Computational protocol: Association between Secreted Phosphoprotein-1 (SPP1) Polymorphisms and Low Bone Mineral Density in Women

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Protocol publication

[…] Common (frequency ≥0.05) SNPs in SPP1 were identified from genotyping data of Han Chinese in Beijing, China (CHB) of the International HapMap Project (http://hapmap.ncbi.nlm.nih.gov). Haplotype block was defined by Haploview program (http://www.broadinstitute.org/haploview/haploview) using modified Gabriel algorithm , . Three representative htSNPs [rs11730582 in 5′untranslated region (UTR), rs6839524 in intron, and rs4754 in exon] were selected from 12 common SNPs using tagSNP program based on the common disease/common variant hypothesis . TaqMan Assay was used to determine genotypes using HT7900 (Applied Biosystems Inc., CA, USA). Genotyping success rate was greater than 95% for each SNP. Quality control samples were replicates of 5% study participants and the concordance rate was 100%. […]

Pipeline specifications

Software tools Haploview, SNPinfo
Databases International HapMap Project
Application GWAS
Organisms Homo sapiens
Diseases Bone Diseases, Osteoporosis, Fractures, Bone