The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism.
Parkinson disease
dopaminergic neurons
genetic risk
induced pluripotent stem cell
omics single-cell RNA sequencing single-cell ATAC sequencing SNCA LRRK2 GBA1
Journal
Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676
Informations de publication
Date de publication:
08 Mar 2023
08 Mar 2023
Historique:
received:
15
09
2022
revised:
22
09
2022
accepted:
12
01
2023
entrez:
23
3
2023
pubmed:
24
3
2023
medline:
24
3
2023
Statut:
epublish
Résumé
The Foundational Data Initiative for Parkinson Disease (FOUNDIN-PD) is an international collaboration producing fundamental resources for Parkinson disease (PD). FOUNDIN-PD generated a multi-layered molecular dataset in a cohort of induced pluripotent stem cell (iPSC) lines differentiated to dopaminergic (DA) neurons, a major affected cell type in PD. The lines were derived from the Parkinson's Progression Markers Initiative study, which included participants with PD carrying monogenic PD variants, variants with intermediate effects, and variants identified by genome-wide association studies and unaffected individuals. We generated genetic, epigenetic, regulatory, transcriptomic, and longitudinal cellular imaging data from iPSC-derived DA neurons to understand molecular relationships between disease-associated genetic variation and proximate molecular events. These data reveal that iPSC-derived DA neurons provide a valuable cellular context and foundational atlas for modeling PD genetic risk. We have integrated these data into a FOUNDIN-PD data browser as a resource for understanding the molecular pathogenesis of PD.
Identifiants
pubmed: 36950378
doi: 10.1016/j.xgen.2023.100261
pii: S2666-979X(23)00017-4
pmc: PMC10025424
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100261Références
Neurobiol Dis. 2020 Dec;146:105088
pubmed: 32977020
J Vis Exp. 2020 Aug 6;(162):
pubmed: 32831313
Nature. 2011 Nov 06;480(7378):547-51
pubmed: 22056989
Nature. 2017 May 4;545(7652):48-53
pubmed: 28445462
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Cell. 2019 Jun 13;177(7):1888-1902.e21
pubmed: 31178118
Bioinformatics. 2010 Sep 15;26(18):2336-7
pubmed: 20634204
Nat Genet. 2020 May;52(5):482-493
pubmed: 32341526
Mov Disord. 2018 May;33(5):771-782
pubmed: 29572948
Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3840-5
pubmed: 15738408
Parkinsonism Relat Disord. 2018 Nov;56:9-15
pubmed: 29934196
Cell Stem Cell. 2021 Feb 4;28(2):343-355.e5
pubmed: 33545081
Commun Biol. 2019 May 1;2:155
pubmed: 31069265
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Mov Disord. 2021 Apr;36(4):842-851
pubmed: 33513272
Nat Methods. 2021 Nov;18(11):1333-1341
pubmed: 34725479
PLoS Comput Biol. 2015 Apr 17;11(4):e1004219
pubmed: 25885710
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
J Stat Softw. 2010;33(1):1-22
pubmed: 20808728
Genome Biol. 2011 Aug 22;12(8):R83
pubmed: 21859476
Genome Biol. 2019 Nov 1;20(1):228
pubmed: 31675989
Brain. 2019 Jan 1;143(1):234-248
pubmed: 31755958
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
Mov Disord. 2019 Sep;34(9):1354-1364
pubmed: 31361367
Bioinformatics. 2012 May 15;28(10):1353-8
pubmed: 22492648
Nat Genet. 2021 Mar;53(3):304-312
pubmed: 33664506
Genome Res. 2005 Aug;15(8):1034-50
pubmed: 16024819
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10
pubmed: 27137889
Lancet Neurol. 2016 Nov;15(12):1257-1272
pubmed: 27751556
Lancet Neurol. 2019 Dec;18(12):1091-1102
pubmed: 31701892
Nucleic Acids Res. 2018 Jul 2;46(W1):W11-W16
pubmed: 29901812
Cell Stem Cell. 2022 Dec 1;29(12):1685-1702.e22
pubmed: 36459969
Stem Cell Reports. 2019 Nov 12;13(5):924-938
pubmed: 31668852
Mov Disord. 2020 Nov;35(11):2056-2067
pubmed: 32864809
Nat Methods. 2019 Dec;16(12):1289-1296
pubmed: 31740819
Neurobiol Aging. 2017 Sep;57:247.e9-247.e13
pubmed: 28602509
Cell. 2016 Oct 6;167(2):566-580.e19
pubmed: 27716510
Nature. 2004 Oct 14;431(7010):805-10
pubmed: 15483602
Cell Rep. 2020 Oct 13;33(2):108263
pubmed: 33053338
Nat Commun. 2020 Aug 21;11(1):4183
pubmed: 32826893
J Cell Biol. 2017 Jul 3;216(7):1993-2009
pubmed: 28592444
Nat Biotechnol. 2019 Aug;37(8):925-936
pubmed: 31375813
Sci Rep. 2020 Oct 7;10(1):16672
pubmed: 33028846
Lancet Neurol. 2020 Feb;19(2):170-178
pubmed: 31521533
Nucleic Acids Res. 2019 Jan 8;47(D1):D135-D139
pubmed: 30371849
Cell. 2018 Apr 19;173(3):792-803.e19
pubmed: 29656897
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Nat Neurosci. 2015 Dec;18(12):1707-12
pubmed: 26605881
Nat Genet. 2019 May;51(5):768-769
pubmed: 31043754
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Bioinformatics. 2018 Dec 1;34(23):3983-3989
pubmed: 29931280
Stem Cell Reports. 2018 Oct 9;11(4):897-911
pubmed: 30245212
Sci Data. 2020 Oct 12;7(1):340
pubmed: 33046718
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Mov Disord. 2020 May;35(5):774-780
pubmed: 31958187
Cell Stem Cell. 2017 Jan 5;20(1):29-40
pubmed: 28094018
Nat Commun. 2012;3:1070
pubmed: 22990866
Prog Neurobiol. 2011 Dec;95(4):629-35
pubmed: 21930184
Nat Methods. 2017 Apr;14(4):417-419
pubmed: 28263959
Science. 2002 Feb 15;295(5558):1306-11
pubmed: 11847345
Sci Adv. 2020 Jul 22;6(30):eaba2619
pubmed: 32832661
Bioinformatics. 2021 Apr 20;37(3):422-423
pubmed: 32745185
Front Cell Dev Biol. 2022 Mar 04;10:804164
pubmed: 35317387
Nat Commun. 2017 Jan 16;8:14049
pubmed: 28091601