Procjena DNA ROH segmenata iz simuliranih podataka putem HMM i klasičnih programskih paketa

master's thesis

• Title (english): Evaluation of DNA ROH segments from simulated data through HMM and classic software packages
• Author: Kristina Strelar
• Mentor: Maja Ferenčaković (mentor)
• Committee member: Maja Ferenčaković (predsjednik povjerenstva)
• Committee member: Ino Čurik (član povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Animal Science); Zagreb
• Defense date and country: 2020-09-30, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Runs of homozygosity (ROH) javljaju se u genomu kao dugi neprekinuti segmenti homozigotnih genotipova koji omogućuju pouzdanu procjenu razine inbreedinga. Danas imaju široku primjenu, pomoću njih otkrivamo i učinke autozigotnosti, no još uvijek postoje polemike oko toga koji je način njihove detekcije optimalan. Cilj ovog rada bio je usporedba triju programskih paketa s različitim algoritmom za detekciju ROH segmenata i to su cgaTOH, PLINK i RZooROH. U tu svrhu je putem programskog paketa AlphaSimR simulirano 60 populacija s različitim efektivnim veličinama (Ne=25 i Ne=300) kroz 50 generacija te su na njima detektirani ROH segmenti sa svakim programskim paketom, a rezultati uspoređeni Tukey-Kramer HSD testom. Rezultati usporedbe programskih paketa pokazuju statistički značajnu razliku (p < 0,01) srednjih vrijednosti malih i srednjih segmenata populacija s Ne = 25 dobivenih programskim paketom RZooROH naspram cgaTOH i PLINK dok se oni međusobno ne razlikuju. Kod populacija s Ne = 300 statistički se značajno razlikuju sva tri programska paketa (p < 0,01) kod malih segmenata dok kod velikih nema razlike ili je ona prisutna kod RZooROH. Svojim algoritmom RZooROH puno restriktivnije određuje ROH segmente i proglašava ih identičnima po porijeklu, pogotovo kod segmenata veličine do 8MB. Kod velikih segmenata i manje očekivane autozigotnosti te su razlike manje. Grafičkim prikaz statusa homozigotnosti simuliranih genoma naspram procjene putem programskih paketa to također potvrđuje. Svakako su potrebna daljnja istraživanja koja bi uključivala simulaciju segregacije segmenata kroz generacije i potom sposobnost detekcije tih segmenata programskim paketima.

Abstract (english)

Runs of homozygosity (ROH) occur in the genome as long continuous segments of homozygous genotypes that allow a reliable assessment of inbreeding levels. Today, they are widely used, and we can use them to detect the effects of autozygosity, although there is still controversy about which method of their detection is optimal. The goal of this paper was to compare three software packages with different algorithms for detection of ROH segments, namely cgaTOH, PLINK and RZooROH. For this purpose, 60 populations with different effective sizes (Ne=25 and Ne=300) were simulated through the AlphaSimR software package over 50 generations, and ROH segments with each software package were detected on them, and the results were compared with the Tukey-Kramer HSD test. Comparison results of software packages show a statistically significant difference (p < 0.01) of the mean values of small and medium segments of populations with Ne=25 obtained by the software package RZooROH versus cgaTOH and PLINK until they differ from each other. In populations with Ne=300, all three software packages are statistically significantly different (p < 0.01) in small segments, while in large segments there is no difference, or it is present in RZooROH. With its algorithm, RZooROH determines ROH segments much more restrictively and declares them identical in origin, especially for segments up to 8MB in size. For large segments and less expected autozygosity, these differences are smaller. A graphical representation of the homozygosity status of the simulated genomes versus estimation via software packages also confirms this. Further research is certainly needed that would include simulating the segregation of segments across generations and then the ability to detect those segments by software packages.

• Keywords: ROH; cgaTOH; PLINK; RZooROH; simulacija
• Keywords (english): ROH; cgaTOH; PLINK; RZooROH; simulation
• Language: croatian
• URN:NBN: urn:nbn:hr:204:413740
• 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: Open access; Embargo expiration date: 2022-01-13
• Created on: 2021-01-13 09:54:37