title: Hypervariable intronic region in NCX1 is enriched in short insertion-deletion polymorphisms and showed association with cardiovascular traits.
abstract: BACKGROUND
  Conserved non-coding regions (CNR) have been shown to harbor gene expression regulatory elements. Genetic variations in these regions may potentially contribute to complex disease susceptibility.
  
  
  METHODS
  We targeted CNRs of cardiovascular disease (CVD) candidate gene, Na(+)-Ca(2+) exchanger (NCX1) with polymorphism screening among CVD patients (n = 46) using DHPLC technology. The flanking region (348 bp) of the 14 bp indel in intron 2 was further genotyped by DGGE assay in two Eastern-European CVD samples: essential hypertension (HYPEST; 470 cases, 652 controls) and coronary artery disease, CAD (CADCZ; 257 cases, controls 413). Genotype-phenotype associations were tested by regression analysis implemented in PLINK. Alignments of primate sequences were performed by ClustalW2.
  
  
  RESULTS
  Nine of the identified NCX1 variants were either singletons or targeted by commercial platforms. The 14 bp intronic indel (rs11274804) was represented with substantial frequency in HYPEST (6.82%) and CADCZ (14.58%). Genotyping in Eastern-Europeans (n = 1792) revealed hypervariable nature of this locus, represented by seven alternative alleles. The alignments of human-chimpanzee-macaque sequences showed that the major human variant (allele frequency 90.45%) was actually a human-specific deletion compared to other primates. In humans, this deletion was surrounded by other short (5-43 bp) deletion variants and a duplication (40 bp) polymorphism possessing overlapping breakpoints. This indicates a potential indel hotspot, triggered by the initial deletion in human lineage. An association was detected between the carrier status of 14 bp indel ancestral allele and CAD (P = 0.0016, OR = 2.02; Bonferroni significance level alpha = 0.0045), but not with hypertension. The risk for the CAD development was even higher among the patients additionally diagnosed with metabolic syndrome (P = 0.0014, OR = 2.34). Consistent with the effect on metabolic processes, suggestive evidence for the association with heart rate, serum triglyceride and LDL levels was detected (P = 0.04).
  
  
  CONCLUSIONS
  Compared to SNPs targeted by large number of locus-specific and genome-wide assays, considerably less attention has been paid to short indel variants in the human genome. The data of genome dynamics, mutation rate and population genetics of short indels, as well as their impact on gene expressional profile and human disease susceptibility is limited. The characterization of NCX1 intronic hypervariable non-coding region enriched in human-specific indel variants contributes to this gap of knowledge.
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Katrin
authors.initials: K
authors.lastname: Kepp
authors.forename: Elin
authors.initials: E
authors.lastname: Org
authors.forename: Siim
authors.initials: S
authors.lastname: Sõber
authors.forename: Piret
authors.initials: P
authors.lastname: Kelgo
authors.forename: Margus
authors.initials: M
authors.lastname: Viigimaa
authors.forename: Gudrun
authors.initials: G
authors.lastname: Veldre
authors.forename: Neeme
authors.initials: N
authors.lastname: Tõnisson
authors.forename: Peeter
authors.initials: P
authors.lastname: Juhanson
authors.forename: Margus
authors.initials: M
authors.lastname: Putku
authors.forename: Andreas
authors.initials: A
authors.lastname: Kindmark
authors.forename: Viktor
authors.initials: V
authors.lastname: Kozich
authors.forename: Maris
authors.initials: M
authors.lastname: Laan
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000818:Animals; D002318:Cardiovascular Diseases / Q000097:blood / Q000235:genetics* / Q000378:metabolism / Q000503:physiopathology; D002851:Chromatography, High Pressure Liquid; D017124:Conserved Sequence; D006801:Humans; D054643:INDEL Mutation; D007438:Introns / Q000235:genetics*; D008875:Middle Aged; D009691:Nucleic Acid Denaturation; D010641:Phenotype; D011110:Polymorphism, Genetic; D011323:Primates / Q000235:genetics; D019831:Sodium-Calcium Exchanger / Q000235:genetics*; D013045:Species Specificity; D055815:Young Adult
chemical_list: D019831:Sodium-Calcium Exchanger; C110374:sodium-calcium exchanger 1