A5081497892- Mitochondrial Function and Pathology
- Metabolism and Genetic Disorders
- Forensic and Genetic Research
- Cancer Genomics and Diagnostics
- SARS-CoV-2 and COVID-19 Research
- Glioma Diagnosis and Treatment
- Genetic Associations and Epidemiology
- Genetic diversity and population structure
- Rangeland Management and Livestock Ecology
- SARS-CoV-2 detection and testing
- Medical Imaging and Pathology Studies
- Biosensors and Analytical Detection
- Forensic Anthropology and Bioarchaeology Studies
- ATP Synthase and ATPases Research
- Genomics and Rare Diseases
- Digestive system and related health
- Molecular Biology Techniques and Applications
- Yersinia bacterium, plague, ectoparasites research
- Chromatin Remodeling and Cancer
- Animal Diversity and Health Studies
- interferon and immune responses
- Sarcoma Diagnosis and Treatment
- Cancer, Hypoxia, and Metabolism
- PARP inhibition in cancer therapy
- Linguistics and Cultural Studies
CeMM Research Center for Molecular Medicine
2021-2023
Austrian Academy of Sciences
2022-2023
Medical University of Vienna
2022-2023
Czech Academy of Sciences, Institute of Archaeology, Prague
2020-2022
Charles University
2019-2022
University Hospital in Motol
2020
Children's Hospital of Los Angeles
2017-2019
University of Southern California
2019
Universidade do Porto
2014-2017
IPO Porto
2014-2017
Genome-wide studies of African populations have the potential to reveal powerful insights into evolution our species, as these diverse been exposed intense selective pressures imposed by infectious diseases, diet, and environmental factors. Within Africa, Sahel Belt extensively overlaps geographical center several endemic infections such malaria, trypanosomiasis, meningitis, hemorrhagic fevers. We screened 2.5 million single nucleotide polymorphisms in 161 individuals from 13 Sahelian...
Ethnic groups can display differential genetic susceptibility to infectious diseases. The arthropod-born viral dengue disease is one such disease, with empirical and limited evidence showing that African ancestry may be protective against the haemorrhagic phenotype. Global analysis based on high-throughput genotyping in admixed populations used test this hypothesis, while admixture mapping map candidate genes. A Cuban fever cohort was genotyped using a 2.5 million SNP chip. ascertained...
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any family. We investigated connections between Kets Siberian North American populations, emphasis on Mal'ta Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples 42 their neighboring groups (Uralic-speaking Nganasans, Enets, Selkups). genotyped over 130,000 autosomal SNPs, identified mitochondrial...
The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves Turkic Uralic-speaking migrants well eastward Europeans. Unfortunately, material records this region are not dense enough to reconstruct details population history. These considerations stimulate growing interest obtain a genetic picture demographic migrations admixture in Northern Eurasia. We genotyped...
At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over generations. Estimating timing impact of these multiple migrations are important steps in reconstructing key demographic events human history. However, current methods based on genome-wide information identify admixture inefficiently, tending to estimate only more recent ages, as here case across Red Sea (∼8–37 generations for African input into Arabia, 30–90...
Little is known about the spectrum of mitochondrial DNA (mtDNA) mutations across pediatric malignancies. In this study, we analyzed matched tumor and normal whole genome sequencing data from 616 patients with hematopoietic malignancies, solid tumors, brain tumors. We identified 391 mtDNA in 284 tumors including 45 loss-of-function mutations, which clustered at four statistically significant hotspots MT-COX3, MT-ND4, MT-ND5, a mutation hotspot MT-tRNA-MET. A skewed ratio (4.83) nonsynonymous...
The genetic structure of human populations is extraordinarily complex and fundamental importance to studies anthropology, evolution, medicine. As increasingly many individuals are mixed origin, there an unmet need for tools that can infer multiple origins. Misclassification such lead incorrect costly misinterpretations genomic data, primarily in disease drug trials. We present advanced tool ancestry identify the biogeographic origins highly individuals. reAdmix incorporate individual's...
Abstract The Sahel/Savannah belt harbors diverse populations with different demographic histories and subsistence patterns. However, from this large African region are notably under-represented in genomic research. To investigate the population structure adaptation history of space, we generated dense genome-wide genotype data 327 individuals—comprising 14 ethnolinguistic groups, including 10 previously unsampled populations. Our results highlight fine-scale complex patterns admixture,...
Fusion of the ZNF384 gene as 3' partner to several different 5' genes occurs recurrently in B-cell precursor acute lymphoblastic and mixed phenotype B/myeloid leukemia. These canonical fusions (ZNF384r) contain complete coding sequence are associated with a specific expression signature. Cases this signature, but without (ZNF384r-like cases), have been described previously. Although some shown harbor ZNF362 fusions, primary aberrations remain unknown major proportion. We studied 3 patients...
Abstract SARS-CoV-2 surveillance is crucial to identify variants with altered epidemiological properties. Wastewater-based epidemiology (WBE) provides an unbiased and complementary approach sequencing individual cases. Yet, national WBE programs have not been widely implemented data analyses remain challenging. We deep-sequenced 2,093 wastewater samples representing 95 municipal catchments, covering >57% of Austria’s population, from December 2020 September 2021. Our Va riant Qu...
Abstract Objectives The Sahel belt is occupied by populations who use two types of subsistence strategy, nomadic pastoralism and sedentary farming, belong to three linguistic families, Niger‐Congo, Nilo‐Saharan, Afro‐Asiatic. Little known, however, about the origins these their mutual genetic relationships. Materials Methods We have built a large dataset mitochondrial DNA sequences Y chromosomal STR haplotypes pastoralists farmers belonging all phyla in western, central, eastern parts Sahel....
Mitochondrial proteins are coded by nuclear (nDNA) and mitochondrial (mtDNA) genes, implying a complex cross-talk between the two genomes. Here we investigated diversity displayed in 104 nuclear-coded from 1,092 individuals 1000 Genomes dataset, order to evaluate if these genes under effects of purifying selection how that compares with their encoded counterparts. Only very rare variants (frequency < 0.1%) nDNA indistinguishable random set all possible terms predicted pathogenicity score,...
Based on current studies, the incidence of Ewing sarcoma (ES) varies significantly by race and ethnicity, with disease being most common in patients European ancestry. However, race/ethnicity has generally been self-reported rather than formally evaluated at a population level using DNA evidence. Additionally, mitochondrial dysfunction is hallmark ES, yet there have no reported studies genetics ES. Thus, we both nuclear ancestries 420 pediatric ES United States whole-genome sequencing. We...
Abstract SARS-CoV-2 has evolved rapidly towards higher infectivity and partial immune escape over the course of pandemic. This evolution is driven by enormous virus population, that infected close to 200 million people now. Therefore, cost effective scalable methods are needed monitor viral globally. Mutation-specific PCR approaches have become inadequate distinguish variety circulating variants unable detect novel ones. Conversely, whole genome sequencing protocols remain too labor-...
Abstract Background We previously established the landscape of mitochondrial DNA (mtDNA) mutations in 23 subtypes pediatric malignancies, characterized mtDNA mutation profiles among these subtypes, and provided statistically significant evidence for a contributory role to malignancies. Methods To further delineate spectrum CNS tumors, we analyzed 545 tumor-normal paired whole genome sequencing data sets from Children’s Brain Tumor Tissue Consortium. Results Germline variants were used...
Abstract The genetic structure of human populations is extraordinarily complex and fundamental importance to studies anthropology, evolution, medicine. As increasingly many individuals are mixed origin, there an unmet need for tools that can infer multiple origins. Misclassification such lead incorrect costly misinterpretations genomic data, primarily in disease drug trials. We present advanced tool ancestry identify the biogeographic origins highly individuals. reAdmix incorporate...
Mode of subsistence is an important factor influencing dietary habits and the genetic structure various populations through differential intensity gene flow selection pressures. Previous studies suggest that in Africa Taste 2 Receptor Member 16 (TAS2R16), which encodes 7-transmembrane receptor protein for bitterness, might also be under positive pressure.However, since sampling coverage was limited, we created a new TAS2R16 population dataset from across African Sahel/Savannah belt...
Abstract Integrative analyses of CRISPR/Cas9 screening datasets from different sources revealed - besides known oncogenes a series transcriptional master regulators as most prominent context-specific dependencies in cancer that remained largely inaccessible to conventional drug discovery approaches. New chemical entities (NCEs) specifically interfere with transcription factor (TF) at any level should induce and be detectable based on selective effects their primary biochemical activity i.e.,...
e17519 Background: The clinical management of testicular germ cell tumors (TGCT) has not changed much for decades; most importantly, novel prognostic factors indicating the need adjuvant chemotherapy and related to development cisplatin resistance would be needed. Circulating free tumor DNA (cfDNA) is an easily available valuable source genetic material, which may bring clinically relevant information. Methods: After ethical committee approval patient informed consent, peripheral blood (PB)...
Abstract The Kets, an ethnic group in the Yenisei River basin, Russia, are considered last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any family. We investigated connections between Kets Siberian North American populations, emphasis on Mal’ta Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples 42 their neighboring groups (Uralic-speaking Nganasans, Enets, Selkups). genotyped over 130,000 autosomal SNPs, identified...