In linkage analysis, patterns of inheritance for genetic markers across the genome are examined in families. Statistical genetic probabilities about allele sharing and the concept of “identical by descent” (IBD) are the basis for this analysis. For example, when siblings inherit the same marker allele from the same parent, that allele is said to be IBD. When a marker is near a gene that influences a phenotype of interest, then siblings who are more similar to one another on that phenotype are expected to share more IBD marker alleles. Likewise, siblings who are less like one another on that phenotype are expected to share fewer IBD marker alleles. A “linkage peak” is an indication that a particular section of a chromosome co-segregates with the trait within families. The degree to which this co-segregation deviates from chance is quantified using a logarithm base 10 of odds (lod) score. Typically, lod scores of 2.2, 3.6, and 5.4 are considered the cutoffs for evidence of suggestive, significant, and highly significant linkage for genetically complex (i.e., multifactorial) behaviors and traits (Lander and Kruglyak, 1995).
