Computational protocol: Genetic Differences between the Determinants of Lipid Profile Phenotypes in African and European Americans: The Jackson Heart Study

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Protocol publication

[…] The ANCESTRYMAP software was used for all analyses. The program generates local ancestry estimates by integrating information from a panel of densely spaced markers differentiated in frequency between African and European populations. The 4464 JHS individuals were genotyped on one of two panels of markers informative for West African vs. European ancestry : 976 were genotyped on an older “Phase 2” Panel of 1536 markers, and 3488 were genotyped on an updated “Phase 3” Panel of 1536 markers. After quality checks, 1408 SNPs in the “Phase 2” Panel and 1447 SNPs in the “Phase 3” Panel were used for subsequent analyses. The LOD score for association, defined as the log ratio of the likelihood of the data under a disease model divided by the likelihood of the data under no disease model, was evaluated at equally spaced points across the genome. At each of these points, the disease likelihood was evaluated with a multiplicative risk model, with risk of disease integrated over the inheritance of 0, 1, and 2 copies of an African ancestral allele. Being based on Bayesian statistics, the ANCESTRYMAP software requires specification of a prior distribution of risk models; we used a range of ten risk models from 1.5-fold increased risk due to inheritance of one African ancestral allele to 1.5-fold increased risk due to inheritance of one European allele, with cases, controls, or both used in the analysis. For each point in the genome, we averaged the Bayes factors generated for each risk model, with the LOD score corresponding to the log-base-10 of this number. [...]˜reich for our ANCESTRYMAP software. […]

Pipeline specifications

Software tools ANCESTRYMAP, GenePath
Application Population genetic analysis
Organisms Homo sapiens
Chemicals Cholesterol, Triglycerides