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.2023 Oct 5;110(10):1704-1717.
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

Yuxuan Wang  1Margaret Sunitha Selvaraj  2Xihao Li  3Zilin Li  4Jacob A Holdcraft  1Donna K Arnett  5Joshua C Bis  6John Blangero  7Eric Boerwinkle  8Donald W Bowden  9Brian E Cade  10Jenna C Carlson  11April P Carson  12Yii-Der Ida Chen  13Joanne E Curran  7Paul S de Vries  8Susan K Dutcher  14Patrick T Ellinor  15James S Floyd  16Myriam Fornage  17Barry I Freedman  18Stacey Gabriel  19Soren Germer  20Richard A Gibbs  21Xiuqing Guo  13Jiang He  22Nancy Heard-Costa  23Bertha Hildalgo  24Lifang Hou  25Marguerite R Irvin  24Roby Joehanes  26Robert C Kaplan  27Sharon Lr Kardia  28Tanika N Kelly  29Ryan Kim  30Charles Kooperberg  31Brian G Kral  32Daniel Levy  33Changwei Li  34Chunyu Liu  35Don Lloyd-Jone  25Ruth Jf Loos  36Michael C Mahaney  7Lisa W Martin  37Rasika A Mathias  32Ryan L Minster  38Braxton D Mitchell  39May E Montasser  39Alanna C Morrison  8Joanne M Murabito  40Take Naseri  41Jeffrey R O'Connell  39Nicholette D Palmer  9Michael H Preuss  42Bruce M Psaty  43Laura M Raffield  44Dabeeru C Rao  45Susan Redline  46Alexander P Reiner  47Stephen S Rich  48Muagututi'a Sefuiva Ruepena  49Wayne H-H Sheu  50Jennifer A Smith  28Albert Smith  51Hemant K Tiwari  52Michael Y Tsai  53Karine A Viaud-Martinez  54Zhe Wang  42Lisa R Yanek  32Wei Zhao  28NHLBI Trans-Omics for Precision Medicine (TOPMed) ConsortiumJerome I Rotter  13Xihong Lin  55Pradeep Natarajan  2Gina M Peloso  56
Affiliations

Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study

Yuxuan Wang et al. Am J Hum Genet..

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.

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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.

Figures

Figure 1
Figure 1
A schematic illustration of the study We performed the rare-variant association tests of 165,000 curated lncRNA genes with lipid phenotypes (i.e., LDL-C, HDL-C, TC, and TG) using the TOPMed freeze 8 data. A total of 66,329 participants from 21 studies with WGS and measured blood lipid levels were analyzed using STAAR framework. We further conducted a series of conditional analyses adjusting for known lipid GWAS variants and the nearby protein-coding genes (rare nonsynonymous, rare synonymous, and rare pLoF variants, separately). We replicated the results using an independent UKB WGS cohort. Finally, gene expression levels of the significantly lipid-associated lncRNAs were investigated in FHS RNA-seq data. TOPMed, Trans-Omics for Precision Medicine; UKB, UK Biobank; FHS, Framingham Heart Study; GLGC, Global Lipids Genetics Consortium; HDL-C, high-density lipoprotein cholesterol; LDL-C, low-density lipoprotein cholesterol; TC, total cholesterol; TG, triglycerides; lncRNA, long non-coding RNA; GWAS, genome wide association study; STAAR, variant-set test for association using annotation information; pLoF, predicted loss-of-function; MAF, minor allele frequency; SNVs, single-nucleotide variants.
Figure 2
Figure 2
Significantly associated lncRNAs with four blood lipid traits The significantly associated lncRNA genes (STAAR-O p value< 4.5 × 1007) are ordered by chromosome, followed by genomic positions. Dots in red and blue represent the −log10(STAAR-O p value) of the STAAR unconditional and conditional analysis adjusting for known lipid-associated GWAS variants, respectively. The black dashed line is the Bonferroni correction level of 0.05/83 = 6.0 × 1004. Arrows indicate at least 104-fold change of STAAR-O p values comparing the unconditional analysis and conditional analysis adjusting for known lipid-associated GWAS variants.
Figure 3
Figure 3
lncRNAs in theAPOE region associated with LDL-C Upper shows the −log10(STAAR-O p value) of the STAAR unconditional analysis, STAAR conditional analysis adjusting on known lipid GWAS variants, and STAAR conditional analysis adjusting for rare non-synonymous variants within the closest protein-coding gene and nearby genes associated with monogenic lipid disorders. The bottom is the nearby protein-coding genes with the genomic coordinates. The vertical dashed line is the position of the known GWAS variants that were conditioned on. The black horizontal dashed line is the Bonferroni correction level of 0.05/111,550 = 4.5 × 1007, and the gray horizontal dashed line is the Bonferroni correction level of 0.05/83 = 6.0 × 1004.
See this image and copyright information in PMC

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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