title: Gene-set based genome-wide association analysis for the speed of sound in two skeletal sites of Korean women.
abstract: The speed of sound (SOS) value is an indicator of bone mineral density (BMD). Previous genome-wide association (GWA) studies have identified a number of genes, whose variations may affect BMD levels. However, their biological implications have been elusive. We re-analyzed the GWA study dataset for the SOS values in skeletal sites of 4,659 Korean women, using a gene-set analysis software, GSA-SNP. We identified 10 common representative GO terms, and 17 candidate genes between these two traits (PGS ＜ 0.05). Implication of these GO terms and genes in the bone mechanism is well supported by the literature survey. Interestingly, the significance levels of some member genes were inversely related, in several gene-sets that were shared between two skeletal sites. This implies that biological process, rather than SNP or gene, is the substantial unit of genetic association for SOS in bone. In conclusion, our findings may provide new insights into the biological mechanisms for BMD.
authors.affiliation: Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Republic of Korea.
authors.forename: Ji-Sun
authors.initials: JS
authors.lastname: Kwon
authors.affiliation: Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Republic of Korea.
authors.forename: Sangsoo
authors.initials: S
authors.lastname: Kim
mesh_terms: D000328:Adult; D000368:Aged; D044466:Asian People / Q000235:genetics; D015519:Bone Density; D001842:Bone and Bones / Q000000981:diagnostic imaging; D015331:Cohort Studies; D030541:Databases, Genetic; D005260:Female; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D056910:Republic of Korea; D012984:Software; D014463:Ultrasonography; D014930:Women