1. Creating the Slovenian genome database and browser as a source of comprehensive variation of the Slovenian populationAleš Maver, Peter Juvan, Urška Kotnik, Luca Lovrečić, Gaber Bergant, Borut Peterlin, 2025, original scientific article Abstract: The genomic data of Central European populations is underrepresented in the publicly available databases. We present the comprehensive genomic variation of the Slovenian population, based on the genomic sequencing of 9425 non-related individuals, i.e. more than 0.44% of the Slovenian population. Over 30 million unique single nucleotide and small indel (30.8 million), copy number (217.6 thousand), and mitochondrial variants (3.3 thousand) were uncovered and annotated by analysing the whole genome of 619 individuals and the whole exome of 8806 individuals. This population variation, including 3,9 million novel variants, is presented in a publicly available genome variant browser, the SloGenVar (https://slogenvar.si). We used this newly developed resource to reveal the population frequency of pathogenic variants in the genes associated with recessive conditions. The Slovenian genome database and browser offer the largest and the most comprehensive publicly available Central European population genomic variant resource, providing an important asset for genomic studies and as a control variant database for variant interpretation in the region and beyond.
Keywords: population genomic variation, whole genome sequencing, genome browser, Slovenian genome database
Published in DiRROS: 22.12.2025; Views: 879; Downloads: 419
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2. Increased burden of rare variants in GWAS associated genes in familial multiple sclerosisAleksander Turk, Aleš Maver, Peter Juvan, Jelena Drulović, Sarlota Mesaros, Ivana Novaković, Nada Starčević-Čizmarević, Smiljana Ristić, Ivana Stanković Matić, Borut Peterlin, 2025, original scientific article Abstract: Multiple sclerosis (MS) is an immune-mediated neurodegenerative disease affecting the central nervous system with many known genetic risk factors. Although genome-wide association studies (GWAS) have identified common genetic variants with small effects associated with MS, the role of rare variants with large effects in MS aetiology remains underexplored. We hypothesized that rare variants in MS-associated genes from GWAS studies (GWAS-associated genes) are more likely to contribute to familial MS (FMS) risk than to sporadic MS (SMS). Therefore, we aimed to assess the burden of rare, predicted pathogenic (RPP) variants in GWAS-associated genes in FMS and SMS patients compared to controls. Rare genetic variants in 111 GWAS-associated genes were assessed in 87 FMS, 89 SMS and 3866 control cases. We demonstrate that RPP variants were significantly overrepresented in the FMS cohort whereas their frequency was not increased in the SMS cohort compared to controls (p-values 5.27 × 10− 74 and 1.00, respectively). Six genes (ALPK2, ANKRD55, INTS8, IQCB1, JADE2, and MALT1) significantly contributed to the burden of RPP in the FMS group. We conclude that rare variants in genes identified by GWAS might contribute to the genetic predisposition of familial MS patients.
Keywords: multiple sclerosis, burden analysis, whole exome sequencing (WES), rare variants, rare pathological changes, candidate genes
Published in DiRROS: 12.11.2025; Views: 659; Downloads: 379
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3. Contrasting effect of recombinant human erythropoietin on breast cancer cell response to cisplatin induced cytotoxicityNina Trošt, Peter Juvan, Gregor Serša, Nataša Debeljak, 2012, original scientific article Abstract: Background. Human recombinant erythropoietin (rHuEpo) that is used for the treatment of the chemotherapy-induced anaemia in cancer patients was shown to cause detrimental effects on the course of disease due to increased adverse events inflicting patient's survival, potentially related to rHuEpo-induced cancer progression. In this study, we elucidate the effect of rHuEpo administration on breast cancer cell proliferation and gene expression after cisplatin (cDDP) induced cytotoxicity. Materials and methods. Two breast carcinoma models, MCF-7 and MDA-MB-231 cell lines, were used differing in oestrogen (ER) and progesterone (PR) receptors and p53 status. Cells wer e cultured with or without rHuEpo for 24 h or 9 weeks and their growth characteristics after cDDP treatment were assessed together with expression ofgenes involved in the p53-signaling pathway. Results. Short-term exposure ofbreast cancer cells to rHuEpo lowers their proliferation and reduces cDDP cytotoxic potency. In contrast, long-term exposure of MCF-7 cells to rHuEpo increases proliferation and predisposes MCF-7 cells to cDDP cytotoxicity, but has no effect on MDA-MB-231 cells. MDA-MB-231 cells show altered level of ERK phosphorylation, indicating involvement of MAPK signalling pathway. Gene expression analysis of p53-dependent genes and bcl-2 gene family members confirmed differences between long and short-term rHuEpo effects, indicating the most prominent changes in BCL2 and BAD expression. Conclusions. Proliferation and survival characteristics of MCF-7 cells are reversely modulated by the length of the rHuEpo exposure. On the other hand, MDA-MB-231 cells are almost irresponsive to long-term rHuEpo, supposedly due to the mutated p53 and ER(+)/PR(-) status. The p53 and ER/PR status may predict tumour response on rHuEpo and cDDP treatment.
Keywords: breast cancer, erythropoietin, cisplatin, cytotoxicity
Published in DiRROS: 22.03.2024; Views: 1721; Downloads: 483
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