title: Targeted exonic sequencing of GWAS loci in the high extremes of the plasma lipids distribution.
abstract: Genome-wide association studies (GWAS) for plasma lipid levels have mapped numerous genomic loci, with each region often containing many protein-coding genes. Targeted re-sequencing of exons is a strategy to pinpoint causal variants and genes.
  
  
  
  We performed solution-based hybrid selection of 9008 exons at 939 genes within 95 GWAS loci for plasma lipid levels and sequenced using next-generation sequencing technology individuals with extremely high as well as low to normal levels of low-density lipoprotein cholesterol (LDL-C, n = 311; mean low = 71 mg/dl versus high = 241 mg/dl), triglycerides (TG, n = 308; mean low = 75 mg/dl versus high = 1938 mg/dl), and high-density lipoprotein cholesterol (HDL-C, n = 684; mean low = 32 mg/dl versus high = 102 mg/dl). We identified 15,002 missense, nonsense, or splice site variants with a frequency <5%. We tested whether coding sequence variants, individually or aggregated within a gene, were associated with plasma lipid levels. To replicate findings, we performed sequencing in independent participants (n = 6424).
  
  
  
  Across discovery and replication sequencing, we found 6 variants with significant associations with plasma lipids. Of these, one was a novel association: p.Ser147Asn variant in APOA4 (14.3% frequency, TG OR = 0.49, P = 7.1 × 10(-4)) with TG. In gene-level association analyses where rare variants within each gene are collapsed, APOC3 (P = 2.1 × 10(-5)) and LDLR (P = 5.0 × 10(-12)) were associated with plasma lipids.
  
  
  
  After sequencing genes from 95 GWAS loci in participants with extremely high plasma lipid levels, we identified one new coding variant associated with TG. These results provide insight regarding design of similar sequencing studies with respect to sample size, follow-up, and analysis methodology.
authors.affiliation: Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
authors.forename: Aniruddh P
authors.initials: AP
authors.lastname: Patel
authors.affiliation: Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
authors.forename: Gina M
authors.initials: GM
authors.lastname: Peloso
authors.affiliation: Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Pirruccello
authors.affiliation: Department of Medicine, Western University, London, Ontario, Canada.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Johansen
authors.affiliation: Department of Medicine, Western University, London, Ontario, Canada.
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Dubé
authors.affiliation: Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA.
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Larach
authors.affiliation: Department of Medicine, Western University, London, Ontario, Canada.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Ban
authors.affiliation: Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: Geesje M
authors.initials: GM
authors.lastname: Dallinge-Thie
authors.affiliation: Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
authors.forename: Namrata
authors.initials: N
authors.lastname: Gupta
authors.affiliation: Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Boehnke
authors.affiliation: Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Gonçalo R
authors.initials: GR
authors.lastname: Abecasis
authors.affiliation: Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: John J P
authors.initials: JJ
authors.lastname: Kastelein
authors.affiliation: Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: G Kees
authors.initials: GK
authors.lastname: Hovingh
authors.affiliation: Department of Medicine, Western University, London, Ontario, Canada.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Hegele
authors.affiliation: Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Rader
authors.affiliation: Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. Electronic address: Sekar@broadinstitute.org.
authors.forename: Sekar
authors.initials: S
authors.lastname: Kathiresan
mesh_terms: D000328:Adult; D000368:Aged; D008076:Cholesterol, HDL / Q000097:blood; D008078:Cholesterol, LDL / Q000097:blood; D002874:Chromosome Mapping; D015331:Cohort Studies; D005091:Exons; D005260:Female; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006801:Humans; D008075:Lipoproteins, HDL / Q000097:blood / Q000235:genetics*; D008077:Lipoproteins, LDL / Q000097:blood / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D011786:Quality Control; D017422:Sequence Analysis, DNA; D014280:Triglycerides / Q000097:blood / Q000235:genetics*
chemical_list: D008076:Cholesterol, HDL; D008078:Cholesterol, LDL; D008075:Lipoproteins, HDL; D008077:Lipoproteins, LDL; D014280:Triglycerides
keywords: Genetic techniques; Genomics; Human genetics; Lipids