Computational protocol: COGA phenotypes and linkages on chromosome 2

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Protocol publication

[…] We performed model-free linkage analyses using the program SIBPAL, part of the SAGE analysis package []. Initial analyses used only microsatellite data. This was later followed up with a combination of microsatellite and Affymetrix single-nucleotide polymorphism (SNP) data using the microsatellite map and the latest SNP map supplied with the data. Data preparation and analyses that did not require accounting for family structure were performed with SAS version 9.0 []. This included use of the procedures CANDISC to perform canonical discriminant analysis based on canonical correlation, and PRINCOMP to perform principal components analysis. These techniques were used only as convenient data summary and reduction techniques. Requirements that would make either canonical discriminant analysis or principal component analysis statistically valid (i.e., normality, independence) were not met; however, because we were not directly forming inferences from these results, this is not a major consideration in the current work. SIBPAL performs linkage analysis based on the Haseman-Elston technique [,]. Family-based tests of association were performed with the program FBAT [-]. Haplotype block structure of the SNPs was explored with the program HAPLOVIEW [] using the algorithm defined by Gabriel et al. []. […]

Pipeline specifications

Software tools FBAT, Haploview
Application GWAS
Diseases Alcoholism