Nichols B E, Sheffield V C, Stone E M
Department of Ophthalmology, University of Iowa Hospitals and Clinics, Iowa City 52242.
Comput Appl Biosci. 1993 Dec;9(6):757-9. doi: 10.1093/bioinformatics/9.6.757.
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 polymorphic 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.(ABSTRACT TRUNCATED AT 250 WORDS)
大量信息丰富的遗传标记的出现，使得人类连锁分析的执行变得更快且更容易。然而，当前的连锁分析软件并未提供一个组织化的数据库，大量的连锁数据无法轻松存储和操作。这种连锁数据的手动录入和编辑通常很耗时，而且容易出现录入错误。此外，为了在跨越较大遗传距离的多个基因座上进行连锁分析，许多这些标记中的大量等位基因必须减少。等位基因数量的这种减少往往既困难又容易造成混淆，尤其是在大型家系中。我们利用基于Macintosh的Hypercard程序开发了一个界面，通过该界面可以轻松存储、检索和编辑连锁数据。对于每个家系，家系的组成部分，包括身份证号码、性别和患病状况，只需录入一次。每次输入新的多态性标记数据时，该程序（连锁界面）都会检索此信息。连锁界面具有灵活的编辑功能，允许用户更改家系的任何部分，包括添加或删除家庭成员，而不会影响先前输入的基因型数据。连锁界面还可以分析家系和标记数据，并将检测遗传模式中的任何不一致之处。此外，该程序可以减少多态性标记的等位基因数量。然后，连锁界面会将“简化”后的数据与原始标记数据进行比较，并通过指出哪些减数分裂变得无信息来协助维持所有信息性减数分裂。（摘要截短于250字）
