Computational protocol: HOXB13 is a susceptibility gene for prostate cancer: results from the International Consortium for Prostate Cancer Genetics (ICPCG)

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Protocol publication

[…] Frequency of the G84E mutation was determined at either family level or individual level. At a family level, the proportion of families with at least one G84E mutation carrier was determined for the entire set as well as for each ICPCG group. The difference in the proportion among different ICPCG groups was tested using Chi-square with a degree of freedom (df) of 14. At an individual level, the proportion of G84E mutation carriers was compared among men with a diagnosis of prostate cancer (affecteds) and the remaining men within the families (unknowns). The difference of G84E mutation carrier rate between affected and unknown men was tested based on a marginal model that accounts for relatedness of subjects within families using generalized estimating equations (GEE). An exchangeable working correlation matrix was assumed.A family-based association test was performed to test association of the G84E mutation and other SNPs with prostate cancer by assessing over-transmission of alleles from parents to affected offspring using the computer program FBAT (Xu et al. ). Empirical variance test statistics were used to account for the correlation of transmitted alleles among multiple affected individuals in the same family.Haplotypes of each individual based on these 15 SNPs were estimated using Genehunter-plus (Kruglyak et al. ) and PLINK (Purcell et al. ). The haplotypes with the highest likelihood were selected. For subjects whose inferred haplotypes were different based on these two methods, manual inspection was performed to resolve the difference, with priority given to haplotypes based on linkage disequilibrium among markers in this study population. […]

Pipeline specifications

Software tools GeneHunter, PLINK
Application GWAS
Organisms Homo sapiens
Diseases Neoplasms, Prostatic Neoplasms