Solving patients with rare diseases through programmatic reanalysis of genome-phenome data
Leslie Matalonga, Carles Hernandéz-Ferrer, Davide Piscia, Solve-RD SNV-indel working group, Enzo Cohen, Isabel Cuesta, Daniel Danis, Anne‐Sophie Denommé‐Pichon, Yannis Duffourd, Christian Gilissen, Mridul Johari, Steven Laurie, Shuang Li, Leslie Matalonga, Isabelle Nelson, Sophia Peters, Ida Paramonov, Prasanth Sivakumar, Peter N. Robinson, Karolis Sablauskas, Marco Savarese, Wouter Steyaert, Joeri K. van der Velde, Antonio Vitobello, Rebecca Schüle, Matthis Synofzik, Ana Töpf, Lisenka E.L.M. Vissers, Richarda de Voer, Solve-RD DITF-GENTURIS, Stefan Aretz, Gabriel Capellá, Richarda M. de Voer, D. Gareth Evans, Jose Garcia Pelaez, Elke Holinski‐Feder, Nicoline Hoogerbrugge, Andreas Laner, Carla Oliveíra, Andreas Rump, Evelin Schröck, Anna Katharina Sommer, Verena Steinke‐Lange, Iris te Paske, Marc Tischkowitz, Laura Valle, Solve-RD DITF-ITHACA, Siddharth Banka, Elisa Benetti, Giorgio Casari, Andrea Ciolfi, Jill Clayton-Smith, Bruno Dallapiccola, Elke de Boer, Anne‐Sophie Denommé‐Pichon, Kornelia Ellwanger, Laurence Faivre, Holm Graessner, Tobias B. Haack, Anna Hammarsjö, Markéta Havlovičová, Alexander Hoischen, Anne Hugon, Adam Jackson, Tjitske Kleefstra, Anna Lindstrand, Estrella López‐Martín, Milan Macek, Manuela Morleo, Vicenzo Nigro, Ann Nordgren, Maria Pettersson, Michele Pinelli, Simone Pizzi, Manuel Posada, Francesca Clementina Radio, Alessandra Renieri, Caroline Rooryck, Lukáš Ryba, Martin Schwarz, Marco Tartaglia, Christel Thauvin, Annalaura Torella, Aurélien Trimouille, Alain Verloès, Lisenka E.L.M. Vissers, Antonio Vitobello, Pavel Votýpka, Klea Vyshka, Birte Zurek, Solve-RD DITF-euroNMD, Jonathan Baets, Danique Beijer, Gisèle Bonne, Enzo Cohen, Judith Cossins, Teresinha Evangelista, Alessandra Ferlini, Peter Hackman, Michael G. Hanna
Abstract
Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics.