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2.1 Phenotypes and Genotypes

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• Numbered alleles. These are codominant alleles at a single locus. The numbers run consecutively from 1 to the maximum number of alleles observed. The phenotype consists of two allele numbers corresponding to a genotype. An unknown genotype is coded as 0 0.

• Binary factors. In this coding scheme a series of binary codes (1 or 0) indicates the presence or absence of a phenotype factor. This system is useful for describing either codominant or recessive/dominant systems. The phenotype is entered as a binary string.

• Affection status. The presence or absence of disease (or other qualitative phenotypes) is described by a numbered code. A risk or liability class can also be included as a separate numeric code.

• Quantitative traits. One or more quantitative measurements can be used as a phenotype description.

The phenotypic codes for each of these types of data are described in more detail below.

NOTE: The present version of LINKAGE does not allow mixtures of affection status and quantitative variables, except in the case of sex-linked traits as described below. A future version will incorporate a modification allowing such mixtures for autosomal data.