Marian Baldovic

A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe.

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe

A large part of Y chromosome lineages in East European and East Asian human populations belong to haplogroup (hg) NO, which is composed of two sister clades N-M231 and O-M175. The O-clade is relatively old (around 30 thousand years (ky)) and encompasses the vast majority of east and Southeast Asian male lineages, as well as significant proportion of those in Oceanian males. On the other hand, our detailed analysis of hg N suggests that its high frequency in east Europe is due to its more recent expansion westward on a counter-clock northern route from inner Asia/southern Siberia, approximately 12–14 ky ago. The widespread presence of hg N in Siberia, together with its absence in Native Americans, implies its spread happened after the founder event for the Americas. The most frequent subclade N3, arose probably in the region of present day China, and subsequently experienced serial bottlenecks in Siberia and secondary expansions in eastern Europe. Another branch, N2, forms two distinctive subclusters of STR haplotypes, Asian (N2-A) and European (N2-E), the latter now mostly distributed in Finno-Ugric and related populations. These phylogeographic patterns provide evidence consistent with male-mediated counter-clockwise late Pleistocene–Holocene migratory trajectories toward Northwestern Europe from an ancestral East Asian source of Paleolithic heritage.

Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a

Human Y-chromosome haplogroup structure is largely circumscribed by continental boundaries. One notable exception to this general pattern is the young haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestry of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorly understood as no marker has yet been described that would distinguish European R1a chromosomes from Asian. Here we present frequency and haplotype diversity estimates for more than 2000 R1a chromosomes assessed for several newly discovered SNP markers that introduce the onset of informative R1a subdivisions by geography. Marker M434 has a low frequency and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.

A database of mitochondrial DNA hypervariable regions I and II sequences of individuals from Slovakia.

In order to identify polymorphic positions and to determine their frequencies and the frequency of haplotypes in the human mitochondrial control region, two hypervariable regions (HV1 and HV2) of the mitochondrial DNA (mtDNA) of 374 unrelated individuals from Slovakia were amplified and sequenced. Sequence comparison led to the identification of 284 mitochondrial lineages as defined by 163 variable sites. Genetic diversity (GD) was estimated at 0.997 and the probability of two randomly selected individuals from population having identical mtDNA types (random match probability, RMP) for the both regions is 0.60%.

Analysis of Leucine-rich repeat kinase 2 (LRRK2) and Parkinson protein 2 (parkin, PARK2) genes mutations in Slovak Parkinson disease patients

Parkinson disease (PD) is a chronic neurodegenerative movement disorder characterized by selective loss of nigrostriatal dopaminergic neurons and formation of Lewy bodies. Clinical manifestations include motor impairments involving tremor, bradykinesia, postural instability and rigidity. Using dHPLC method we screened exons 31, 35, 41, 48 of the Leucine-rich repeat kinase 2 (LRRK2) gene and exons 2, 6 and 7 of Parkinson protein 2 (parkin, PARK2) genes in a cohort of 216 consecutive, unrelated Slovak patients with familial or sporadic PD, including early and late onset. By this means we aimed to detect the most common pathogenic mutations within LRRK2 (Arg1441Cys, Arg1441Gly, Arg1628Pro, Tyr1699Cys, Gly2019Ser, Ile2020Thr, Gly2385Arg) and parkin genes responsible for late and early onset forms of disease, respectively. However, none of these mutations was identified in our cohort. Heterozygous point mutation p.Arg275Trp in exon 7 of parkin gene was identified in one patient with age at onset 61 years. Furthermore, we observed the presence of one exonic (LRRK2 ex 48: 7155A>G) and eight intronic polymorphisms (in LRRK2: IVS35+23T>A, IVS47-91insGCCAT, IVS47-91insGCAT, IVS47-41A>G, IVS47-9delT, IVS47-20C>T, IVS47-90A>G, in parkin: IVS2+25T>C), three of which were novel.

Comprehensive genetic study of cystic fibrosis in Slovak patients in 25 years of genetic diagnostics

Cystic fibrosis (CF) has one of the longest histories in hereditary disease molecular diagnostics. However, identification of causative mutations in the CFTR gene is complicated by over 2000 currently identified mutations; with more still being discovered. Knowledge of mutation spectrum may improve effective routine diagnostics and is obligatory in mutation‐specific treatment.

7 Twenty-five years' experience in genetic testing of cystic fibrosis in Slovakia – update on mutation spectrum

mutations. Point mutations were tested by allele-specific ligation, followed by PCR amplification. Results: The 2013 year CF Registry contains the data of 1968 patients from 74 regions of RF. Genetic testing was performed in 88.7% of patients (87.5% in children and 91.0% in adults). Total frequency of identified alleles was 80.5% (77.6% in children and 87.5% in adults). Two mutations were detected in 68.3% of patients, one mutation in 24.5% of patients, a single mutation failed to identify in 7.2% of patients. In total 112 different mutations was determined, of which 10 mutations (up to a frequency of 1%) were 70.25%. Registered 21 mutations with frequency from 1% to 0.09%, 9 mutations (0.09%), 10 mutations (0.06%), 62 mutations (0.03%). The first 10 mutations were distributed as follows: F508del 52.21%, CFTRdele2,3(21kb) 5.94%, E92K 2.58%, 3849+10kbC>T 2.18%, 2184insA 1.69%, 2143delT 1.67%, N1303K 1.46%, W1282X 1.43%, G542X 1.09%, L138ins 1.00%. Conclusion: The spectrum of mutations in the CFTR gene in the Russian Federation is characterized by a great variety. Mutation F508del occurs at a low frequency. There is a particular frequency distribution for the common CF mutations in the RF. These characteristics are determined by the historical singularities and significant ethnic diversity of the RF population.

Molecular detection of Mycobacterium tuberculosis complex in the 8th century skeletal remains from the territory of Slovakia

Abstract DNA was extracted using a Silica Bead Extraction kit from bone samples taken from a Slavonic-Avar individual found at the archaeological site of Cífer-Pác. The analysed skeletal remains from the grave number 62/79 belong to a young adult male (20–30 years at death) and are dated to the 8th–9th century anno Domini. The isolated ancient DNA (aDNA) was amplified by a targeted PCR with a primer pair designed to recognize the Mycobacterium tuberculosis complex insertion sequence IS6110. The aim of this molecular approach was to test and optimize a methodology for aDNA M. tuberculosis complex extraction from bone samples with osteological evidence of tuberculosis. Despite of the currently biased authenticity of the mentioned fragment, in this case study we prove that macroscopic evidence for tuberculosis additionally supported by a positive result of molecular testing can be considered authentic enough to be the proof of a tuberculosis infection caused by MTBC (Mycobacterium tuberculosis complex) bacteria when additional skeletal trauma and changes potentially caused by MOTT (mycobacteria other than tuberculosis) bacteria can be excluded. Positivity was confirmed in all of the three samples (thoracic vertebrae, lumbar vertebrae and right femur). Our results confirmed the diagnosis of tuberculosis of the spine and right hip joint. This is the first molecular evidence for the occurrence of tuberculosis on the territory of Slovakia. Through this bio-molecular approach we wish to provide a basis for aDNA examinations on other skeletal collections and provide epidemiological data concerning historical populations living on the territory of Slovakia.