Computational protocol: Further analysis of previously implicated linkage regions for Alzheimer's disease in affected relative pairs

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Protocol publication

[…] Family structures were verified through the Graphical relationship representation software (GRR) []. Mendelian errors were identified and allele frequencies for selected microsatellite markers were calculated including all available individuals using the MENDEL v8.0 software []. Allele frequencies were calculated for the total sample as well as for each of the analyzed subgroups: SWE, UK USA, APOE ε4+ (ARPs where both individuals have at least one APOE ε4 allele), and APOE ε4- (ARPs where neither individual has an APOE ε4 allele). File conversion was performed using Mega v4.0 [].Allele sharing multipoint LOD scores (MLS) and two-point LOD scores (TLS) were calculated for all groups using the Allegro v2.0 software []. As suggested by the software authors, an exponential model with scoring function Spairs and family weighting option "power: 0.5" was used. Significance levels of detected MLSs in the total sample and the analyzed subgroups were simulated through 1000 replications using the actual data set from the selected chromosomes. […]

Pipeline specifications

Software tools MEGA-V, Allegro
Application GWAS
Diseases Alzheimer Disease
Chemicals Amphotericin B