1. Optical genome mapping : a new approach in laboratory and clinical geneticsAnja Kovanda, Borut Peterlin, 2026, review article Abstract: Optical genome mapping (OGM) is a novel method based on image acquisition of single, enzyme labelled, high-molecular-weight DNA molecules, that enables the detection of structural variants (SV). This includes copy neutral SV such as inversions, insertions and balanced translocations in size ranges that typically represent a challenge for sequence, array or PCR based methods, making the method applicative in the field of haematological and constitutional genetic testing alike. In constitutional setting, OGM is particularly useful for facioscapulohumeral dystrophy testing, validation of suspected variants from other technologies, as well as testing of rare-disease patients with previously negative genetic testing results.
Keywords: duplication, insertion, inversion, optical genome mapping, structural genomic variants, translocation
Published in DiRROS: 03.09.2026; Views: 116; Downloads: 49
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2. Oral microbiome and preterm birthMarijana Vidmar Šimic, Aleš Maver, Ana Nyasha Zimani, Keli Hočevar, Borut Peterlin, Tanja Premru-Sršen, 2023, original scientific article Abstract: Background: The etiology of preterm birth (PTB) is heterogeneous and not yet well known. Maternal periodontal disease has been investigated for decades and is a known risk factor for adverse pregnancy outcomes. However, no particular bacterial species or higher taxonomic order has been found as causative of PTB, leading to studies of the whole oral microbiome. In order to determine if and how the composition of the oral microbiome is associated with PTB, we performed a large case–control study including women with term (TB) and PTB. Methods: We compared oral microbiomes in PTB to TB, to examine differences in the microbial richness, diversity, and differential abundance of specific taxa. We obtained oral swab samples from 152 Caucasian pregnant women who were classified as either PTB (≤36 6/7 weeks, n = 61) or TB (≥38 0/7 weeks, n = 91) in exclusion of any other major medical or obstetric conditions. The oral microbiomes of these women were characterized by 16S ribosomal RNA (rRNA) gene sequencing of the V3–V4 region on the MiSeq platform. Results: The dominant microorganisms at the phylum level in all pregnant women regardless of birth week outcomes as belonging to Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria. The phyla Firmicutes and Bacteroidetes were relatively more abundant in women with a PTB than in women with a TB, while Proteobacteria was less prevalent in women with a PTB. At the genus level, Veillonella, Prevotella, and Capnocytophaga were enriched in the PTB, and while many of the members of these genera could not be resolved to the species level, Veillonella massillensis was shown to be increased in the PTB group. Conclusion: We identified the genera Veillonella, Prevotella, and Capnocytophaga in the maternal oral microbiome as being associated with PTB independently of clinically apparent infection, uterine anomalies, and other pregnancy complications, including placenta previa, and placental abruption. The clarification of the role of those taxa in the etiology of PTB merits further research.
Keywords: preterm delivery, microbiome, 16S rRNA gene, 16S rDNA, oral microbiome, pregnancy
Published in DiRROS: 01.09.2026; Views: 174; Downloads: 78
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3. Genomic landscape of susceptibility to severe Covid-19 in the Slovenian populationAnja Kovanda, Tadeja Lukežič, Aleš Maver, Hana Vokač Križaj, Mojca Čižek-Sajko, Julij Šelb, Matija Rijavec, Barbara Bitežnik, Boštjan Rituper, Peter Korošec, Borut Peterlin, 2024, original scientific article Abstract: Determining the genetic contribution of susceptibility to severe SARS-CoV-2 infection outcomes is important for public health measures and individualized treatment. Through intense research on this topic, several hundred genes have been implicated as possibly contributing to the severe infection phenotype(s); however, the findings are complex and appear to be population- dependent. We aimed to determine the contribution of human rare genetic variants associated with a severe outcome of SARS-CoV-2 infections and their burden in the Slovenian population. A panel of 517 genes associated with severe SARS-CoV-2 infection were obtained by combining an extensive review of the literature, target genes identified by the COVID-19 Host Genetic Initiative, and the curated Research COVID-19 associated genes from PanelApp, England Genomics. Whole genome sequencing was performed using PCR-free WGS on DNA from 60 patients hospitalized due to severe COVID-19 disease, and the identified rare genomic variants were analyzed and classified according to the ACMG criteria. Background prevalence in the general Slovenian population was determined by comparison with sequencing data from 8025 individuals included in the Slovenian genomic database (SGDB). Results show that several rare pathogenic/likely pathogenic genomic variants in genes CFTR, MASP2, MEFV, TNFRSF13B, and RNASEL likely contribute to the severe infection outcomes in our patient cohort. These results represent an insight into the Slovenian genomic diversity associated with a severe COVID-19 outcome.
Keywords: severe COVID-19, severe outcome of SARS-CoV-2 infection, whole-genome sequencing, genetic susceptibility, rare variants, human rare genomic variants
Published in DiRROS: 11.06.2026; Views: 370; Downloads: 272
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4. GiOPARK Project : the genetic study of Parkinson’s Disease in the Croatian populationValentino Rački, Gaber Bergant, Eliša Papić, Anja Kovanda, Mario Hero, Gloria Rožmarić, Nada Starčević-Čizmarević, Smiljana Ristić, Saša Ostojić, Miljenko Kapović, Aleš Maver, Borut Peterlin, Vladimira Vuletić, 2024, original scientific article Keywords: Parkinson’s disease, genetic testing, whole-exome sequencing
Published in DiRROS: 09.06.2026; Views: 413; Downloads: 195
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5. Biallelic RFC1 expansions are a rare cause of early-onset and familial Parkinson's diseaseAnja Kovanda, Lara Šušmelj, Helena Jaklič, Tadeja Lukežič, Aleš Maver, Igor N. Petrović, Borut Peterlin, 2026, other scientific articles Keywords: CANVAS, neurodegenerative disease, vestibular areflexia syndrome, CANVAS, RFC1, PCR
Published in DiRROS: 18.03.2026; Views: 531; Downloads: 478
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6. Microbial diversity in drug-naïve Parkinson’s disease patientsEliša Papić, Valentino Rački, Mario Hero, Ana Nyasha Zimani, Mojca Čižek-Sajko, Gloria Rožmarić, Nada Starčević-Čizmarević, Saša Ostojić, Miljenko Kapović, Goran Hauser, Aleš Maver, Borut Peterlin, Anja Kovanda, Vladimira Vuletić, 2025, original scientific article Abstract: Parkinson’s disease (PD) is a neurological disorder characterized by rigidity, bradykinesia and tremor. Several genetic and environmental causes of PD are known, and there is emerging evidence of the possible contribution of the gut microbiome to the disease onset, severity, and response to therapy. While previous research has shown several differences in the microbiome of PD patients under therapy as opposed to healthy controls, few prospective studies have included drug-naïve patients. In order to evaluate the gut microbiome composition prior to therapy initiation, we collected and performed 16S rRNA gene sequencing of the stool samples from 49 drug-naïve PD patients and compared them to 34 diet and lifestyle-matched controls from the Croatian population (GiOPARK Project). While no significant alpha diversity difference was observed between the patients and controls, the differential relative abundance analysis showed an increase in Bacteroides fluxus, B. interstinalis, B. eggerthii, and Dielma fastidiosa in the drug-naïve PD patients compared to controls, while Alistipes, Barnesiella and Dialister spp. were decreased in patients compared to controls. Despite preserved overall diversity, these changes may indicate early microbial dysbiosis and represent a foundation for future studies exploring microbiome changes across disease progression and treatment.
Keywords: Parkinson’s disease, neurological disorder, gut microbiome, microbial diversity, microbial dysbiosis
Published in DiRROS: 23.02.2026; Views: 648; Downloads: 305
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7. Value of optical genome mapping (OGM) for diagnostics of rare diseases : a family case reportAnja Kovanda, Olivera Miljanović, Luca Lovrečić, Aleš Maver, Alenka Hodžić, Borut Peterlin, 2024, other scientific articles Abstract: Optical genome mapping (OGM) is a novel method enabling the detection of structural genomic variants. The method is based on the laser image acquisition of single, labeled, high-molecular-weight DNA molecules and can detect structural genomic variants such as translocations, inversions, insertions, deletions, duplications, and complex structural rearrangements. We aim to present our experience with OGM at the Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slovenia. Since its introduction in 2021, we have used OGM for the testing of facioscapulohumeral muscular dystrophy 1, characterization and resolution of variants identified by other technologies such as microarrays, exome and genome next-generation sequencing, karyotyping, as well as testing of rare disease patients in whom no genetic cause could be identified using these methods. We present an example family case of two previously undiagnosed male siblings with an overlapping clinical presentation of thrombocytopenia, obesity, and presacral teratoma. After karyotyping, microarray analysis and next-generation sequencing, by using OGM, a maternally inherited cryptic translocation t(X;18)(q27.1;q12.2) was identified in both brothers. Despite an extended segregation analysis, based on strictly applied ACMG criteria and ClinGen guidelines, the identified translocation remains a variant of unknown significance. Despite the remaining limitations of OGM, which will hopefully be resolved by improvements in databases of known benign SV variation and the establishment of official guidelines on the clinical interpretation of OGM variants, our work highlights the complexity of the diagnostic journey, including this novel method, in rare disease cases.
Keywords: optical genome mapping, OGM, structural variants, SV, genomic variants, rare disease genetic testing
Published in DiRROS: 04.12.2025; Views: 674; Downloads: 427
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