Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans

Christy L. Avery, Praveen Sethupathy, Steven Buyske, Qianchuan He, Dan Yu Lin, Dan E. Arking, Cara L. Carty, David Duggan, Megan D. Fesinmeyer, Lucia A. Hindorff, Janina M. Jeff, Liviu Klein, Kristen K. Patton, Ulrike Peters, Ralph V. Shohet, Nona Sotoodehnia, Alicia M. Young, Charles Kooperberg, Christopher A. Haiman, Karen L. MohlkeEric A. Whitsel, Kari E. North

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


The QT interval (QT) is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death. Most genetic studies of QT have examined European ancestral populations; however, the increased genetic diversity in African Americans provides opportunities to narrow association signals and identify population-specific variants. We therefore evaluated 6,670 SNPs spanning eleven previously identified QT loci in 8,644 African American participants from two Population Architecture using Genomics and Epidemiology (PAGE) studies: the Atherosclerosis Risk in Communities study and Women's Health Initiative Clinical Trial. Of the fifteen known independent QT variants at the eleven previously identified loci, six were significantly associated with QT in African American populations (P≤1.20×10-4): ATP1B1, PLN1, KCNQ1, NDRG4, and two NOS1AP independent signals. We also identified three population-specific signals significantly associated with QT in African Americans (P≤1.37×10-5): one at NOS1AP and two at ATP1B1. Linkage disequilibrium (LD) patterns in African Americans assisted in narrowing the region likely to contain the functional variants for several loci. For example, African American LD patterns showed that 0 SNPs were in LD with NOS1AP signal rs12143842, compared with European LD patterns that indicated 87 SNPs, which spanned 114.2 Kb, were in LD with rs12143842. Finally, bioinformatic-based characterization of the nine African American signals pointed to functional candidates located exclusively within non-coding regions, including predicted binding sites for transcription factors such as TBX5, which has been implicated in cardiac structure and conductance. In this detailed evaluation of QT loci, we identified several African Americans SNPs that better define the association with QT and successfully narrowed intervals surrounding established loci. These results demonstrate that the same loci influence variation in QT across multiple populations, that novel signals exist in African Americans, and that the SNPs identified as strong candidates for functional evaluation implicate gene regulatory dysfunction in QT prolongation.

Original languageEnglish (US)
Article numbere1002870
JournalPLoS genetics
Issue number8
StatePublished - Aug 2012

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research


Dive into the research topics of 'Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans'. Together they form a unique fingerprint.

Cite this