title: F9 Malmö, factor IX and deep vein thrombosis.
abstract: BACKGROUND
  We recently reported the association between the Malmö sequence variant in F9 (rs6048) and deep vein thrombosis.
  
  
  METHODS
  We aimed to study whether the association between F9 Malmö and deep vein thrombosis is explained by linkage disequilibrium with nearby single-nucleotide polymorphisms, and whether the association is explained biologically by F9 Malmö affecting factor IX antigen levels or activation of factor IX. We investigated the association of F9 Malmö and 28 nearby single-nucleotide polymorphisms with deep vein thrombosis in men from two case-control studies, LETS (n=380) and MEGA (n=1,469). We assessed the association of F9 Malmö with factor IX antigen level in male control subjects from LETS (n=191) and two subsets of MEGA (n=823 and n=484) and the association with endogenous thrombin potential in LETS control men. We studied the association between F9 Malmö and factor IX activation peptide in 1,199 healthy middle-aged men from the NPHS-II cohort.
  
  
  RESULTS
  In the combined LETS and MEGA studies, the odds ratio (95% confidence interval) for the G allele of F9 Malmö, compared with the A allele, was 0.80 (0.69-0.93). One single-nucleotide polymorphism in F9, rs422187, was strongly linked to F9 Malmö (r(2)=0.94) and was similarly associated with deep vein thrombosis. No other single-nucleotide polymorphism or haplotype tested was more strongly associated. Factor IX antigen level, factor IX activation peptide levels and endogenous thrombin potential did not differ between F9 Malmö genotypes.
  
  
  CONCLUSIONS
  The F9 Malmö sequence variant was the most strongly associated with deep vein thrombosis among common single-nucleotide polymorphisms in the region. However, the biological mechanism by which F9 Malmö affects risk remains unknown.
authors.affiliation: Department of Clinical Epidemiology, C7-P Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Irene D
authors.initials: ID
authors.lastname: Bezemer
authors.forename: Andre R
authors.initials: AR
authors.lastname: Arellano
authors.forename: Carmen H
authors.initials: CH
authors.lastname: Tong
authors.forename: Charles M
authors.initials: CM
authors.lastname: Rowland
authors.forename: Helen A
authors.initials: HA
authors.lastname: Ireland
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Bauer
authors.forename: Joseph
authors.initials: J
authors.lastname: Catanese
authors.forename: Pieter H
authors.initials: PH
authors.lastname: Reitsma
authors.forename: Carine J M
authors.initials: CJ
authors.lastname: Doggen
authors.forename: James J
authors.initials: JJ
authors.lastname: Devlin
authors.forename: Frits R
authors.initials: FR
authors.lastname: Rosendaal
authors.forename: Lance A
authors.initials: LA
authors.lastname: Bare
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D016022:Case-Control Studies; D041321:Chromosomes, Human, X / Q000235:genetics; D005164:Factor IX / Q000235:genetics* / Q000378:metabolism; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D008875:Middle Aged; D016017:Odds Ratio; D020641:Polymorphism, Single Nucleotide; D012307:Risk Factors; D020246:Venous Thrombosis / Q000097:blood / Q000235:genetics*; D055815:Young Adult
chemical_list: D005164:Factor IX