Vladimír Ferák

Phylogeography of Y-Chromosome Haplogroup I Reveals Distinct Domains of Prehistoric Gene Flow in Europe

To investigate which aspects of contemporary human Y-chromosome variation in Europe are characteristic of primary colonization, late-glacial expansions from refuge areas, Neolithic dispersals, or more recent events of gene flow, we have analyzed, in detail, haplogroup I (Hg I), the only major clade of the Y phylogeny that is widespread over Europe but virtually absent elsewhere. The analysis of 1,104 Hg I Y chromosomes, which were identified in the survey of 7,574 males from 60 population samples, revealed several subclades with distinct geographic distributions. Subclade I1a accounts for most of Hg I in Scandinavia, with a rapidly decreasing frequency toward both the East European Plain and the Atlantic fringe, but microsatellite diversity reveals that France could be the source region of the early spread of both I1a and the less common I1c. Also, I1b*, which extends from the eastern Adriatic to eastern Europe and declines noticeably toward the southern Balkans and abruptly toward the periphery of northern Italy, probably diffused after the Last Glacial Maximum from a homeland in eastern Europe or the Balkans. In contrast, I1b2 most likely arose in southern France/Iberia. Similarly to the other subclades, it underwent a postglacial expansion and marked the human colonization of Sardinia approximately 9,000 years ago.

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.

Identification of a single ancestral CYP1B1 mutation in Slovak Gypsies (Roms) affected with primary congenital glaucoma

Primary congenital glaucoma (PCG) is an autosomal recessive eye disease that occurs at an unusually high frequency in the ethnic isolate of Roms (Gypsies) in Slovakia. Recently, we linked the disease in this population to the GLC3A locus on 2p21. At this locus, mutations in the cytochrome P4501B1 (CYP1B1) gene have been identified as a molecular basis for this condition. Here, we report the results of CYP1B1 mutation screening of 43 PCG patients from 26 Slovak Rom families. A homozygous G→A transition at nucleotide 1505 in the highly conserved region of exon 3 was detected in all families. This mutation results in the E387K substitution, which affects the conserved K helix region of the cytochrome P450 molecule. Determination of the CYP1B1 polymorphic background showed a common DNA haplotype in all patients, thus indicating that the E387K mutation in Roms has originated from a single ancestral mutational event. The Slovak Roms represent the first population in which PCG is found to result from a single mutation in the CYP1B1 gene, so that a founder effect is the most plausible explanation of its increased incidence. An ARMS-PCR assay has been developed for fast detection of this mutation, thus allowing direct DNA based prenatal diagnosis as well as gene carrier detection in this particular population. Screening of 158 healthy Roms identified 17 (10.8%) mutation carriers, indicating that the frequency of PCG in this population may be even higher than originally estimated.

High Frequency of Alkaptonuria in Slovakia: Evidence for the Appearance of Multiple Mutations in HGO Involving Different Mutational Hot Spots

Alkaptonuria (AKU) is an autosomal recessive disorder caused by the deficiency of homogentisate 1,2 dioxygenase (HGO) activity. AKU shows a very low prevalence (1:100,000-250,000) in most ethnic groups. One notable exception is in Slovakia, where the incidence of AKU rises to 1:19,000. This high incidence is difficult to explain by a classical founder effect, because as many as 10 different AKU mutations have been identified in this relatively small country. We have determined the allelic associations of 11 HGO intragenic polymorphisms for 44 AKU chromosomes from 20 Slovak pedigrees. These data were compared to the HGO haplotype data available in our laboratory for >80 AKU chromosomes from different European and non-European countries. The results show that common European AKU chromosomes have had only a marginal contribution to the Slovak AKU gene pool. Six of the ten Slovak AKU mutations, including the prevalent G152fs, G161R, G270R, and P370fs mutations, most likely originated in Slovakia. Data available for 17 Slovak AKU pedigrees indicate that most of the AKU chromosomes have their origins in a single very small region in the Carpathian mountains, in the northwestern part of the country. Since all six Slovak AKU mutations are associated with HGO mutational hot spots, we suggest that an increased mutation rate at the HGO gene is responsible for the clustering of AKU mutations in such a small geographical region.

Reconstructing the population history of European Romani from genome-wide data

The Romani, the largest European minority group with approximately 11 million people, constitute a mosaic of languages, religions, and lifestyles while sharing a distinct social heritage. Linguistic and genetic studies have located the Romani origins in the Indian subcontinent. However, a genome-wide perspective on Romani origins and population substructure, as well as a detailed reconstruction of their demographic history, has yet to be provided. Our analyses based on genome-wide data from 13 Romani groups collected across Europe suggest that the Romani diaspora constitutes a single initial founder population that originated in north/northwestern India ~1.5 thousand years ago (kya). Our results further indicate that after a rapid migration with moderate gene flow from the Near or Middle East, the European spread of the Romani people was via the Balkans starting ~0.9 kya. The strong population substructure and high levels of homozygosity we found in the European Romani are in line with genetic isolation as well as differential gene flow in time and space with non-Romani Europeans. Overall, our genome-wide study sheds new light on the origins and demographic history of European Romani.

Linkage of Autosomal Recessive Primary Congenital Glaucoma to the GLC3A Locus in Roms (Gypsies) from Slovakia

The autosomal recessive form of primary congenital glaucoma (gene symbol GLC3) has been recently mapped to two different loci, GLC3A (at 2p21), and GLC3B (at 1p36), respectively, on families of Turkish and Saudi Arabian provenance. This disorder is known to occur with an extremely high incidence in Roms (Gypsies) in Slovakia. We performed a standard linkage analysis on a sample of 7 Slovak Gypsy families comprising 18 affected members, and found significant linkage with four STR markers from the chromosomal region of 2p21 (D2S1788, D2S1346, D2S2328, and D2S1356), without heterogeneity. This finding demonstrates that in the Rom population of Slovakia, primary congenital glaucoma is due to the locus GLC3A, and consequently, to the mutation(s) in the cytochrome P4501B1 gene, which has been recently identified as the principal cause of the disease. Roms represent the third population, in which the disorder has been mapped to GLC3A.

Novel mutations in the homogentisate- 1,2-dioxygenase gene identified in Slovak patients with alkaptonuria

Editor—Alkaptonuria (AKU, McKusick No 203500), a rare autosomal recessive disorder (1:250 000),1 is a classical example of a specific biochemical lesion leading to degenerative disease. As a result of deficiency of homogentisic acid 1,2-dioxygenase activity (HGO, E.C. 1.13.11.5), AKU patients are unable to degrade homogentisic acid (HGA), an intermediary metabolite in phenylalanine and tyrosine catabolism.2 Accumulated HGA is excreted into the urine in large amounts, which darkens on standing. Over the years, benzoquinone acetic acid, an oxidation product of HGA, is deposited in connective tissues, causing their pigmentation (ochronosis), which leads to painful and disabling arthropathy of the large joints and spine (ochronotic arthropathy). AKU was the first disease interpreted in terms of Mendelian inheritance.3 The HGO gene in humans is located on chromosome 3q21-23.1 4 5Fernandez-Canon et al 5 cloned the human HGO gene and by identifying the first loss of function mutations also provided formal proof that AKU results from a defect in this gene. So far, 24 different mutations have been identified in the HGO gene in patients from various populations.5-10 Notable exceptions to the low prevalence of AKU in all ethnic groups studied are the Dominican Republic and Slovakia (1:19 000).11 12 Founder effects as the consequence of genetic isolation have been postulated to explain this observation. Here, we present results of mutation screening of the HGO gene in 32 AKU chromosomes carried by 17 Slovak AKU patients (in two families, one chromosome was shared by two patients from different generations). All 14 exons of the HGO gene were amplified from genomic DNA, using PCR primers and conditions as described by Fernandez-Canon et al. 5 PCR products were analysed for the presence of mutations by non-radioactive single strand conformation polymorphism analysis …

PKU in Slovakia: mutation screening and haplotype analysis

The restriction fragment length polymorphism haplotypes and seven common mutations in the phenylalanine hydroxylase gene were analysed in 49 unrelated Slovak phenylketonuria (PKU) families of Caucasian origin. The predominant mutation in this population sample is R408W, with a frequency of 45.9%. In addition, four other mutations have been identified at relatively high frequencies: IVS12nt1, 10.2%; R158Q, 7.1%; R261Q, 7.1%; R252W, 2.0%. The mutation-haplotype associations correspond to those described in other European populations. The high proportion of mutations (72.4%) amenable to simple rapid detection based on the polymerase chain reaction provides a good basis for direct DNA-diagnosis of PKU in the Slovak population.

Genetic distances, geographic distances and migration between four villages of a single region in Slovakia

Abstract Genetic microdifferentiation has been studied among four endogamous villages of the Bystrica Valley in the Kysuce region of northwest Slovakia, which arose from a single ancestral population about 15 generations ago. Genetic distances and sample kinship between the villages were estimated from the gene frequencies of seven serum-group and isozyme genetic markers. The genetic distance was found to correlate positively (though insignificantly) with the geographic distance, and negatively with the intensity of migration between villages; the sample kinship correlates negatively with geography as well as with the genetic distance. This pattern of genetic structure within the area indicates that the genetic variation among the villages is attributable to the genetic drift. Thus, drift has brought about a detectable differentiation in the area within a limited period of approximately 300 years, in spite of the fact that the villages were not completely genetically isolated from each other. The finding of a negative correlation between the sample kinship and geographic distance indicates that the recent breakdown of genetic isolates in Slovakia is likely to be accompanied with an overall increase of heterozygosity.

Genetic screening and genetic services in Slovakia

Before attaining independence in 1993, Slovakia existed as a republic within the Czechoslovak Federation. Slovakia inherited most of its laws and other regulations governing medical practice, including those concerning genetic screening and genetic services, from the former Czechoslovakia. The same holds true for the Czech Republic; and hence the situation in both these countries is very similar.