Targeted deep resequencing identifies coding variants in the PEAR1 gene that play a role in platelet aggregation

PLoS One. 2013 May 21;8(5):e64179. doi: 10.1371/journal.pone.0064179. Print 2013.

Abstract

Platelet aggregation is heritable, and genome-wide association studies have detected strong associations with a common intronic variant of the platelet endothelial aggregation receptor1 (PEAR1) gene both in African American and European American individuals. In this study, we used a sequencing approach to identify additional exonic variants in PEAR1 that may also determine variability in platelet aggregation in the GeneSTAR Study. A 0.3 Mb targeted region on chromosome 1q23.1 including the entire PEAR1 gene was Sanger sequenced in 104 subjects (45% male, 49% African American, age = 52±13) selected on the basis of hyper- and hypo- aggregation across three different agonists (collagen, epinephrine, and adenosine diphosphate). Single-variant and multi-variant burden tests for association were performed. Of the 235 variants identified through sequencing, 61 were novel, and three of these were missense variants. More rare variants (MAF<5%) were noted in African Americans compared to European Americans (108 vs. 45). The common intronic GWAS-identified variant (rs12041331) demonstrated the most significant association signal in African Americans (p = 4.020×10(-4)); no association was seen for additional exonic variants in this group. In contrast, multi-variant burden tests indicated that exonic variants play a more significant role in European Americans (p = 0.0099 for the collective coding variants compared to p = 0.0565 for intronic variant rs12041331). Imputation of the individual exonic variants in the rest of the GeneSTAR European American cohort (N = 1,965) supports the results noted in the sequenced discovery sample: p = 3.56×10(-4), 2.27×10(-7), 5.20×10(-5) for coding synonymous variant rs56260937 and collagen, epinephrine and adenosine diphosphate induced platelet aggregation, respectively. Sequencing approaches confirm that a common intronic variant has the strongest association with platelet aggregation in African Americans, and show that exonic variants play an additional role in platelet aggregation in European Americans.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Black or African American / genetics
  • Cohort Studies
  • Exons / genetics
  • Female
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Linkage Disequilibrium / genetics
  • Male
  • Middle Aged
  • Open Reading Frames / genetics*
  • Platelet Aggregation / genetics*
  • Polymorphism, Single Nucleotide / genetics*
  • Receptors, Cell Surface / genetics
  • White People / genetics

Substances

  • PEAR1 protein, human
  • Receptors, Cell Surface