On the Superior Power of Likelihood-based Linkage Disequilibrium Mapping in Large Multiplex Families Compared to Population Based Case-control Designs

88 In this study, software for automated genome-wide linkage and linkage disequilibrium analysis was developed based on common gene mapping methods for qualitative and quantitative phenotypes. Further, powerful likelihood-based software for joint linkage and/or linkage disequilibrium (LD) analysis in general pedigrees was developed based on a novel variation of the classical lod score approach, the so-called pseudomarker method, and its statistical properties were compared with the existing family-based association methods. In addition, various study designs for association analysis were compared, and investigated statistical properties of the likelihood ratio test for conditional analysis of LD given linkage. These results provide important information for the human genetics community about optimal ways to collect and analyze data.

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