Ancestral DNA Reconstruction Using Pedigrees

Abstract

In this thesis we look at the purpose, process, and application of DNA reconstruction using a known family tree, known as a pedigree. First, we see the applications of having a pedigree with DNA sequences for all individuals in the pedigree since the ultimate goal of DNA reconstruction is to recreate the genome of all members of the pedigree. We do this to better understand trait inheritance, particularly in humans. With a family tree complete with DNA, we can study things such as heritable diseases. Then to better understand how DNA reconstruction is possible, we look at how family relatedness between people in a pedigree can help us understand the connections within their DNA. From that understanding, we will be able to see how DNA reconstruction can be performed on ancestors in a pedigree, given the genome of their descendants. Focusing on an algorithm called "Thread," we see how DNA reconstruction is being applied today. For this work, evaluation was done on the performance of Thread in comparison to Merlin, an implementation of an older algorithm for DNA reconstruction. The experimentation done here reconfirms the greatly more efficient execution time of Thread but exposes weaknesses in its performance under certain circumstances.