Solving the unsolved Rare Diseases

Deliverables

Documents, reports (9)

First training for ePAGs delivered

Training ERN patient representatives in scientific innovation and genome diagnostics.

Guidelines for exome/genome re-analysis

Guidelines for exome/genome re-analysis provided by the Data Analyses Task Force.

All foundational standards selected and implemented across the project

Provide all foundational standards selected and implemented across the project.

Deployment of PhenoTips custom forms according to the ERNs specifications

In this task we will make the necessary adaptations to PhenoTips allowing for the collection of phenotype data from unsolved cases coming from ERNs. The requirements for the templates will be prepared by the ERNs.

Central RD-Connect database serving Solve-RD, including user authentication and authorization

Database and data sharing aspects of the project.

Metadata catalog operational, with initial content

Metadata aspects of the project.

Guidelines for collection of experimental data

Good practice guidance will be provided in order to ensure the quality of data.

Solve-RD communication and dissemination tools

Solve-RD communication and dissemination tools like press releases, research briefs, research summary documents, policy brief, newsletter, publication in popular press, peer-reviewed journals, wide-audience journals with a high impact factor, publication of papers, reviews on different topics, organisation of symposia and presentation meetings, outreach to patient community and health care provider (networking).

Training modules, guidance document and online help module for collection of phenotypes

Training and good practice guidance will be provided in order to ensure the quality of data at the source, based on users’ guides already in place around HPO and PhenoTips

Publications

Peer reviewed articles (24)

Improved ontology-based similarity calculations using a study-wise annotation model

Author(s): Sebastian Köhler
Published in: Database, Issue 2018/1, 2018, ISSN 1758-0463
DOI: 10.1093/database/bay026

Intra-familial phenotypic heterogeneity in a Sudanese family with DARS2-related leukoencephalopathy, brainstem and spinal cord involvement and lactate elevation: a case report

Author(s): Ashraf Yahia, Liena Elsayed, Arwa Babai, Mustafa A. Salih, Sarah Misbah El-Sadig, Mutaz Amin, Mahmoud Koko, Rayan Abubakr, Razaz Idris, Shaimaa Omer M.A. Taha, Salah A. Elmalik, Alexis Brice, Ammar Eltahir Ahmed, Giovanni Stevanin
Published in: BMC Neurology, Issue 18/1, 2018, ISSN 1471-2377
DOI: 10.1186/s12883-018-1180-7

Sensory neuropathy-causing mutations in ATL3 affect ER–mitochondria contact sites and impair axonal mitochondrial distribution

Author(s): Michiel Krols, Bob Asselbergh, Riet De Rycke, Vicky De Winter, Alexandre Seyer, Franz-Josef Müller, Ingo Kurth, Geert Bultynck, Vincent Timmerman, Sophie Janssens
Published in: Human Molecular Genetics, Issue 28/4, 2018, Page(s) 615-627, ISSN 0964-6906
DOI: 10.1093/hmg/ddy352

Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish

Author(s): Aleksandra Siekierska, Hannah Stamberger, Tine Deconinck, Stephanie N. Oprescu, Michèle Partoens, Yifan Zhang, Jo Sourbron, Elias Adriaenssens, Patrick Mullen, Patrick Wiencek, Katia Hardies, Jeong-Soo Lee, Hoi-Khoanh Giong, Felix Distelmaier, Orly Elpeleg, Katherine L. Helbig, Joseph Hersh, Sedat Isikay, Elizabeth Jordan, Ender Karaca, Angela Kecskes, James R. Lupski, Reka Kovacs-Nagy, Patrick M
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-018-07953-w

Challenges in modelling the Charcot-Marie-Tooth neuropathies for therapy development

Author(s): Manisha Juneja, Joshua Burns, Mario A Saporta, Vincent Timmerman
Published in: Journal of Neurology, Neurosurgery & Psychiatry, Issue 90/1, 2018, Page(s) 58-67, ISSN 0022-3050
DOI: 10.1136/jnnp-2018-318834

Loss of Neurological Disease HSAN-I-Associated Gene SPTLC2 Impairs CD8+ T Cell Responses to Infection by Inhibiting T Cell Metabolic Fitness

Author(s): Jingxia Wu, Sicong Ma, Roger Sandhoff, Yanan Ming, Agnes Hotz-Wagenblatt, Vincent Timmerman, Nathalie Bonello-Palot, Beate Schlotter-Weigel, Michaela Auer-Grumbach, Pavel Seeman, Wolfgang N. Löscher, Markus Reindl, Florian Weiss, Eric Mah, Nina Weisshaar, Alaa Madi, Kerstin Mohr, Tilo Schlimbach, Rubí M.-H. Velasco Cárdenas, Jonas Koeppel, Florian Grünschläger, Lisann Müller, Maren Baumeiste
Published in: Immunity, Issue 50/5, 2019, Page(s) 1218-1231.e5, ISSN 1074-7613
DOI: 10.1016/j.immuni.2019.03.005

De novo ITPR1 variants are a recurrent cause of early-onset ataxia, acting via loss of channel function

Author(s): Matthis Synofzik, Katherine L. Helbig, Florian Harmuth, Tine Deconinck, Pranoot Tanpaiboon, Bo Sun, Wenting Guo, Ruiwu Wang, Erika Palmaer, Sha Tang, G. Bradley Schaefer, Janina Gburek-Augustat, Stephan Züchner, Ingeborg Krägeloh-Mann, Jonathan Baets, Peter de Jonghe, Peter Bauer, S. R. Wayne Chen, Ludger Schöls, Rebecca Schüle
Published in: European Journal of Human Genetics, Issue 26/11, 2018, Page(s) 1623-1634, ISSN 1018-4813
DOI: 10.1038/s41431-018-0206-3

Neuropathy-causing mutations in HSPB1 impair autophagy by disturbing the formation of SQSTM1/p62 bodies

Author(s): Mansour Haidar, Bob Asselbergh, Elias Adriaenssens, Vicky De Winter, Jean-Pierre Timmermans, Michaela Auer-Grumbach, Manisha Juneja, Vincent Timmerman
Published in: Autophagy, Issue 15/6, 2019, Page(s) 1051-1068, ISSN 1554-8627
DOI: 10.1080/15548627.2019.1569930

Targeted therapies for congenital myasthenic syndromes: systematic review and steps towards a treatabolome

Author(s): Rachel Thompson, Gisèle Bonne, Paolo Missier, Hanns Lochmüller
Published in: Emerging Topics in Life Sciences, Issue 3/1, 2019, Page(s) 19-37, ISSN 2397-8554
DOI: 10.1042/etls20180100

A nomenclature and classification for the congenital myasthenic syndromes: preparing for FAIR data in the genomic era

Author(s): Rachel Thompson, Angela Abicht, David Beeson, Andrew G. Engel, Bruno Eymard, Emmanuel Maxime, Hanns Lochmüller
Published in: Orphanet Journal of Rare Diseases, Issue 13/1, 2018, ISSN 1750-1172
DOI: 10.1186/s13023-018-0955-7

Congenital myopathy with hanging big toe due to homozygous myopalladin (MYPN) mutation

Author(s): Luciano Merlini, Patrizia Sabatelli, Manuela Antoniel, Valeria Carinci, Fabio Niro, Giuseppe Monetti, Annalaura Torella, Teresa Giugliano, Cesare Faldini, Vincenzo Nigro
Published in: Skeletal Muscle, Issue 9/1, 2019, ISSN 2044-5040
DOI: 10.1186/s13395-019-0199-9

Hereditary spastic paraplegias: time for an objective case definition and a new nosology for neurogenetic disorders to facilitate biomarker/therapeutic studies

Author(s): Liena E. O. Elsayed, Isra Z. M. Eltazi, Ammar E. M. Ahmed, Giovanni Stevanin
Published in: Expert Review of Neurotherapeutics, Issue 19/5, 2019, Page(s) 409-415, ISSN 1473-7175
DOI: 10.1080/14737175.2019.1608824

Loss of paraplegin drives spasticity rather than ataxia in a cohort of 241 patients with SPG7

Author(s): Giulia Coarelli, Rebecca Schule, Bart P.C. van de Warrenburg, Peter De Jonghe, Claire Ewenczyk, Andrea Martinuzzi, Matthis Synofzik, Elisa G. Hamer, Jonathan Baets, Mathieu Anheim, Ludger Schöls, Tine Deconinck, Pegah Masrori, Bertrand Fontaine, Thomas Klockgether, Maria Grazia D'Angelo, Marie-Lorraine Monin, Jan De Bleecker, Isabelle Migeotte, Perrine Charles, Maria Teresa Bassi, Thomas Klopstoc
Published in: Neurology, Issue 92/23, 2019, Page(s) e2679-e2690, ISSN 0028-3878
DOI: 10.1212/wnl.0000000000007606

Update on the Genetics of Spastic Paraplegias

Author(s): Maxime Boutry, Sara Morais, Giovanni Stevanin
Published in: Current Neurology and Neuroscience Reports, Issue 19/4, 2019, ISSN 1528-4042
DOI: 10.1007/s11910-019-0930-2

Truncating Mutations in UBAP1 Cause Hereditary Spastic Paraplegia

Author(s): Mohammad Ali Farazi Fard, Adriana P. Rebelo, Elena Buglo, Hamid Nemati, Hassan Dastsooz, Ina Gehweiler, Selina Reich, Jennifer Reichbauer, Beatriz Quintáns, Andrés Ordóñez-Ugalde, Andrea Cortese, Steve Courel, Lisa Abreu, Eric Powell, Matt C. Danzi, Nicole B. Martuscelli, Dana M. Bis-Brewer, Feifei Tao, Fariba Zarei, Parham Habibzadeh, Majid Yavarian, Farzaneh Modarresi, Mohammad Silawi, Zahra
Published in: The American Journal of Human Genetics, Issue 104/4, 2019, Page(s) 767-773, ISSN 0002-9297
DOI: 10.1016/j.ajhg.2019.03.001

Recommendations for patient screening in ultra-rare inherited metabolic diseases: what have we learned from Niemann-Pick disease type C?

Author(s): María-Jesús Sobrido, Peter Bauer, Tom de Koning, Thomas Klopstock, Yann Nadjar, Marc C Patterson, Matthis Synofzik, Chris J Hendriksz
Published in: Orphanet Journal of Rare Diseases, Issue 14/1, 2019, ISSN 1750-1172
DOI: 10.1186/s13023-018-0985-1

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Author(s): Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A McMurry, David Osumi-Sutherland, Valentina Cipriani, James P Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh Dawkins, Michael Segal, Anna C Jansen, Ahmed Muaz, Willie H Chang, Jenna Bergers
Published in: Nucleic Acids Research, Issue 47/D1, 2018, Page(s) D1018-D1027, ISSN 0305-1048
DOI: 10.1093/nar/gky1105

Increasing phenotypic annotation improves the diagnostic rate of exome sequencing in a rare neuromuscular disorder

Author(s): Rachel Thompson, Anastasios Papakonstantinou Ntalis, Sergi Beltran, Ana Töpf, Eduardo de Paula Estephan, Kiran Polavarapu, Peter A. C. ’t Hoen, Paolo Missier, Hanns Lochmüller
Published in: Human Mutation, 2019, ISSN 1059-7794
DOI: 10.1002/humu.23792

226th ENMC International Workshop:

Author(s): Annemieke Aartsma-Rus, Alessandra Ferlini, Elizabeth M. McNally, Pietro Spitali, H. Lee Sweeney, Annemieke M. Aartsma-Rus, Christina Al-Khalili Szigyarto, Luca Bello, Abby Bronson, Kristy Brown, Filippo Buccella, Jessica Chadwick, Alessandra Ferlini, Diane Frank, Eric Hoffman, Jane Larkindale, G. McClorey, Elizabeth McNally, Rick Munschauer, Francesco Muntoni, Jane Owens, Ulrike Schara, Pietro Spi
Published in: Neuromuscular Disorders, Issue 28/1, 2018, Page(s) 77-86, ISSN 0960-8966
DOI: 10.1016/j.nmd.2017.10.002

Phenotero: Annotate as you write

Author(s): Daniela Hombach, Jana M. Schwarz, Ellen Knierim, Markus Schuelke, Dominik Seelow, Sebastian Köhler
Published in: Clinical Genetics, Issue 95/2, 2019, Page(s) 287-292, ISSN 0009-9163
DOI: 10.1111/cge.13471

RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants

Author(s): Jana Marie Schwarz, Daniela Hombach, Sebastian Köhler, David N Cooper, Markus Schuelke, Dominik Seelow
Published in: Nucleic Acids Research, Issue 47/W1, 2019, Page(s) W106-W113, ISSN 0305-1048
DOI: 10.1093/nar/gkz327

Long-Read Sequencing Emerging in Medical Genetics

Author(s): Tuomo Mantere, Simone Kersten, Alexander Hoischen
Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021
DOI: 10.3389/fgene.2019.00426

Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

Author(s): Peer Arts, Annet Simons, Mofareh S. AlZahrani, Elanur Yilmaz, Eman AlIdrissi, Koen J. van Aerde, Njood Alenezi, Hamza A. AlGhamdi, Hadeel A. AlJubab, Abdulrahman A. Al-Hussaini, Fahad AlManjomi, Alaa B. Alsaad, Badr Alsaleem, Abdulrahman A. Andijani, Ali Asery, Walid Ballourah, Chantal P. Bleeker-Rovers, Marcel van Deuren, Michiel van der Flier, Erica H. Gerkes, Christian Gilissen, Murad K. Habazi
Published in: Genome Medicine, Issue 11/1, 2019, ISSN 1756-994X
DOI: 10.1186/s13073-019-0649-3

Somatic mutational signatures in polyposis and colorectal cancer

Author(s): Judith E. Grolleman, Marcos Díaz-Gay, Sebastià Franch-Expósito, Sergi Castellví-Bel, Richarda M. de Voer
Published in: Molecular Aspects of Medicine, 2019, ISSN 0098-2997
DOI: 10.1016/j.mam.2019.05.002