On Genotype-Phenotype Association using SAS

Jing Hua Zhao, Ruth J.F. Loos, and Nick Wareham


Genetics and genomics, Bioinformatics, Genome-wide association studies, Meta-analysis, Mixed models, Pedigree analysis


We provide updates on various aspects that have been described in two previous papers concerning about the utility of general software systems in analysis of complex traits and the experiences from the European Prospective Investigation of Cancer (EPIC) Norfolk, a large population-based cohort study (http://www.srl.cam.ac.uk/epic/). Our current focus is restricted to SAS (http://www.sas.com) including data handling, foreign language calling, statistical modelling, and a brief comparison with other software such as R (http://www.r-project.org). We give examples on exact test of Hardy-Weinberg equilibrium, meta-analysis, and test of genettype-phenotype association involving family data including kinship calculation. Advantages, limitations and future work are also indicated. We believe these will be of general interest and practical use.

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