Chapter 6

Extensions

This chapter of Extensions includes things which are under development and/or are special topics and procedures which have very specific application.

6.1 Inheritance Images

6.1.1 Inheritance: Background

A local genetic linkage study prompted the addition of this feature to DNA/GUI which we vaguely label "inheritance". However, the feature is quite limited and for a very specific application. The inheritance logic is limited to 2 alleles across 3 generations (grandparents, parents, children).
Each experimental lane in the image belongs to one person. There are specific inheritance codes which are used to identify which lanes belong to which generations; these codes are included with the lane-label information in the gel-format file. There should be at least 1 band and at most 2 bands in each experimental lane. Bands of the same sizes, across lanes, are said to have the same allele.
The inheritance algorithm is applied to the detected experimental bands. Parent band fragment sizes are confirmed, and the child band fragment sizes checked against the parents. Bands which should appear to be inherited from parents but have a small discrepancy (e.g. 1 base pair), because of poor image quality, image warp, etc., will have their sizes edited to conform to natural inheritance. Missing data and ambiguities are reported. The inheritance algorithms and analysis procedures for band sizing and allele assignment follow in the sections below.

6.1.2 Inheritance: Algorithms

In practice, the parent sizes must be known; the child checks are not applied until the user confirms parent sizes. Discrepancies between grandparents and parents are noted, but will not keep the program from the ultimate parent/child checks. In fact, grandparent information need not be present. Here's a brief summary of the inheritance logic.

6.1.3 Inheritance: Band-Sizing and Allele Assignment

Figure 6.1: Lane-Index, Lane-Label, and Inheritance Stripes.

Figure 6.2: The Allele Window.

Figure 6.3: The Allele Summary.


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