title: Molecular prioritization strategies to identify functional genetic variants in the cardiovascular disease-associated expression QTL Vanin-1.
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.
authors.affiliation: School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia.
authors.forename: Belinda J
authors.initials: BJ
authors.lastname: Kaskow
authors.affiliation: School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia.
authors.forename: Luke A
authors.initials: LA
authors.lastname: Diepeveen
authors.affiliation: Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA.
authors.forename: J Michael
authors.initials: JM
authors.lastname: Proffitt
authors.affiliation: School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Rea
authors.affiliation: School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia.
authors.forename: Daniela
authors.initials: D
authors.lastname: Ulgiati
authors.affiliation: Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA.
authors.forename: John
authors.initials: J
authors.lastname: Blangero
authors.affiliation: Centre for Genetic Origins of Health and Disease (GOHaD), University of Western Australia, Crawley, WA, Australia.
authors.forename: Eric K
authors.initials: EK
authors.lastname: Moses
authors.affiliation: 1] School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia [2] Centre for Genetic Origins of Health and Disease (GOHaD), University of Western Australia, Crawley, WA, Australia.
authors.forename: Lawrence J
authors.initials: LJ
authors.lastname: Abraham
mesh_terms: D000483:Alleles; D000581:Amidohydrolases / Q000235:genetics*; D001483:Base Sequence; D002318:Cardiovascular Diseases / Q000235:genetics*; D002843:Chromatin / Q000235:genetics; D019175:DNA Methylation; D058851:GPI-Linked Proteins / Q000235:genetics; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D014644:Genetic Variation; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D040641:Quantitative Trait Loci
chemical_list: D002843:Chromatin; D058851:GPI-Linked Proteins; D000581:Amidohydrolases; C022314:pantetheinase
references.citation: Mol Cell Biol. 1982 Sep;2(9):1044-51
references.pmid: 6960240
references.citation: Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3740-5
references.pmid: 11891299
references.citation: Mol Immunol. 2012 Oct;52(3-4):165-73
references.pmid: 22673213
references.citation: Hum Mol Genet. 2010 Oct 15;19(R2):R204-9
references.pmid: 20846943
references.citation: Biochim Biophys Acta. 2006 Jan;1762(1):17-28
references.pmid: 16297602
references.citation: Biochem Biophys Res Commun. 2012 Jan 13;417(2):653-8
references.pmid: 22155241
references.citation: Nat Biotechnol. 2011 Jan;29(1):24-6
references.pmid: 21221095
references.citation: Anal Biochem. 1988 Nov 15;175(1):5-13
references.pmid: 3072883
references.citation: Eur J Hum Genet. 2009 Nov;17(11):1454-62
references.pmid: 19471307
references.citation: Trends Genet. 2004 Mar;20(3):113-6
references.pmid: 15049300
references.citation: Cytokine. 2000 Feb;12(2):110-9
references.pmid: 10671295
references.citation: J Clin Invest. 1985 Oct;76(4):1665-72
references.pmid: 4056044
references.citation: Eur J Biochem. 1970 Nov;16(3):571-8
references.pmid: 5477303
references.citation: Ann Hum Genet. 1986 May;50(2):181-94
references.pmid: 3435047
references.citation: Science. 1985 Jan 18;227(4684):266-70
references.pmid: 3917575
references.citation: FEBS Lett. 2000 Oct 20;483(2-3):149-54
references.pmid: 11042271
references.citation: Nucleic Acids Res. 1981 Dec 11;9(23):6505-25
references.pmid: 6275366
references.citation: Nature. 2010 Oct 28;467(7319):1061-73
references.pmid: 20981092
references.citation: Am J Hum Genet. 1998 May;62(5):1198-211
references.pmid: 9545414
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):308-11
references.pmid: 11125122
references.citation: Nature. 2004 Aug 12;430(7001):743-7
references.pmid: 15269782
references.citation: Eur J Hum Genet. 2000 Jul;8(7):545-51
references.pmid: 10909856
references.citation: Nat Genet. 2008 Jul;40(7):904-8
references.pmid: 18568024
references.citation: Mutat Res. 2008 Jul-Aug;659(1-2):147-57
references.pmid: 18565787
references.citation: J Pathol. 2008 Jan;214(1):65-74
references.pmid: 17973241
references.citation: Biochem Biophys Res Commun. 2008 Mar 7;367(2):349-55
references.pmid: 18164259
references.citation: BMC Genet. 2005 Dec 30;6 Suppl 1:S91
references.pmid: 16451707
references.citation: Genome Res. 2012 Sep;22(9):1790-7
references.pmid: 22955989
references.citation: Biotechniques. 2007 Feb;42(2):217-24
references.pmid: 17373487
references.citation: Immunity. 1996 Nov;5(5):391-405
references.pmid: 8934567
references.citation: J Immunol. 2001 Oct 15;167(8):4494-503
references.pmid: 11591776
references.citation: Environ Toxicol Pharmacol. 1998 Aug 4;6(1):59-66
references.pmid: 21781882
references.citation: Nat Genet. 2007 Oct;39(10):1208-16
references.pmid: 17873875
references.citation: Clin Sci (Lond). 2003 May;104(5):493-501
references.pmid: 12513691
references.citation: Circulation. 1996 Nov 1;94(9):2159-70
references.pmid: 8901667
references.citation: Nat Rev Genet. 2011 Aug 18;12(9):628-40
references.pmid: 21850043
references.citation: BMC Bioinformatics. 2010 May 06;11:230
references.pmid: 20459626
references.citation: Nucleic Acids Res. 1981 Jul 10;9(13):3047-60
references.pmid: 6269071