Sirvi Autor "Abner, Erik, juhendaja" järgi

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Genome-wide association study for detecting autoimmune-disease-associated genetic pattern differences in specific HLA type carriers
(Tartu Ülikool, 2023) Kukkonen, Arne; Abner, Erik, juhendaja
The HLA locus variants are one of the strongest genetic predictors for most, if not all, human autoimmune diseases. The HLA locus genes include the antigen-presenting cell surface peptide encoding genes, which form an essential component in the maturation of the T-cell population in the thymus, and their subsequent activation in the periphery. Leveraging the modern population-wide genotype information that capture even the most polymorphic loci, this work sets the aim to design a case-control genome-wide association study (GWAS), that would result in the detection of non-HLA genetic variants that have a statistically different effect on an autoimmune disease in the carriers of certain HLA types, in comparison to the non-carriers. For the purpose of this aim, study groups are assembled based on specific HLA allele doses, so that for 42 HLA allele typesselected for this study there are 42 HLA-specific groups where every individual is a carrier of at least one copy of the HLA allele type. The effect sizes from the summary statistics of the HLA-specific GWASs are compared to a general population GWAS (which is done on all the participants of the Estonian Biobank in this case). The variants are considered relevant to this aim if their effect size is statisticallt different in the HLA-specific groups than they are in the general population GWAS.
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Identifying Microproteins with Genetic Association Data
(Tartu Ülikool, 2025) Savchak, Sviatoslav-Oleh; Alekseienko, Anastasiia, juhendaja; Abner, Erik, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Bioinseneeria instituut
The annotation of the human genome is an ongoing process, continually refined as new functional elements are discovered. In recent years, regions previously classified as long non-coding RNAs have gained attention as many of them contain sequences that are actively translated. In this work, we mapped single-nucleotide variants (SNVs) listed in the GWAS Catalog to 7,264 previously undescribed open reading frames (ORFs) identified from the human genome. From this analysis, we identified six final microprotein encoding candidates that are likely to be associated with diseases or traits linked to their corresponding SNVs. These findings will hopefully contribute to the expanding functional annotation of the human genome and highlight the potential biological relevance of previously overlooked potential new microgenes.
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Kronotüübi ja erinevate haiguste põdemise seoste uurimine TÜ Eesti geenivaramu andmetel
(2023) Kivi, Kadi-Liis; Abner, Erik, juhendaja; Kolde, Anastassia, juhendaja; Tartu Ülikool. Matemaatika ja statistika instituut; Tartu Ülikool. Loodus- ja täppisteaduste valdkond
Terminit kronotüüp kasutatakse uneharjumuste kirjeldamise vahendina, mis näitab, millal inimene magab. Bakalaureusetöö eesmärk on logistilise regressiooni mudeli abil uurida kronotüübi seost erinevate haiguste põdemisega, valideerida varasemalt näidatud seost hilise kronotüübi ja lühi- ja kaugelenägevuse vahel ning analüüsida uinumise kellaaega alternatiivse krononotüübina. Lühinägevuse puhul näidati hilise kronotüübi ja haiguse põdemise positiivset seost, ent kaugelenägevuse puhul statistilselt olulist seost ei avaldunud. Uinumise kellaaeg osutus heaks potentsiaalseks kronotüübi definitsiooni alternatiiviks.
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Lyme disease: modeling and analyzing long-term costs related to the infection based on Estonian Biobank data
(Tartu Ülikool, 2025) Raak, Sten; Abner, Erik, juhendaja; Fischer, Krista, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Matemaatika ja statistika instituut
Lyme disease is a prevalent vector-borne illness with significant public health implications due to its potential for multisystem effects and persistent symptoms. Understanding the associated economic burden is crucial for healthcare planning. This thesis investigates the temporal dynamics of healthcare costs surrounding a Lyme disease diagnosis, aiming to quantify whether cost increases are primarily acute or persist over a longer period, which contributes to understanding the extended healthcare services utilization potentially linked to the condition. Using longitudinal health data from the Estonian Biobank, this study uses a relative time scale indexed to the year of first diagnosis. Linear Mixed-Effects (LME) models serve as the primary analytical framework to handle correlated repeated measures and model cost trajectories. The analysis compares diagnosed individuals to a reference group over a defined time window surrounding diagnosis. The thesis includes a background on the disease and methods, details the analysis, and presents results within the Estonian context.
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Puukborrelioos: geneetilised riskitegurid ja nakkusega seotud terviseriskid TÜ Eesti geenivaramu andmete põhjal
(2023) Raak, Sten; Abner, Erik, juhendaja; Fischer, Krista, juhendaja; Tartu Ülikool. Matemaatika ja statistika instituut; Tartu Ülikool. Loodus- ja täppisteaduste valdkond
Bakalaureusetöö eesmärk on uurida puukborrelioosiga kaasnevaid terviseriske ning nakkusest tulenevaid haigestumisriske. Soovitakse leida põhjapanevaid tulemusi, mida Eesti meditsiinisüsteem saaks kasutada raskemate haiguste ennetuseks. Töös kasutatakse peamiselt hii-ruut testi ning logistilist regressiooni seose tugevuse hindamiseks. Lisaks on rakendatud eraldi PheWASi, mille järel on kasutatud Mendeli randomiseerimist põhjusliku seose tugevuse jaoks. Esmalt antakse töös ülevaade puukborrelioosist ning sellega tulenevatest terviseprobleemidest. Seejärel kirjeldatakse seoseuuringute tüüpe GWAS ja PheWAS, miks neid kasutatakse ning nende erinevusi. Lõpuks tehakse kokkuvõte töös kasutatavatest meetoditest, näiteks hii-ruut test, logistiline regressioon, mitmese testimise probleem ning Mendeli randomiseerimine. Nende meetodite põhjal teostatakse analüüs puukborrelioosi ning puukborrelioosi soodustavale geneetilise riskiteguri mõjule teistele haigustele, kasutades Tartu Ülikooli Eesti geenivaramu andmeid.
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Systematic interpretation of large-scale GWAS analyses of 5,035 phenotypes
(Tartu Ülikool, 2024) Alekseienko, Anastasiia; Võsa, Urmo, juhendaja; Abner, Erik, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
This thesis presents the systematic interpretation of 5,035 genome-wide association studies (GWAS) conducted within the Estonian Biobank, aiming to elucidate the genetic determinants influencing a diverse array of phenotypic traits. Through a review of existing literature and the application of advanced bioinformatic tools, the work done in this thesis outlined the results of main post-GWAS methods, such as the identification of novel variants, SNP heritability estimation, fine-mapping of causal variants, and prioritization of genes associated with complex traits. Around 26% of the variants identified as lead ones in this work are novel and had not been implicated by GWASs before. Fine mapping prioritized single genetic variants for 10.3% of investigated loci, providing hypotheses for further functional studies, and the gene prioritization approach identified the 2,402 lead variants to be related to 804 genes, several of those biologically interpretable. Heritability was reliably inferred for 25% of studied phenotypes, the most heritable traits being “Other specified hypothyroidism” (ICD-10 code E03.8), “Obesity due to excess calories” (E66.0), “Obesity” (E66), “Myopia” (H52.1), and “Hypertension” (I10). These findings are a good starting point for a more in-depth interpretation of loci associated with complex diseases in the Estonian Biobank.