Bioinformatics Applications SPLINK

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SPLINK is a program for linkage analysis using affected sib pairs. It uses the method of maximum likelihood to estimate the probability that two affected sibs share 0, 1 or 2 autosomal marker haplotypes identically by descent (IBD). For marker haplotypes on the X-chromosome, IBD sharing of maternal haplotypes only is considered. Parental marker data need not be present (although, of course, they help) and neither IBD status or phase of marker haplotype need be known. When full parental data are not available, the uncertainty in assigning parental haplotypes may be reduced by including data on sibs who are either unaffected or of unknown affection status. When all available data still permit ambiguity for parental haplotypes, the population haplotype frequencies become relevant, and these are estimated internally, again using the method of maximum likelihood.

Affected sib trios (and larger groupings) are dealt with approximately by treating all pairwise comparisons as independent. Since this device does not correspond to a genuine likelihood, in this more general case the method should be referred to as maximum pseudo-likelihood. It has been become conventional to weight the individual sibpair comparisons in larger sets of affected sibs by 2/A where A is the number of affected sibs in the family. However the grounds for this are not clear and there may be good reasons to prefer the unweighted approach.

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