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Interdisciplinary Training in High-Throughput Sequencing, Bioinformatics and Model Systems: Moving towards Clinical applications of Genomics

Deliverables

Report on bioinformatis curriculum and training activities

A bioinformatics training curriculum will be set-up for UoM researchers. A report will be generated on the setting up on this curriculum and related training activities

Minutes of Project meeting 3

Minutes of 3rd project meeting

Report attesting that Task 1.6 has been completed

Introduce in the reporting tool on the Participant Portal all relevant publications of the Coordinator during the 3 years preceding the start date of the project

Interim report on monthly online mentoring on HTS analysis pipelines

An interim report will be submitted detailing the online mentoring activities held on HTS analysis pipelines.

A record of the dissemination activities undertaken: 1

A record of the dissemination activities undertaken during the first half of the project will be submitted

Minutes of Project meeting 2

Minutes of the 2nd project meeting

Minutes of Project meeting 1

minutes of the 1st project meeting

A report on planned and completed communication activities

A report will be compiled and submitted detailing the planned and completed communication activities.

A record of the dissemination activities undertaken: 2

A record of the dissemination activities undertaken during the second half of the project will be submitted

Minutes of Project meeting 5

Minutes of the 5th project meeting

A report on dissemination activities undertaken

A report highlighting all the dissemination activities undertaken as part of this project will be compiled and submitted

Reports from all scientists attended courses or conferences through this grant

Every scientist who attends a course or conference through this funding will submit a report. These reports will be compiled into a report for this deliverable.

Minutes of Project meeting 4

Minutes of 4th Project meeting

Final report on training visit by a postdoc or researcher from UoM to a UCAM group

A final report detailing the activities of a training visit by a UoM scientist (graduate student post-doc or researcher) to a UCAM group.

Report on training visit to KULeuven

A report on training visit by a UoM scientist (graduate student, post-doc or researcher) to KULeuven for zebrafish training.

Final report on monthly online mentoring on HTS analysis pipelines

A final report will be submitted detailing the online mentoring activities held on HTS analysis pipelines.

Dissemination of survey results to consortium members

Task 2.1 consists of determining the bioinformatics and statistical needs of scientists and students at UoM. The results of this survey will be distributed to the consortium members

Interim report on training visit by a post-doc or researcher from UoM to a UCAM group

An interim report detailing the activities of a training visit by a UoM scientist (graduate student post-doc or researcher) to a UCAM group.

Report on training visit to UCAM

A report on training visit by a UoM scientist (graduate student, post-doc or researcher) to UCAM for iPSC training.

Minutes of Project meeting 6

Minutes of 6th project meeting

Publication of research and review papers

Scientific publications enabled or facilitated through the training activities of the project

Copies of articles in local magazines and/or newspapers

Copies of all articles published in local magazines or newspapers, as part of the dissemination activities of the project, will be compiled and submitted to the commission.

Attendance at international conferences Year3

A list of the conferences (and courses) attended during months 25 to 36 of the project.

Summer school in HTS bioinformatics core skills

A summer school focusing on core skills in HTS bioinformatics will be organised and delivered during the first 12 months of the project.

Attendance at international conferences Year2

A list of the conferences (and courses) attended during months 13 to 24 of the project.

Attendance at international conferences Year1

A list of the conferences (and courses) attended during the first 12 months of the project.

"""Train the Trainer"" event in Malta"

"A ""Train the Trainer"" event will be held in Malta, targeting UoM scientists interested in becoming training instructors in HTS data analysis and delivering future training courses at UoM."

Summer school in Model Systems

A summer school will be organised and held. The focus will be on imparting the basics in the utilisation of model systems for the elucidation of the function of mutations within candidate genes

Summer school on epigenomic data generation and analysis

A summer school focussing on the generation and analysis of epigenomic data will be organised and delivered by the end of the project

Depositing of training information on webpage: 3

Training information will be deposited on the project webpage. This will occur periodically throughout the final year of the project

Set-up of a project website

The setting-up of a project website where training material can be deposited (as part of WP5 - dissemination activities)

Depositing of training information on webpage: 1

Training information will be deposited on the project webpage. This will occur periodically throughout the first year of the project

Depositing of training information on webpage: 2

Training information will be deposited on the project webpage. This will occur periodically throughout the second year of the project

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Publications

The impact of passive and active smoking on inflammation, lipid profile and the risk of myocardial infarction

Author(s): Ritienne Attard, Philip Dingli, Carine J M Doggen, Karen Cassar, Rosienne Farrugia, Stephanie Bezzina Wettinger
Published in: Open Heart, Issue 4/2, 2017, Page(s) e000620, ISSN 2053-3624
DOI: 10.1136/openhrt-2017-000620

Genetic causes of Parkinson’s disease in the Maltese: a study of selected mutations in LRRK2, MTHFR, QDPR and SPR

Author(s): Charmaine Zahra, Christine Tabone, Graziella Camilleri, Alex E. Felice, Rosienne Farrugia, Stephanie Bezzina Wettinger
Published in: BMC Medical Genetics, Issue 17/1, 2016, ISSN 1471-2350
DOI: 10.1186/s12881-016-0327-x

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Author(s): Romina Petersen, John J. Lambourne, Biola M. Javierre, Luigi Grassi, Roman Kreuzhuber, Dace Ruklisa, Isabel M. Rosa, Ana R. Tomé, Heather Elding, Johanna P. van Geffen, Tao Jiang, Samantha Farrow, Jonathan Cairns, Abeer M. Al-Subaie, Sofie Ashford, Antony Attwood, Joana Batista, Heleen Bouman, Frances Burden, Fizzah A. Choudry, Laura Clarke, Paul Flicek, Stephen F. Garner, Matthias Haimel, Carly
Published in: Nature Communications, Issue 8, 2017, Page(s) 16058, ISSN 2041-1723
DOI: 10.1038/ncomms16058

Individualizing fetal hemoglobin augmenting therapy for β-type hemoglobinopathies patients

Author(s): Aikaterini Gravia, Vasiliki Chondrou, Argyro Sgourou, Ioanna Papantoni, Joseph Borg, Theodora Katsila, Adamantia Papachatzopoulou, George P Patrinos
Published in: Pharmacogenomics, Issue 15/10, 2014, Page(s) 1355-1364, ISSN 1462-2416
DOI: 10.2217/pgs.14.101

Personalized pharmacogenomics profiling using whole-genome sequencing

Author(s): Clint Mizzi, Brock Peters, Christina Mitropoulou, Konstantinos Mitropoulos, Theodora Katsila, Misha R Agarwal, Ron HN van Schaik, Radoje Drmanac, Joseph Borg, George P Patrinos
Published in: Pharmacogenomics, Issue 15/9, 2014, Page(s) 1223-1234, ISSN 1462-2416
DOI: 10.2217/pgs.14.102

Key challenges for next-generation pharmacogenomics: Science & Society series on Science and Drugs

Author(s): K. Kampourakis, E. Vayena, C. Mitropoulou, R. H. van Schaik, D. N. Cooper, J. Borg, G. P. Patrinos
Published in: EMBO reports, Issue 15/5, 2014, Page(s) 472-476, ISSN 1469-221X
DOI: 10.1002/embr.201438641

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

Author(s): Ioannis Karageorgos, Clint Mizzi, Efstathia Giannopoulou, Cristiana Pavlidis, Brock A. Peters, Zoi Zagoriti, Peter D. Stenson, Konstantinos Mitropoulos, Joseph Borg, Haralabos P. Kalofonos, Radoje Drmanac, Andrew Stubbs, Peter van der Spek, David N. Cooper, Theodora Katsila, George P. Patrinos
Published in: Human Genomics, Issue 9/1, 2015, ISSN 1479-7364
DOI: 10.1186/s40246-015-0034-2

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Author(s): Belinda Giardine, Joseph Borg, Emmanouil Viennas, Cristiana Pavlidis, Kamran Moradkhani, Philippe Joly, Marina Bartsakoulia, Cathy Riemer, Webb Miller, Giannis Tzimas, Henri Wajcman, Ross C. Hardison, George P. Patrinos
Published in: Nucleic Acids Research, Issue 42/D1, 2013, Page(s) D1063-D1069, ISSN 0305-1048
DOI: 10.1093/nar/gkt911

Aip regulates cAMP signalling and GH secretion in GH3 cells

Author(s): R. Formosa, A. Xuereb-Anastasi, J. Vassallo
Published in: Endocrine Related Cancer, Issue 20/4, 2013, Page(s) 495-505, ISSN 1351-0088
DOI: 10.1530/ERC-13-0043

Whole‐genome sequencing identifies EN1 as a determinant of bone density and fracture

Author(s): Hou‐Feng Zheng, Vincenzo Forgetta, Yi‐Hsiang Hsu, Karol Estrada, Alberto Rosello‐Diez, Paul J. Leo, Chitra L. Dahia, Kyung Hyun Park‐Min, Jonathan H. Tobias, Charles Kooperberg, Aaron Kleinman, Unnur Styrkarsdottir, Ching‐Ti Liu, Charlotta Uggla, Daniel S. Evans, Carrie M. Nielson, Klaudia Walter, Ulrika Pettersson‐Kymmer, Shane McCarthy, Joel Eriksson, Tony Kwan, Mila Jhamai, Katerina
Published in: Nature, Issue 526/7571, 2015, Page(s) 112-117, ISSN 0028-0836
DOI: 10.1038/nature14878

Genomic variation in the MAP3K5 gene is associated with β-thalassemia disease severity and hydroxyurea treatment efficacy

Author(s): Christina Tafrali, Arsinoi Paizi, Joseph Borg, Milena Radmilovic, Marina Bartsakoulia, Emily Giannopoulou, Olga Giannakopoulou, Maja Stojiljkovic-Petrovic, Branka Zukic, Konstantinos Poulas, Eleana F Stavrou, Polyxeni Lambropoulou, Alexandra Kourakli, Alexander E Felice, Adamantia Papachatzopoulou, Sjaak Philipsen, Sonja Pavlovic, Marianthi Georgitsi, George P Patrinos
Published in: Pharmacogenomics, Issue 14/5, 2013, Page(s) 469-483, ISSN 1462-2416
DOI: 10.2217/pgs.13.31

Genetic associations of Nrf2-encoding NFE2L2 variants with Parkinson’s disease – a multicenter study

Author(s): Malin von Otter, Petra Bergström, Aldo Quattrone, Elvira Valeria De Marco, Grazia Annesi, Peter Söderkvist, Stephanie Bezzina Wettinger, Marek Drozdzik, Monika Bialecka, Hans Nissbrandt, Christine Klein, Michael Nilsson, Ola Hammarsten, Staffan Nilsson, Henrik Zetterberg
Published in: BMC Medical Genetics, Issue 15/1, 2014, ISSN 1471-2350
DOI: 10.1186/s12881-014-0131-4

Transfusion-independent β0-thalassemia after bone marrow transplantation failure: proposed involvement of high parental HbF and an epigenetic mechanism

Author(s): Katia Paciaroni, Guido Lucarelli, Fabrizio Martelli, Anna Rita Migliaccio, Marieke von Lindern, Joseph Borg, Nynke Gillemans, Thamar B van Dijk, Sjaak Philipsen
Published in: Am J Blood Res, Issue 4(1), 2014, Page(s) 27-32, ISSN 2160-1992