Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol.

Leslie A Lange, Youna Hu, He Zhang, Chenyi Xue, Ellen M Schmidt, Zheng-Zheng Tang, Chris Bizon, Ethan M Lange, Joshua D Smith, Emily H Turner, Goo Jun, Hyun Min Kang, Gina Peloso, Paul Auer, Kuo-Ping Li, Jason Flannick, Ji Zhang, Christian Fuchsberger, Kyle Gaulton, Cecilia LindgrenAdam Locke, Alisa Manning, Xueling Sim, Manuel A Rivas, Oddgeir L Holmen, Omri Gottesman, Yingchang Lu, Douglas Ruderfer, Eli A Stahl, Qing Duan, Yun Li, Peter Durda, Shuo Jiao, Aaron Isaacs, Albert Hofman, Joshua C Bis, Adolfo Correa, Michael E Griswold, Johanna Jakobsdottir, Albert V Smith, Pamela J Schreiner, Mary F Feitosa, Qunyuan Zhang, Jennifer E Huffman, Jacy Crosby, Christina L Wassel, Ron Do, Nora Franceschini, Lisa W Martin, Jennifer G Robinson, Themistocles L Assimes, David R Crosslin, Elisabeth A Rosenthal, Michael Tsai, Mark J Rieder, Deborah N Farlow, Aaron R Folsom, Thomas Lumley, Ervin R Fox, Christopher S Carlson, Ulrike Peters, Rebecca D Jackson, Cornelia M van Duijn, André G Uitterlinden, Daniel Levy, Jerome I Rotter, Herman A Taylor, Vilmundur Gudnason, David S Siscovick, Myriam Fornage, Ingrid B Borecki, Caroline Hayward, Igor Rudan, Y Eugene Chen, Erwin P Bottinger, Ruth J F Loos, Pål Sætrom, Kristian Hveem, Michael Boehnke, Leif Groop, Mark McCarthy, Thomas Meitinger, Christie M Ballantyne, Stacey B Gabriel, Christopher J O'Donnell, Wendy S Post, Kari E North, Alexander P Reiner, Eric Boerwinkle, Bruce M Psaty, David Altshuler, Sekar Kathiresan, Dan-Yu Lin, Gail P Jarvik, L Adrienne Cupples, Charles Kooperberg, James G Wilson, Deborah A Nickerson, Goncalo R Abecasis, Stephen S Rich, Russell P Tracy, Cristen J Willer

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168 Citations (SciVal)


Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98(th) or <2(nd) percentile). Follow-up analyses included sequencing of 1,302 additional individuals and genotype-based analysis of 52,221 individuals. We observed significant evidence of association between LDL-C and the burden of rare or low-frequency variants in PNPLA5, encoding a phospholipase-domain-containing protein, and both known and previously unidentified variants in PCSK9, LDLR and APOB, three known lipid-related genes. The effect sizes for the burden of rare variants for each associated gene were substantially higher than those observed for individual SNPs identified from GWASs. We replicated the PNPLA5 signal in an independent large-scale sequencing study of 2,084 individuals. In conclusion, this large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL-C and provides unique insight into the design and analysis of similar experiments.
Original languageEnglish
Pages (from-to)233-245
JournalAmerican Journal of Human Genetics
Issue number2
Publication statusPublished - 2014

Subject classification (UKÄ)

  • Medical Genetics


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