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© Oxford University Press

A user-friendly Hypercard interface for human linkage analysis

B.E. Nichols , V.C. Sheffield 1 and E.M. Stone 2

Departments of Ophthalmology Iowa City, 14 52242, USA
1Pediatrics, University of Iowa Hospitals and Clinics Iowa City, 14 52242, USA

2To whom correspondence should be addressed

The availability of a large number of highly informative genetic markers has made human linkage analysis faster and easier to perform. However, current linkage analysis software does not provide an organizational database into which a large body of linkage data can be easily stored and manipulated. This manual entry and editing of linkage data is often time consuming and prone to typing errors. In addition, the large number of alleles in many of these markers must be reduced in order to perform linkage analysis with multiple loci across large genetic distances. This reduction in allele number is often difficult and confusing, especially in large pedigrees. We have taken advantage of the Macintosh-based Hypercard program to develop an interface with which linkage data can be easily stored, retrieved and edited. For each family, the components of the pedigree, including ID numbers, sex and affection status, only need to be entered once. The program (Linkage Interface) retrieves this information each time the data from a new polymorphic marker is entered. Linkage Interface has flexible editing capabilities that allow the user to change any portion of the pedigree, including the addition or deletion of family members, without affecting previously entered genotype data. Linkage Interface can also analyze both the pedigree and marker data and will detect any inconsistencies in inheritance patterns. In addition, the program can reduce the number of alleles for a polynwrphic marker. Linkage Interface will then compare the ‘reduced’ data to the original marker data and assists in maintaining all informative meioses by pointing out which meioses have become non-informative. Once polymorphic marker data are entered, the pedigree data, including the marker genotypes, are easily exported to a text file. This text file can be transferred to an IBM-compatible computer for direct use with DOS-based linkage programs.

Received on September 30, 1992; accepted on March 7, 1993

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