Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study
- PMID:37802043
- PMCID: PMC10577076
- DOI: 10.1016/j.ajhg.2023.09.003
Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study
Abstract
Long non-coding RNAs (lncRNAs) are known to perform important regulatory functions in lipid metabolism. Large-scale whole-genome sequencing (WGS) studies and new statistical methods for variant set tests now provide an opportunity to assess more associations between rare variants in lncRNA genes and complex traits across the genome. In this study, we used high-coverage WGS from 66,329 participants of diverse ancestries with measurement of blood lipids and lipoproteins (LDL-C, HDL-C, TC, and TG) in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) program to investigate the role of lncRNAs in lipid variability. We aggregated rare variants for 165,375 lncRNA genes based on their genomic locations and conducted rare-variant aggregate association tests using the STAAR (variant-set test for association using annotation information) framework. We performed STAAR conditional analysis adjusting for common variants in known lipid GWAS loci and rare-coding variants in nearby protein-coding genes. Our analyses revealed 83 rare lncRNA variant sets significantly associated with blood lipid levels, all of which were located in known lipid GWAS loci (in a ±500-kb window of a Global Lipids Genetics Consortium index variant). Notably, 61 out of 83 signals (73%) were conditionally independent of common regulatory variation and rare protein-coding variation at the same loci. We replicated 34 out of 61 (56%) conditionally independent associations using the independent UK Biobank WGS data. Our results expand the genetic architecture of blood lipids to rare variants in lncRNAs.
Keywords: association; blood lipid; cholesterol; lncRNA; rare variants; whole-genome sequencing.
Copyright © 2023 American Society of Human Genetics. All rights reserved.
Conflict of interest statement
Declaration of interests P.N. reports research grants from Allelica, Apple, Amgen, Boston Scientific, Genentech/Roche, and Novartis; personal fees from Allelica, Apple, AstraZeneca, Blackstone Life Sciences, Eli Lilly & Co, Foresite Labs, Genentech/Roche, GV, HeartFlow, Magnet Biomedicine, and Novartis; scientific advisory board membership of Esperion Therapeutics, Preciseli, and TenSixteen Bio; scientific co-founder of TenSixteen Bio; equity in MyOme, Preciseli, and TenSixteen Bio; and spousal employment at Vertex Pharmaceuticals, all unrelated to the present work. B.M.P. serves on the Steering Committee of the Yale Open Data Access Project funded by Johnson & Johnson. L.M.R., S.S.R., and R.M. are consultants for the TOPMed Administrative Coordinating Center (through Westat). M.E.M. receives funding from Regeneron Pharmaceutical Inc. unrelated to this work. X. Lin is a consultant of AbbVie Pharmaceuticals and Verily Life Sciences. P.T.E. receives sponsored research support from Bayer AG, IBM Research, Bristol Myers Squibb, Pfizer, and Novo Nordisk; he has also served on advisory boards or consulted for Bayer AG, MyoKardia, and Novartis. A.P.C. previously received investigator-initiated grant support from Amgen, Inc. unrelated to the present work.
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Update of
- Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study.Wang Y, Selvaraj MS, Li X, Li Z, Holdcraft JA, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Cade BE, Carlson JC, Carson AP, Chen YI, Curran JE, de Vries PS, Dutcher SK, Ellinor PT, Floyd JS, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, Guo X, He J, Heard-Costa N, Hildalgo B, Hou L, Irvin MR, Joehanes R, Kaplan RC, Kardia SL, Kelly TN, Kim R, Kooperberg C, Kral BG, Levy D, Li C, Liu C, Lloyd-Jone D, Loos RJ, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Murabito JM, Naseri T, O'Connell JR, Palmer ND, Preuss MH, Psaty BM, Raffield LM, Rao DC, Redline S, Reiner AP, Rich SS, Ruepena MS, Sheu WH, Smith JA, Smith A, Tiwari HK, Tsai MY, Viaud-Martinez KA, Wang Z, Yanek LR, Zhao W; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Rotter JI, Lin X, Natarajan P, Peloso GM.Wang Y, et al.medRxiv [Preprint]. 2023 Jun 29:2023.06.28.23291966. doi: 10.1101/2023.06.28.23291966.medRxiv. 2023.Update in:Am J Hum Genet. 2023 Oct 5;110(10):1704-1717. doi: 10.1016/j.ajhg.2023.09.003.PMID:37425772Free PMC article.Updated.Preprint.
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