Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.

TitleIdentification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.
Publication TypeJournal Article
Year of Publication2021
AuthorsBonder, MJan, Smail, C, Gloudemans, MJ, Frésard, L, Jakubosky, D, D'Antonio, M, Li, X, Ferraro, NM, Carcamo-Orive, I, Mirauta, B, Seaton, DD, Cai, N, Vakili, D, Horta, D, Zhao, C, Zastrow, DB, Bonner, DE, Wheeler, MT, Kilpinen, H, Knowles, JW, Smith, EN, Frazer, KA, Montgomery, SB, Stegle, O
Corporate AuthorsHipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium
JournalNat Genet
Volume53
Issue3
Pagination313-321
Date Published2021 03
ISSN1546-1718
KeywordsBardet-Biedl Syndrome, Calcium Channels, Cell Line, Cerebellar Ataxia, DNA Methylation, Gene Expression, Genetic Variation, Humans, Induced Pluripotent Stem Cells, Polymorphism, Single Nucleotide, Proteins, Quantitative Trait Loci, Rare Diseases, Regulatory Sequences, Nucleic Acid, Sequence Analysis, RNA, Whole Genome Sequencing
Abstract

Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.

DOI10.1038/s41588-021-00800-7
Alternate JournalNat Genet
PubMed ID33664507
PubMed Central IDPMC7944648
Grant ListU01 DK105541 / DK / NIDDK NIH HHS / United States
DP3 DK112155 / DK / NIDDK NIH HHS / United States
U01 HG007708 / HG / NHGRI NIH HHS / United States
R01 DK107437 / DK / NIDDK NIH HHS / United States
U01 HG010218 / HG / NHGRI NIH HHS / United States
R01 HL142015 / HL / NHLBI NIH HHS / United States
U01 HG009080 / HG / NHGRI NIH HHS / United States
R01 DK116750 / DK / NIDDK NIH HHS / United States
R01 AG066490 / AG / NIA NIH HHS / United States
P30 DK116074 / DK / NIDDK NIH HHS / United States
U01 HL107388 / HL / NHLBI NIH HHS / United States
T32 LM012409 / LM / NLM NIH HHS / United States
WT098503 / WT / Wellcome Trust / United Kingdom
U01 HG009431 / HG / NHGRI NIH HHS / United States
R01 HG008150 / HG / NHGRI NIH HHS / United States
R01 DK106236 / DK / NIDDK NIH HHS / United States
U01 HL107442 / HL / NHLBI NIH HHS / United States
R01 DK120565 / DK / NIDDK NIH HHS / United States
T15 LM007033 / LM / NLM NIH HHS / United States
/ MR / Medical Research Council / United Kingdom
WT090851 / WT / Wellcome Trust / United Kingdom
S10 OD023452 / OD / NIH HHS / United States
/ WT / Wellcome Trust / United Kingdom