Publications and open tools

Using semantic web knowledge graphs to harmonise case-mix and outcome data across STRONG AYA's federated cancer infrastructure.

Hogenboom, J.; Gouthamchand, V.; Cairns, C.; Janssen, S.H.M.; Way, K.; Dekker, A.L.A.J.; Van Der Graaf, W.T.A.; Darlington, A.-S.; Husson, O.; Wee, L.Y.L.; Van Soest, J.; Lobo Gomes, A.

Detecting complete and mosaic aneuploidies in autosomes and sex chromosomes directly from routine exome sequencing coverage data.

Barco-Armengol, N.; Yubero, D.; Xiol, C.; Catasús, N.; Martí-Sánchez, L.; Armstrong, J.; Palau, F.; Fernandez, G.

Cataloguing 1062 disease-causing variants across 20 Israeli ethnic groups to map the genetics of inherited retinal disease.

Shalom, S.; Gradstein, L.; Pras, E.; Valensi, J.; Birk, O.S.; Blumenfeld, A.; Eilat, A.; Macarov, M.; Poleg, T.; Cremers, F.P.M.; Roosing, S.; Panneman, D.M.; Hollander, N.; Goldenberg-Cohen, N.; Yahalom, C.; Banin, E.; Ben-Yosef, T.; Sharon, D.

Showing how ATP hydrolysis gates the COQ8 pocket that chaperones coenzyme Q intermediates and senses the finished product.

Gottinger, A.; Malatesta, M.; Nicoll, C.R.; Ansari, G.; Quinodoz, M.; Kaminska, K.; Tang, R.W.C.; Tan, T.-E.; Fenner, B.J.; Barberán-Martínez, P.; García-García, G.; Millán, J.M.; Pfau, M.; Burbach, N.E.; Cecchini, D.; Rivolta, C.; Mattevi, A.

Identifying biallelic DDX41 variants in eight families as a new cause of early-onset retinal dystrophy involving Müller cells.

Mars, Z.; Zanetti, A.; Kaminska, K.; Miyagawa, T.; Liu, D.; Antonio, A.; Arno, G.; Audo, I.; Ayuso, C.; Muhammad Jafar Hussain, H.; Bao, X.; Barberán-Martínez, P.; Bocquet, B.; Boguszewska-Chachulska, A.; Condroyer, C.; David, P.; Dollfus, H.; Fares-Taie, L.; Fernández-Caballero, L.; García-García, G.; Michel, V.; Guerrera, C.I.; Jung, V.; Kessel, L.; Gioja, L.; Lin, S.; Matczynska, E.; Millán, J.M.; Moye, A.R.; Martín-Gutiérrez, M.P.; Quinodoz, M.; Robert, M.P.; Roger, J.E.; Sousa-Luis, R.; Swafiri, S.T.; Teper, S.; Meunier, I.; Patat, O.; Pennesi, M.E.; Wadt, K.A.W.; Wang, M.; Webster, A.R.; Yang, P.; Yumei, L.; Zeitz, C.; Rieux-Laucat, F.; Giraudier, S.; Chen, R.; Fica, S.M.; Rivolta, C.; Sebert, M.; Rozet, J.-M.; Perrault, I.

Reviewing automated variant interpretation tools and benchmarking their classifications against ClinGen Expert Panel decisions for 256 variants.

Costa, M.; García S., A.; León, A.; Pastor, O.

Presenting I-ETL, a pipeline that normalises heterogeneous hospital data and metadata so federated analyses become possible.

Barret, N.; Bernasconi, A.; Bikbov, B.; Pinoli, P.

Applying bias-mitigation algorithms to build fairer, gender-debiased machine learning classifiers for diagnosing ADHD in children and adolescents.

Neufang, S.; Li, F.; Akhrif, A.; Beyan, O.D.

Establishing biallelic DARS2 variants as a new cause of childhood-onset axonal Charcot–Marie–Tooth disease in five patients.

Estévez-Arias, B.; Sarv, S.; Bonello-Palot, N.; Carrera-García, L.; Ortez, C.; Expósito-Escudero, J.; Yubero, D.; Muchart, J.; Delmont, E.; Õiglane-Shlik, E.; Meren, T.; Puusepp, S.; Murumets, Ü.; Salomons, G.S.; Udd, B.; Väli, L.; Cantarero, L.; Bönnemann, C.G.; Nascimento, A.; Ramón-Maiques, S.; Õunap, K.; Hoenicka, J.; Natera-de Benito, D.; Palau, F.

Presenting RetiGene, an expert-curated atlas bringing together variant, expression and functional data for inherited retinal disease genes.

Quinodoz, M.; Celik, E.; Kamdar, D.; Cancellieri, F.; Kaminska, K.; Ullah, M.; Barberán-Martínez, P.; Bouckaert, M.; Cortón, M.; Delanote, E.; Fernández-Caballero, L.; García García, G.; Holtes, L.K.; Karali, M.; Lopez, I.; Peter, V.G.; Schneider, N.; Vincke, L.; Ayuso, C.; Banfi, S.; Bocquet, B.; Coppieters, F.; Cremers, F.P.M.; Inglehearn, C.F.; Iwata, T.; Kalatzis, V.; Koenekoop, R.K.; Millán, J.M.; Sharon, D.; Toomes, C.; Rivolta, C.

Setting out BETTER's vision for a FAIR data infrastructure and Personal Health Train analytics platform for rare diseases.

Bregonzio, M.; Bernasconi, A.; Pinoli, P.

Proposing a dual-pathway deep learning model that combines noise and context to denoise multiple medical imaging modalities.

Fartiyal, J.; Freire, P.; Whayeb, Y.; Wolffsohn, J.S.; Turitsyn, S.K.; Sokolovski, S.G.

Reporting incidence and distribution of inborn errors of metabolism among 343,507 newborns screened in Lombardy, 2016–2020.

Berardo, C.; Vasco, A.; Mauri, A.; Lucchi, S.; Cappelletti, L.; Saielli, L.; Rizzetto, M.; Biganzoli, D.; Montrasio, C.; Postorivo, D.; Perrone Donnorso, M.; Pratiffi, E.; Meta, A.; Carelli, S.; Amorosi, A.; Paci, S.; Cefalo, G.; Furlan, F.; Menni, F.; Gasperini, S.; Crescitelli, V.; Banderali, G.; Zuccotti, G.; Alberti, L.; Cereda, C.

Introducing VarClaMM, a meta-model that formalises DNA variant classification to expose inconsistencies and support automation.

Costa, M.; García S., A.; León, A.; Bernasconi, A.; Pastor, O.

Reporting two new TBC1D32 variants in a patient with oro-facial-digital syndrome, adding hearing loss to the known phenotype.

García-Bohórquez, B.; Marín-Reina, P.; Aller, E.; Barberán-Martínez, P.; Armengot, M.; Llorens-Salvador, R.; Almor-Palacios, I.C.; Millán, J.M.; García-García, G.

Screening non-coding USH2A variants in Usher syndrome and designing antisense oligonucleotides that successfully redirect splicing in vitro.

García-Bohórquez, B.; Barberán-Martínez, P.; Aller, E.; Jaijo, T.; Mínguez, P.; Rodilla, C.; Fernández-Caballero, L.; Blanco-Kelly, F.; Ayuso, C.; Sanchis-Juan, A.; Broekman, S.; de Vrieze, E.; van Wijk, E.; García-García, G.; Millán, J.M.

Comparing plasma amino acid profiles in 1242 autistic and 488 non-autistic children, revealing distinct neurological and nutritional subgroups.

Ferraro, S.; Saielli, L.; Biganzoli, D.; Tosi, M.; Guidi, L.; Longo, R.; Severino, F.; Carelli, S.; Rossi, M.; Pisciotta, L.; Ricci, E.; Brustia, F.; Verduci, E.; Zuccotti, G.; Mussap, M.; Cereda, C.

Showing that DNA from dried blood spots supports exome sequencing, opening the way to genomic newborn screening.

Mauri, A.; Berardo, C.; Biganzoli, D.; Meta, A.; Benedetti, S.; Rey, F.; Messa, L.; Zuccotti, G.V.; Carelli, S.; Alberti, L.; Cereda, C.

Describing five patients whose heterozygous MAP3K20 variants cause a new syndrome with craniosynostosis, hearing loss and limb anomalies.

Brooks, D.; Burke, E.; Lee, S.; Eble, T.N.; O'Leary, M.; Osei-Owusu, I.; Rehm, H.L.; Dhar, S.U.; Emrick, L.; Bick, D.; Nehrebecky, M.; Macnamara, E.; Casas-Alba, D.; Armstrong, J.; Prat, C.; Martínez-Monseny, A.F.; Palau, F.; Liu, P.; Adams, D.; Undiagnosed Diseases Network; Lalani, S.; Rosenfeld, J.A.; Burrage, L.C.