005 Sep;16(9):3951-62
pubmed: 15958490
Hum Mol Genet. 2008 Mar 1;17(5):768-74
pubmed: 18057069
Philos Trans R Soc Lond B Biol Sci. 2006 Sep 29;361(1473):1545-64
pubmed: 16939974
Med Genet. 2018;30(2):252-258
pubmed: 30220791
Front Genet. 2020 Jun 30;11:654
pubmed: 32695141
Neuron. 2011 Oct 20;72(2):257-68
pubmed: 21944779
Nat Commun. 2021 Nov 16;12(1):6622
pubmed: 34785650
Mol Neurobiol. 2017 Jul;54(5):3162-3179
pubmed: 27052956
Genet Epidemiol. 2010 Apr;34(3):201-12
pubmed: 19810024
Nat Genet. 2013 Oct;45(10):1238-1243
pubmed: 24013639
Nat Rev Dis Primers. 2017 Oct 05;3:17071
pubmed: 28980624
BMC Bioinformatics. 2013 Apr 15;14:128
pubmed: 23586463
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W77-83
pubmed: 23703215
Gigascience. 2019 Jul 1;8(7):
pubmed: 31307061
PLoS Comput Biol. 2015 Oct 05;11(10):e1004467
pubmed: 26436655
Cell Mol Neurobiol. 2018 Apr;38(3):635-639
pubmed: 28639078
Mol Neurobiol. 2015 Feb;51(1):361-9
pubmed: 24647822
Nat Rev Genet. 2009 Nov;10(11):769-82
pubmed: 19823194
Nucleic Acids Res. 2019 Jul 2;47(W1):W191-W198
pubmed: 31066453
N Engl J Med. 2001 May 31;344(22):1688-700
pubmed: 11386269
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Curr Opin Cell Biol. 2020 Apr;63:57-67
pubmed: 31972475
Neuroepidemiology. 2013;41(2):118-30
pubmed: 23860588
Am J Hum Genet. 2007 Dec;81(6):1278-83
pubmed: 17966091
Nucleic Acids Res. 2017 Jan 4;45(D1):D833-D839
pubmed: 27924018
Lancet Neurol. 2007 Apr;6(4):322-8
pubmed: 17362836
J Pers Med. 2020 Aug 25;10(3):
pubmed: 32854276
Nat Commun. 2017 Sep 20;8(1):611
pubmed: 28931804
Chest. 2019 Feb;155(2):401-408
pubmed: 29990478
J Neurol Neurosurg Psychiatry. 2017 Dec;88(12):1042-1044
pubmed: 28642287
Sci Adv. 2021 Jan 15;7(3):
pubmed: 33523907
Nat Genet. 2016 Sep;48(9):1043-8
pubmed: 27455348
Hum Genet. 2009 Aug;126(2):289-301
pubmed: 19408013
Nat Rev Neurol. 2011 Oct 11;7(11):603-15
pubmed: 21989245
J Neurol Sci. 2019 Apr 15;399:217-226
pubmed: 30870681
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W437-43
pubmed: 21622953
Lancet Neurol. 2018 Jan;17(1):94-102
pubmed: 29154141
Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361
pubmed: 27899662
Brain Commun. 2021 Oct 07;3(4):fcab236
pubmed: 34708205
Genome Med. 2020 May 18;12(1):44
pubmed: 32423490
Neuroscience. 2007 Feb 9;144(3):991-1003
pubmed: 17150307
J Pers Med. 2020 Nov 26;10(4):
pubmed: 33256133
Cell Syst. 2015 Dec 23;1(6):417-425
pubmed: 26771021
J Pers Med. 2018 Dec 13;8(4):
pubmed: 30551677
Nat Commun. 2017 Nov 28;8(1):1826
pubmed: 29184056
Am J Psychiatry. 2017 Sep 1;174(9):850-858
pubmed: 28494655
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Neuron. 2018 Mar 21;97(6):1268-1283.e6
pubmed: 29566793
Nat Genet. 2015 Dec;47(12):1385-92
pubmed: 26523775
Bioinformatics. 2007 Apr 15;23(8):980-7
pubmed: 17303618
Nat Genet. 2021 Dec;53(12):1636-1648
pubmed: 34873335
Neurobiol Aging. 2014 Jul;35(7):1778.e9-1778.e23
pubmed: 24529757
Nucleic Acids Res. 2017 Jan 4;45(D1):D896-D901
pubmed: 27899670
Nucleic Acids Res. 2009 Jan;37(1):1-13
pubmed: 19033363
Nat Rev Neurol. 2017 Feb;13(2):96-104
pubmed: 27982040
Front Neurol. 2019 May 14;10:400
pubmed: 31139131
Nat Rev Genet. 2016 Apr 12;17(6):353-64
pubmed: 27070863
Front Neurosci. 2021 Apr 30;15:657465
pubmed: 33994932
Nucleic Acids Res. 2020 Jan 8;48(D1):D845-D855
pubmed: 31680165
Am J Med Genet B Neuropsychiatr Genet. 2015 Oct;168(7):517-27
pubmed: 26059482
Nat Neurosci. 2014 Jan;17(1):17-23
pubmed: 24369373
Cell. 2010 Aug 6;142(3):350-1; author reply 353-5
pubmed: 20691890
Genet Mol Res. 2015 Jun 11;14(2):6429-38
pubmed: 26125848
Nat Rev Genet. 2019 Aug;20(8):467-484
pubmed: 31068683
Commun Biol. 2020 Sep 23;3(1):526
pubmed: 32968195
Nat Commun. 2016 Aug 11;7:12408
pubmed: 27510634
Amyotroph Lateral Scler. 2009 Oct-Dec;10(5-6):310-23
pubmed: 19922118
NeuroRx. 2004 Apr;1(2):255-62
pubmed: 15717026