Izomdystrophiák differenciál-diagnosztikai vizsgálata molekuláris genetikai, valamint immunhisztokémiai és immunoblot analízisek segítségével = Differential diagnostic study of muscle dystrophies by molecular genetic, immunohystochemical and Western-blot analyses

A DMD/BMD betegségben célul tűzték ki a cDNS próbák alkalmazását a hordozósági státusz vizsgálatára és a deléciók pontos méretének meghatározására. Az újonnan bevezetett MLPA módszer segítségével a teljes dystrophin gén feltérképezésére, bizonyos pont mutációk kiszűrésére, a deléciók és duplikációk pontos analízisére, továbbá a hordozóság gyors szűrésére is vállalkozhattak. Összesen 120 beteg és 89 női hozzátartozó molekuláris analízisét végezték el a pályázat támogatásával. Az FSHD betegségben a komplex genetikai háttér miatt szükséges a molekuláris diagnosztikus kritériumok finomítása. A betegség hátterében álló epigenetikus változások kulcsfontosságúak lehetnek fenotípus kialakulásában. A betegség pathomechanizmusában a D4Z4 szekvenciáktól proximálisan elhelyezkedő gének megváltozott transzkripciójának van szerepe, amelynek vizsgálatára metilációs analízist alkalmaztak. A klinikai diagnózis megerősítésére összesen 90 beteg és 46 tünetmentes hozzátartozó DNS mintáját analizálták. Az LGMD betegségcsoport a betegek differenciál-diagnosztikája jelenleg csak specifikus fehérjedetektálási módszerekkel lehetségesek. Ezeket a módszereket alkalmazták azokban az esetekben, ahol az FSHD és DMD/BMD molekuláris genetikai vizsgálata negatív volt. A vizsgálati periódusban 122 beteg izombiopsziás mintája érkezett, ebből 56 esetben immunhisztokémiai, míg 20 esetben kiegészítő western blot analízis történt. További, DNS szintű analízisek 14 esetben azonosították a patogén mutációt. | The first aim of the study was to introduce cDNA probes for the analysis of DMD/BMD in order to detect carrier status and exact deletion borders. Additionally, the new MLPA technique was first introduced by us in Hungary and enabled the detection of the entire dystrophin gene with highlights on specific pointmutations, exact analysis of the deletions and duplications and moreover, on efficient screening of the carrier status. During the project, 120 affected persons and 89 female relatives were screened. In case of the FSHD molecular genetic criteria have to be improved because of the complexity of the disorder. Epigenetic influences may play a crutial role in modulating phenotype. Altered transcriptional activities of neighbouring genes proximal to the D4Z4 sequences have a key place in the pathomechanism, therefore, this effect was studied by methylation analysis. For confirmation of the clinical diagnosis 90 patients and 46 asymptomatic family members were genetically nalysed. The differential diagnosis of the heterogenous group of LGMD requires at first the specific analysis of the dystrophin-associated glycoproteins. This was used in the case of patients where the establishment of the genetic diagnosis of DMD/BMD or FSHD failed. Muscle biopsies and blood samples of 122 patients were sent to the laboratory; in total 56 immunohistochemical and 20 Western blot analyses have been performed. In 14 patients the exact pathogenic mutation has been identified by DNA sequencing

Upper Palaeolithic genomes reveal deep roots of modern Eurasians.

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.This research was supported by the European Research Council (ERC) Starting Grant to R.P. (ERC-2010-StG 263441). D.B., M.H and AM. were also supported by the ERC (295729-CodeX, 310763-GeneFlow and 647787-LocalAdaptation respectively). The National Geographic Global Exploration Fund funded fieldwork in Satsurblia Cave l from April 2013 to February 2014 (grant- GEFNE78–13). V.S. was supported by a scholarship from the Gates Cambridge Trust and M.G.L. by a BBSRC DTP studentship. C.G. was supported by the Irish Research Council for Humanities and Social Sciences (IRCHSS) ERC Support Programme and the Marie-Curie Intra-European Fellowships (FP7-IEF-328024). R.M. was funded by the BEAN project of the Marie Curie ITN (289966) and L.C. by the Irish Research Council (GOIPG/2013/1219). R.L.M. was funded by the ALS Association of America (2284) and Fondation Thierry Latran (ALSIBD). M.C. was supported by Swiss NSF grant 31003A_156853. We acknowledge Shota Rusataveli Georgian National Science Foundation as well as the DJEI/DES/SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and Science Foundation Ireland (12/ERC/B2227) for provision of sequencing facilities. We thank Valeria Mattiangeli and Matthew D. Teasdale for their assistance.This is the final version of the article. It was first available from NPG via http://dx.doi.org/10.1038/ncomms991

Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago.

Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.V.S. was supported by the Gates Cambridge Trust. R.P. was funded by the European Research Council (ERC) starting grant ADNABIOARC (263441) and the Irish Research Council Advanced Research Project Grant from January 2014 to December 2016. M.H. was supported by ERC Consolidator Grant 310763 “GeneFlow.” This work was supported by the Research Fund (1.140113.01) of Ulsan National Institute of Science and Technology to J.B. This work was also supported by the Research Fund (14-BR-SS-03) of Civil-Military Technology Cooperation Program to J.B. and Y.S.C. M.G.-L. was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnerships studentship. A.M. and A.E. were supported by the ERC Consolidator Grant 647787 “LocalAdaptation.” D.G.B. was funded by ERC Investigator grant 295729-CodeX

Human population history and its interplay with natural selection

The complex demographic changes that underlie the expansion of anatomically modern humans out of Africa have important consequences on the dynamics of natural selection and our ability to detect it. In this thesis, I aimed to refine our knowledge on human population history using ancient genomes, and then used a climate-informed, spatially explicit framework to explore the interplay between complex demographies and selection. I first analysed a high-coverage genome from Upper Palaeolithic Romania from ~37.8 kya, and demonstrated an early diversification of multiple lineages shortly after the out-of-Africa expansion (Chapter 2). I then investigated Late Upper Palaeolithic (~13.3ky old) and Mesolithic (~9.7 ky old) samples from the Caucasus and a Late Upper Palaeolithic (~13.7ky old) sample from Western Europe, and found that these two groups belong to distinct lineages that also diverged shortly after the out of Africa, ~45-60 ky ago (Chapter 3). Finally, I used East Asian samples from ~7.7ky ago to show that there has been a greater degree of genetic continuity in this region compared to Europe (Chapter 4). In the second part of my thesis, I used a climate-informed, spatially explicit demographic model that captures the out-of-Africa expansion to explore natural selection. I first investigated whether the model can represent the confounding effect of demography on selection statistics, when applied to neutral part of the genome (Chapter 5). Whilst the overlap between different selection statistics was somewhat underestimated by the model, the relationship between signals from different populations is generally well-captured. I then modelled natural selection in the same framework and investigated the spatial distribution of two genetic variants associated with a protective effect against malaria, sickle-cell anaemia and $\beta^0$ thalassemia (Chapter 6). I found that although this model can reproduce the disjoint ranges of different variants typical of the former, it is incompatible with overlapping distributions characteristic of the latter. Furthermore, our model is compatible with the inferred single origin of sickle-cell disease in most regions, but it can not reproduce the presence of this disorder in India without long-distance migrations.The Gates Cambridge Trust provided the full funding for my PhD, including funding to attend conferences and workshop, and fourth-year funding. Trinity College helped financially through the External Honorary Research scholarship and travel funding. The Cambridge Philosophical Society contributed to funding in the fourth year of my PhD

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