Molecular prioritization strategies to identify functional genetic variants in the cardiovascular disease-associated expression QTL Vanin-1

Belinda J. Kaskow, Luke A. Diepeveen, J. Michael Proffitt, Alexander J. Rea, Daniela Ulgiati, John Blangero, Eric K. Moses, Lawrence J. Abraham

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

There is now good evidence that non-coding sequence variants are involved in the heritability of many common complex traits. The current 'gold standard' approach for assessing functionality is the in vitro reporter gene assay to assess allelic differences in transcriptional activity, usually followed by electrophoretic mobility shift assays to assess allelic differences in transcription factor binding. Although widely used, these assays have inherent limitations, including the lack of endogenous chromatin context. Here we present a more contemporary approach to assessing functionality of non-coding sequence variation within the Vanin-1 (VNN1) promoter. By combining 'gold standard' assays with in vivo assessments of chromatin accessibility, we greatly increase our confidence in the statistically assigned functional relevance. The standard assays revealed the-137 single nucleotide variant to be functional but the-587 variant to have no functional relevance. However, our in vivo tests show an allelic difference in chromatin accessibility surrounding the-587 variant supporting strong functional potential at both sites. Our approach advances the identification of functional variants by providing strong in vivo biological evidence for function.

Original languageEnglish (US)
Pages (from-to)688-695
Number of pages8
JournalEuropean Journal of Human Genetics
Volume22
Issue number5
DOIs
StatePublished - 2014
Externally publishedYes

Fingerprint

Chromatin
Cardiovascular Diseases
Electrophoretic Mobility Shift Assay
Reporter Genes
Transcription Factors
Nucleotides
In Vitro Techniques

Keywords

  • allele-specific chromatin arrangement
  • cardiovascular disease
  • functional variant
  • pantetheinase

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Medicine(all)

Cite this

Kaskow, B. J., Diepeveen, L. A., Michael Proffitt, J., Rea, A. J., Ulgiati, D., Blangero, J., ... Abraham, L. J. (2014). Molecular prioritization strategies to identify functional genetic variants in the cardiovascular disease-associated expression QTL Vanin-1. European Journal of Human Genetics, 22(5), 688-695. https://doi.org/10.1038/ejhg.2013.208

Molecular prioritization strategies to identify functional genetic variants in the cardiovascular disease-associated expression QTL Vanin-1. / Kaskow, Belinda J.; Diepeveen, Luke A.; Michael Proffitt, J.; Rea, Alexander J.; Ulgiati, Daniela; Blangero, John; Moses, Eric K.; Abraham, Lawrence J.

In: European Journal of Human Genetics, Vol. 22, No. 5, 2014, p. 688-695.

Research output: Contribution to journalArticle

Kaskow, BJ, Diepeveen, LA, Michael Proffitt, J, Rea, AJ, Ulgiati, D, Blangero, J, Moses, EK & Abraham, LJ 2014, 'Molecular prioritization strategies to identify functional genetic variants in the cardiovascular disease-associated expression QTL Vanin-1', European Journal of Human Genetics, vol. 22, no. 5, pp. 688-695. https://doi.org/10.1038/ejhg.2013.208
Kaskow, Belinda J. ; Diepeveen, Luke A. ; Michael Proffitt, J. ; Rea, Alexander J. ; Ulgiati, Daniela ; Blangero, John ; Moses, Eric K. ; Abraham, Lawrence J. / Molecular prioritization strategies to identify functional genetic variants in the cardiovascular disease-associated expression QTL Vanin-1. In: European Journal of Human Genetics. 2014 ; Vol. 22, No. 5. pp. 688-695.
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