Interactive pedigree plotter for genetic analysis
Diseases and traits are often caused by mutations in the genome. A very useful way to try to determine how these mutations occur and are inherited in families is by looking at a pedigree. A pedigree is a diagram that depicts the biological relationship between an individual, its ancestors and other relatives. It is often used to look at the genetic transmission of genetic disorders. The purpose of a pedigree is to have a visually easy-to-read chart that depicts a certain characteristic or disorder in a family. It can be used for a physical characteristic like having a widow‘s peak or attached earlobes, or a genetic disorder like colorblindness or Huntington‘s disease. With technological advances in genetics last two decades such as improved genotyping methods, e.g. by moving from microsatellites and other single marker genotyping methods to chip genotyping and whole genome sequencing, researchers at deCODE now have immense data volume to work with. This gives them much better and more accurate understanding of infrequent variations in the DNA that may be an attributing factor to rare diseases. One method to analyze these rare variants is to use pedigrees, but because of the low penetrance of these variants, the researcher may have to draw very large pedigrees, hundreds or even thousands of individuals, just to understand the inheritance of the variant. This thesis reviews a pedigree plotter, \textit{\softwarenameEN} (IPP), designed by the author, which specializes in large pedigrees; both drawing them and working with them. The \enquote{interactive} refers to allowing the user to, for example, collapse/expand, move and delete certain parts of the descendant tree; a feature that becomes important with increasing pedigree size. The IPP also offers various attribute features such as arbitrary text attributes and multiple symbols, giving the user good tools to distinguish individuals from one another as well as being able to have multiple phenotypes, e.g. several cancer types. To summarize, IPP is a pedigree plotter that is well equipped to handle large and complex pedigrees, enabling researchers to study rare variants. This thesis reviews IPP and its features, and then compares it to several similar pedigree plotters to see whether existing pedigree plotters are sufficiently advanced for the genetic analyses being done at deCODE Genetics.
Heilbrigðisverkfræði, Meistaraprófsritgerðir, Erfðarannsóknir, Gagnvirkni (tölvur), Tækni- og verkfræðideild, Biomedical engineering, Genetic research, Interactive computer systems, School of Science and Engineering
Networked Digital Library of Theses and Dissertations