Genetic Reconstruction in Pedigrees to Study Disease Inheritance
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2021
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Haverford College. Department of Computer Science
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Thesis
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eng
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Dark Archive until 2041-01-01, afterwards Haverford users only.
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Abstract
In this paper we look at ways to reconstruct DNA in a pedigree. We start by discussing what a pedigree is, how it can be used to learn more about a population, and some challenges of reconstructing its genetic information. We then review some of the relevant literature on the topic. First, we motivate pedigree reconstruction with a full bird pedigree being used to study migration. We then look at GERMLINE, an algorithm that finds IBD segments, which are a useful tool for reconstruction. Next we examine thread, an algorithm that uses IBD segments to reconstruct a pedigree. Then we look at HMM, an algorithm that reconstructs a pedigree one generation at a time. Lastly we consider RABBIT, an algorithm that expands on HMM. After the literature review, we propose our work that expands on this research by studying thread's accuracy. We would do so by running thread on the full bird pedigree and comparing it to the real data, and by running thread and HMM on the same dataset to compare the two algorithms. We conclude by considering the future work in this field, including looking at reconstructed DNA for patterns about disease inheritance.