This paper considers questions of standard error and questions of bias in the maximum likelihood estimation of parameters associated with an HLA-linked disease. It is shown that a considerable reduction in standard error is possible using data on population prevalence and parental disease status, if available. Comparison is made with standard errors arising in the shared haplotypes method. The biases considered relate to misspecification of the ascertainment scheme, to incorrect assumptions about parameter values, to the possibility that affected parents have lower fitness than unaffected parents, and to the possibility of within family correlation of penetrance values due to effects of a common environment.
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