title: Characterization of common genetic variants in cathepsin K and testing for association with bone mineral density in a large cohort of perimenopausal women from Scotland.
abstract: BMD values in approximately 3000 perimenopausal Scottish women were adjusted by regression to identify and account for nongenetic factors. Adjusted BMD values were not associated with simple tandem repeat (STR) markers or single nucleotide polymorphisms (SNPs) at the Cathepsin K (CTSK) locus. We present a thorough analysis of common CTSK polymorphisms and genetic relatedness among CTSK haplotypes.
  
  
  BACKGROUND
  CTSK is a cysteine protease of the papain family and is thought to play a critical role in osteoclast-mediated bone degradation. Rare, inactivating mutations in CTSK cause pychodysostosis, an autosomal recessive osteochondrodysplasia characterized by osteosclerosis and short stature. However, there have been no studies of common genetic variants in CTSK and their possible association with bone density in the general population.
  
  
  METHODS
  To identify common single nucleotide polymorphisms (SNPs) and simple tandem repeat (STR) polymorphisms in and around CTSK, we screened all CTSK exons, intron A, all intron-exon boundaries, and the putative CTSK promoter region in 130 random whites using both high-performance liquid chromatography (HPLC) and DNA sequencing. CTSK markers were genotyped in approximately 3000 perimenopausal Scottish women whose hip and spine bone mineral density (BMD) had been measured by DXA. We performed linear regression analysis to identify and adjust for nongenetic predictors of BMD, and adjusted BMD values (regression residuals) were tested for association with individual CTSK markers and haplotypes by ANOVA and the composite haplotype method of Zaykin et al.
  
  
  CONCLUSIONS
  We discovered two intronic SNPs (8% and 9% frequency), but no common exonic SNPs (> 1% frequency), and found that three STRs at the immediate 5' end of the CTSK locus are highly polymorphic. The population frequencies of haplotypes defined by these five polymorphisms were estimated, and a cladogram was derived showing proximity of relationship and likely descent of the 30 most common CTSK haplotypes. Regression analyses revealed that approximately 39% of spine and 19% of hip rate of change in BMD was accounted for by nongenetic factors. For baseline BMD values in premenopausal women, nongenetic predictors explained 11% of the variance at the spine and 13% at the hip. Adjusted BMD values showed no statistically significant association with any of the individual CTSK polymorphisms or CTSK haplotypes.
authors.affiliation: Department of Discovery Genetics, GlaxoSmithKline Research and Development, New Frontiers Science Park, Harlow, United Kingdom.
authors.forename: Fabienne S
authors.initials: FS
authors.lastname: Giraudeau
authors.forename: Ralph E
authors.initials: RE
authors.lastname: McGinnis
authors.forename: Ian C
authors.initials: IC
authors.lastname: Gray
authors.forename: Eamonn J
authors.initials: EJ
authors.lastname: O'Brien
authors.forename: Kim E
authors.initials: KE
authors.lastname: Doncaster
authors.forename: Nigel K
authors.initials: NK
authors.lastname: Spurr
authors.forename: Stuart H
authors.initials: SH
authors.lastname: Ralston
authors.forename: David M
authors.initials: DM
authors.lastname: Reid
authors.forename: John
authors.initials: J
authors.lastname: Wood
mesh_terms: D000704:Analysis of Variance; D001827:Body Height; D015992:Body Mass Index; D001835:Body Weight; D015519:Bone Density; D056657:Cathepsin K; D002403:Cathepsins / Q000235:genetics*; D002979:Climacteric / Q000235:genetics / Q000378:metabolism*; D015331:Cohort Studies; D018900:Dinucleotide Repeats / Q000235:genetics; D005260:Female; D005272:Femur Neck / Q000737:chemistry; D005787:Gene Frequency; D005838:Genotype; D006239:Haplotypes / Q000235:genetics; D020249:Hormone Replacement Therapy; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D008159:Lumbar Vertebrae / Q000737:chemistry; D008875:Middle Aged; D011110:Polymorphism, Genetic / Q000235:genetics* / Q000502:physiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011446:Prospective Studies; D012044:Regression Analysis; D012606:Scotland; D013997:Time Factors
chemical_list: D002403:Cathepsins; C534130:CTSK protein, human; D056657:Cathepsin K