Rare coding variants in 35 genes associate with circulating lipid levels-A multi-ancestry analysis of 170,000 exomes

George Hindy 1Peter Dornbos 2Mark D Chaffin 3Dajiang J Liu 4Minxian Wang 5Margaret Sunitha Selvaraj 6David Zhang 7Joseph Park 7Carlos A Aguilar-Salinas 8Lucinda Antonacci-Fulton 9Diego Ardissino 10Donna K Arnett 11Stella Aslibekyan 12Gil Atzmon 13Christie M Ballantyne 14Francisco Barajas-Olmos 15Nir Barzilai 16Lewis C Becker 17Lawrence F Bielak 18Joshua C Bis 19John Blangero 20Eric Boerwinkle 21Lori L Bonnycastle 22Erwin Bottinger 23Donald W Bowden 24Matthew J Bown 25Jennifer A Brody 19Jai G Broome 26Noël P Burtt 27Brian E Cade 28Federico Centeno-Cruz 15Edmund Chan 29Yi-Cheng Chang 30Yii-Der I Chen 31Ching-Yu Cheng 32Won Jung Choi 33Rajiv Chowdhury 34Cecilia Contreras-Cubas 15Emilio J Córdova 15Adolfo Correa 35L Adrienne Cupples 36Joanne E Curran 20John Danesh 37Paul S de Vries 38Ralph A DeFronzo 39Harsha Doddapaneni 40Ravindranath Duggirala 20Susan K Dutcher 9Patrick T Ellinor 41Leslie S Emery 26Jose C Florez 42Myriam Fornage 43Barry I Freedman 44Valentin Fuster 45Ma Eugenia Garay-Sevilla 46Humberto García-Ortiz 15Soren Germer 47Richard A Gibbs 48Christian Gieger 49Benjamin Glaser 50Clicerio Gonzalez 51Maria Elena Gonzalez-Villalpando 52Mariaelisa Graff 53Sarah E Graham 54Niels Grarup 55Leif C Groop 56Xiuqing Guo 31Namrata Gupta 57Sohee Han 58Craig L Hanis 59Torben Hansen 60Jiang He 61Nancy L Heard-Costa 62Yi-Jen Hung 63Mi Yeong Hwang 58Marguerite R Irvin 64Sergio Islas-Andrade 65Gail P Jarvik 66Hyun Min Kang 67Sharon L R Kardia 18Tanika Kelly 68Eimear E Kenny 69Alyna T Khan 26Bong-Jo Kim 58Ryan W Kim 33Young Jin Kim 58Heikki A Koistinen 70Charles Kooperberg 71Johanna Kuusisto 72Soo Heon Kwak 73Markku Laakso 72Leslie A Lange 74Jiwon Lee 75Juyoung Lee 58Seonwook Lee 33Donna M Lehman 39Rozenn N Lemaitre 19Allan Linneberg 76Jianjun Liu 77Ruth J F Loos 78Steven A Lubitz 41Valeriya Lyssenko 79Ronald C W Ma 80Lisa Warsinger Martin 81Angélica Martínez-Hernández 15Rasika A Mathias 17Stephen T McGarvey 82Ruth McPherson 83James B Meigs 84Thomas Meitinger 85Olle Melander 86Elvia Mendoza-Caamal 15Ginger A Metcalf 40Xuenan Mi 68Karen L Mohlke 87May E Montasser 88Jee-Young Moon 89Hortensia Moreno-Macías 90Alanna C Morrison 38Donna M Muzny 40Sarah C Nelson 26Peter M Nilsson 91Jeffrey R O'Connell 88Marju Orho-Melander 91Lorena Orozco 15Colin N A Palmer 92Nicholette D Palmer 24Cheol Joo Park 33Kyong Soo Park 93Oluf Pedersen 55Juan M Peralta 20Patricia A Peyser 18Wendy S Post 94Michael Preuss 95Bruce M Psaty 96Qibin Qi 89D C Rao 97Susan Redline 28Alexander P Reiner 98Cristina Revilla-Monsalve 99Stephen S Rich 100Nilesh Samani 25Heribert Schunkert 101Claudia Schurmann 102Daekwan Seo 33Jeong-Sun Seo 33Xueling Sim 103Rob Sladek 104Kerrin S Small 105Wing Yee So 80Adrienne M Stilp 26E Shyong Tai 106Claudia H T Tam 80Kent D Taylor 31Yik Ying Teo 107Farook Thameem 108Brian Tomlinson 109Michael Y Tsai 110Tiinamaija Tuomi 111Jaakko Tuomilehto 112Teresa Tusié-Luna 113Miriam S Udler 114Rob M van Dam 115Ramachandran S Vasan 116Karine A Viaud Martinez 117Fei Fei Wang 26Xuzhi Wang 118Hugh Watkins 119Daniel E Weeks 120James G Wilson 121Daniel R Witte 122Tien-Yin Wong 32Lisa R Yanek 17AMP-T2D-GENES, Myocardial Infarction Genetics ConsortiumNHLBI Trans-Omics for Precision Medicine (TOPMed) ConsortiumNHLBI TOPMed Lipids Working GroupSekar Kathiresan 123Daniel J Rader 124Jerome I Rotter 31Michael Boehnke 67Mark I McCarthy 125Cristen J Willer 126Pradeep Natarajan 127Jason A Flannick 2Amit V Khera 3Gina M Peloso 128

Affiliations


Abstract

Large-scale gene sequencing studies for complex traits have the potential to identify causal genes with therapeutic implications. We performed gene-based association testing of blood lipid levels with rare (minor allele frequency < 1%) predicted damaging coding variation by using sequence data from >170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels; some of these genes have not been previously associated with lipid levels when using rare coding variation from population-based samples. We prioritize 32 genes in array-based genome-wide association study (GWAS) loci based on aggregations of rare coding variants; three (EVI5, SH2B3, and PLIN1) had no prior association of rare coding variants with lipid levels. Most of our associated genes showed evidence of association among multiple ancestries. Finally, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes and for genes closest to GWAS index single-nucleotide polymorphisms (SNPs). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels.

Keywords: association; cholesterol; exome sequencing; gene-based association; lipid.

Conflict of interest statement

Declaration of interests The authors declare no competing interests for the present work. P.N. reports investigator-initiated grants from Amgen, Apple, and Boston Scientific; is a scientific advisor to Apple, Blackstone Life Sciences, and Novartis; and has spousal employment at Vertex, all unrelated to the present work. A.V.K. has served as a scientific advisor to Sanofi, Medicines Company, Maze Pharmaceuticals, Navitor Pharmaceuticals, Verve Therapeutics, Amgen, and Color; received speaking fees from Illumina, MedGenome, Amgen, and the Novartis Institute for Biomedical Research; received sponsored research agreements from the Novartis Institute for Biomedical Research and IBM Research; and reports a patent related to a genetic risk predictor (20190017119). C.J.W.’s spouse is employed at Regeneron. L.E.S. is currently an employee of Celgene/Bristol Myers Squibb. Celgene/Bristol Myers Squibb had no role in the funding, design, conduct, and interpretation of this study. M.E.M. receives funding from Regeneron unrelated to this work. E.E.K. has received speaker honoraria from Illumina, Inc and Regeneron Pharmaceuticals. B.M.P. serves on the Steering Committee of the Yale Open Data Access Project funded by Johnson & Johnson. L.A.C. has consulted with the Dyslipidemia Foundation on lipid projects in the Framingham Heart Study. P.T.E. is supported by a grant from Bayer AG to the Broad Institute focused on the genetics and therapeutics of cardiovascular disease. P.T.E. has consulted for Bayer AG, Novartis, MyoKardia, and Quest Diagnostics. S.A.L. receives sponsored research support from Bristol Myers Squibb/Pfizer, Bayer AG, Boehringer Ingelheim, Fitbit, and IBM and has consulted for Bristol Myers Squibb/Pfizer, Bayer AG, and Blackstone Life Sciences. The views expressed in this article are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health. M.I.M. has served on advisory panels for Pfizer, NovoNordisk, and Zoe Global and has received honoraria from Merck, Pfizer, Novo Nordisk, and Eli Lilly and research funding from Abbvie, Astra Zeneca, Boehringer Ingelheim, Eli Lilly, Janssen, Merck, NovoNordisk, Pfizer, Roche, Sanofi Aventis, Servier, and Takeda. As of June 2019, M.I.M. is an employee of Genentech and a holder of Roche stock. M.E.J. holds shares in Novo Nordisk A/S. H.M.K. is an employee of Regeneron Pharmaceuticals; he owns stock and stock options for Regeneron Pharmaceuticals. M.E.J. has received research grants form Astra Zeneca, Boehringer Ingelheim, Amgen, and Sanofi. S.K. is founder of Verve Therapeutics.


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