The Exploration of Genome Rearrangement Through Edit Distance and Combinations of Variants
Open Access
Author:
Diaz, Austin
Graduate Program:
Bioinformatics and Genomics
Degree:
Master of Science
Document Type:
Master Thesis
Date of Defense:
March 20, 2023
Committee Members:
George Perry, Program Head/Chair Santhosh Girirajan, Thesis Advisor/Co-Advisor Mingfu Shao, Committee Member Christian Huber, Committee Member
Keywords:
oligogenic combination variants SAT solving CNF RareComb ICD codes
Abstract:
Genome rearrangement has been a topic of interest for a long time. Researchers have long tried to discover why genome rearrangement happens, how it happens, its effects, and how to determine its existence in a genome. This thesis touches on the classic genome rearrangement problem of finding the edit distance. In addition, an idea stemming from the two-hit model where CNFs, in concert with other variants, show association to disease by oligogenic combinations or inheritance. Potential methods for encoding counting in CNF are discussed so that an exact ILP algorithm for the double-cut-join model used to find the edit distance can be translated to CNF. Also, in a separate study, we find associations of variant combinations of size three to phenotypes of diseases of the respiratory system and mental and behavior disorders. It is also shown that control patients have higher frequencies of a variant combination of size two than cases do among several phenotypes.
