Procjena DNA ROH segmenta pomoću metode skrivenog Markovljevog modela

master's thesis

• Title (english): DNA ROH segment estimation using the hidden Markov model method
• Author: Iva Katić
• Mentor: Maja Ferenčaković (mentor)
• Committee member: Maja Ferenčaković (predsjednik povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Committee member: Ino Čurik (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Department of Animal Science I); Zagreb
• Defense date and country: 2019-09-30, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Run of homozygosity (ROH) se kao dugi neprekidni segmenti homozigotnih genotipova koji omogućuju pouzdanu procjenu razine inbreedinga danas koriste u raznim područjima. Pomoću ROH segmenata otkrivamo učinke autozigotnosti, no nepoznato je koji je program najoptimalniji. U ovom radu procjenjujemo ROH segmente softverom cgaTOH i paketom programa ''R studio'' zvanim ''RZooROH'' koji procjenjuje ROH segmente putem skrivenog Markovljevog Modela (HMM). HMM je model koji funkcionira na način popunjavanja missing SNP-ova, te u ovom radu možemo vidjeti na koji način se to odražava na koeficijent inbreedinga određenog ROH segmenta.

Abstract (english)

Run of homozygosity (ROH) is used as a long continuous segment of homozygous genotypes that allow reliable estimation of the level of inbreeding used in various fields today. Using ROH segments, we detect the effects of autozygosity, but it is unknown which program is the most optimal. In this paper, we evaluate ROH segments by cgaTOH software and an R studio program called "RZooROH" that evaluates runo f homozygosity segments via the hidden Markov Model (HMM). HMM is a model that works by filling in missing SNPs, and in this paper we can see how this reflects on the inbreeding coefficient of a given ROH segment.

• Keywords: Run of homozygosity; skriven Markovljev Model; cgaTOH; RzooROH; inbreeding
• Keywords (english): Run of homozygosity; hidden Markov Model; cgaTOH; RzooROH; inbreeding
• Language: croatian
• URN:NBN: urn:nbn:hr:204:839564
• Study programme: Title: Animal Genetics and Breeding; Study programme type: university; Study level: graduate; Academic / professional title: magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja (magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2019-11-20 10:59:04