Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples

The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples

Small RNA NGS revealed the presence of cherry virus A and little cherry virus 1 on apricots in Hungary

Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation. © 2018 by the authors. Licensee MDPI, Basel, Switzerland

The Development of eServices in an Enlarged EU: A Synthesis Report on eLearning

In 2005, IPTS launched a project which aimed to assess the developments in eGoverment, eHealth and eLearning in the 10 New Member States at national, and at cross-country level. At that time, the 10 New Member States were Cyprus, the Czech Republic, Estonia, Hungary, Latvia, Lithuania, Malta, Poland, Slovenia and Slovakia. A report for each country was produced, describing its educational system and the role played by eLearning within both the formal education system and other aspects of lifelong learning. Each report then analyzed, on the basis of desk research and expert interviews, the major achievements, shortcomings, drivers and barriers in the development of eLearning in one of the countries in question. This synthesis report developed in the final phases of the project offers an integrated view of the developments of eLearning in the New Member States. Furthermore, the project has prepared a prospective report looking across and beyond the development of the eGoverment, eHealth and eLearning areas to summarize policy challenges and options for the development of eServices and the Information Society towards the goals of Lisbon and i2010.JRC.J.4-Information Societ

Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples.

The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples

BC-Monitor: Towards a Routinely Accessible Circulating Tumor DNA-Based Tool for Real-Time Monitoring Breast Cancer Progression and Treatment Effectiveness

, László Tordai 4 , Rozália Tóth 4 , Zsuzsanna Kahán 4 and Lajos Haracska 5,

Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy

DNA transposon-based gene delivery vectors represent a promising new branch of randomly integrating vector development for gene therapy. For the side-by-side evaluation of the piggyBac and Sleeping Beauty systems—the only DNA transposons currently employed in clinical trials—during therapeutic intervention, we treated the mouse model of tyrosinemia type I with liver-targeted gene delivery using both transposon vectors. For genome-wide mapping of transposon insertion sites we developed a new next-generation sequencing procedure called streptavidin-based enrichment sequencing, which allowed us to identify approximately one million integration sites for both systems. We revealed that a high proportion of piggyBac integrations are clustered in hot regions and found that they are frequently recurring at the same genomic positions among treated animals, indicating that the genome-wide distribution of Sleeping Beauty-generated integrations is closer to random. We also revealed that the piggyBac transposase protein exhibits prolonged activity, which predicts the risk of oncogenesis by generating chromosomal double-strand breaks. Safety concerns associated with prolonged transpositional activity draw attention to the importance of squeezing the active state of the transposase enzymes into a narrower time window

A Klimo - könyvtár a tudományos kutatások szolgálatában : A 2001. szeptember 28-án megrendezett konferencia előadásai

Szerkesztő: Csóka-Jaksa Helga | További szerzők: Fischerné Dárdai Ágnes ; Somos Róbert ; Kajtár István ; Béli Gábor; Móró Mária Anna; Priszter Szaniszló; Szabó László Gy.; Jankovits László | Cím: A Klimo - könyvtár a tudományos kutatások szolgálatában | Alcím: A 2001. szeptember 28-án megrendezett konferencia előadásai | Sorozatcím: A Pécsi Egyetemi Könyvtár kiadványai ; 3. | Megjelenési adatok: Pécsi Tudományegyetem Könyvtára, Pécs, 2001. | ISSN: 1587-5202 | ISBN: 963-641869-1 | Leírás: Kötetünkben a Pécsi Tudományegyetem Könyvtára által, 2001. szeptember 28-án megrendezett konferencia előadásainak írott változatát olvashatják. Konferenciánk apropója a Klimo-könyvtár régen várt szerzői betűrendes katalógusának megjelenése volt, amely nem csak a régi könyves szakma figyelmére tarthat számot, hanem más tudományterületek művelői is bizonyára haszonnal forgatják majd. Konferenciánk is ezt példázta, hiszen olyan előadókat hallgathattunk meg, akiknek szakterülete nagyon eltérő. Volt közöttük botanikus, jogász, történész, irodalomtörténész és természetesen könyvtáros is. A Klimo Könyvtár anyaga nem holt állomány tehát, széles körű tudást gyűjtött össze, amelyben a mai kutató is talál feldolgozásra váró anyagot, ötletet. Reméljük, hogy a katalógus, a konferencia és a most megjelent kötet olyan fiatal kutatokat is a Klimo-könyvtárba vezet, akik diákköri dolgozatukhoz, szakdolgozatukhoz, doktori disszertációjukhoz keresnek témát

Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary

Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation