TRANSLATE NAMSE

National action alliance for people with rare diseases

A blue-print for genome diagnostics for patients with rare diseases in Germany (genomDE).

Abstract

Most individuals with rare diseases first contact primary care physicians. Although efficient diagnostic routines exist for a subset of rare diseases, ultra-rare entities often require expert clinical knowledge or comprehensive genetic diagnostics, which poses structural challenges to public healthcare systems. To address these challenges, a novel structured diagnostic concept based on the presence of multidisciplinary expertise at centers for rare diseases (CRDs) that have been established at German university hospitals in recent years, was evaluated in a prospective study (TRANSLATE-NAMSE). Between January 2018 and December 2020, 5652 patients were enrolled in the study and were comprehensively assessed by multidisciplinary teams (MDTs) at ten CRDs. Exome sequencing (ES) was initiated for 268 adult and 1309 pediatric patients and partially complemented by additional molecular tests. Conclusive diagnoses were established in 497 individuals, covering 400 diagnostic-grade genes, suggesting ultra-rare disorders were enriched in this cohort. In addition, we describe 56 novel gene-phenotype associations, mainly in individuals with neurodevelopmental delay. A subcohort of 211 individuals was analyzed with the artificial intelligence–based PEDIA protocol, which integrates next-generation phenotyping on medical imaging and sequencing data. With the entire cohort data, we developed a tool to predict the diagnostic yield from the clinical features of a patient if advanced molecular testing strategies are applied.

Can a genome solve your case?

The diagnostic yield is highly dependent on the disease group and the clinical features and ranged between 0.15 and 0.5. Based on the TRANSLATE NAMSE cohort a tool was developed to predict the diagnostic yield which is based on least absolute shrinkage and selection operator (LASSO). For that purpose the dataset was randomly divided into a training set incorporating 1239 cases (851 unsolved or unclear, 388 solved) and a test set incorporating 326 cases (223 unsolved or unclear, 103 solved). The binary response of a case being solved or not solved was regressed on 49 HPO subcategories using the logit function as a link function and controlling for the age, sex, sequencing laboratory, and the use of the PEDIA workflow. The model was fitted on the training data and the penalty parameter was tuned via ten-fold cross-validation. The resulting model was then applied to the independent test set and validated its predictive performance using the ROC curve. We then refitted the model on the whole cohort of 1565 cases and made the results available in the predictor of diagnostic yield (Pody) web application. Users can specify the age, sex, and assigned HPO terms of their patient while the remaining confounders are estimated as the mean effect of the TRANSLATE NAMSE cohort. The service provides a point estimate of the diagnostic yield as well as a relation to the densities of the diagnostic yields of TRANSLATE NAMSE patients resulting from the model.

Variant analysis

Most exomes were evaluated in VarFish, which is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. VarFish was originally developed in Berlin by CUBI (Core Unit Bioinformatics, BIH) together with the Institute of Medical and Human Genetics, Charite Berlin. Currently, a growing number of genetics institutes and TRANSLATE NAMSE members are is using VarFish and are working on extensions and improvements. You can find out more on the CUBI Website.

Code availability and Software Demos

  • TNAMSE Code Repository
  • PEDIA is provided as a Webservice by GeneTalk. If you are interested in a customized integration of the PEDIA protocol into your diagnostics workflow, please contact info@gene-talk.de.
  • VarFish Demo shows the features of the VarFish software including user-based commenting of variants. This is the “classic” mode where data is uploaded using a back-end API by computational staff.
  • VarFish Kiosk allows users to upload their own cases as VCF files and perform an analysis.

Publications

Hsieh, TC., Bar-Haim, A., Moosa, S. et al., GestaltMatcher facilitates rare disease matching using facial phenotype descriptors. Nat Genet 54, 349–357 (2022). https://doi.org/10.1038/s41588-021-01010-x

Chengyao Peng, Simon Dieck, Alexander Schmid, Ashar Ahmad, Alexej Knaus, Maren Wenzel, Laura Mehnert, Birgit Zirn, Tobias Haack, Stephan Ossowski, Matias Wagner, Theresa Brunet, Nadja Ehmke, Magdalena Danyel, Stanislav Rosnev, Tom Kamphans, Guy Nadav, Nicole Fleischer, Holger Fröhlich, Peter Krawitz, CADA: phenotype-driven gene prioritization based on a case-enriched knowledge graph, NAR Genomics and Bioinformatics, Volume 3, Issue 3, September 2021. https://doi.org/10.1093/nargab/lqab078

Holtgrewe, M.; Stolpe, O.; Nieminen, M.; Mundlos, S.; Knaus, A.; Kornak, U.; Seelow, D.; Segebrecht, L.; Spielmann, M.; Fischer-Zirnsak, B.; Boschann, F.; Scholl, U.; Ehmke, N.; Beule, D. VarFish: Comprehensive DNA Variant Analysis for Diagnostics and Research. Nucleic Acids Research 2020, gkaa241. https://doi.org/10.1093/nar/gkaa241.

Tzung-Chien Hsieh, Martin Atta Mensah et al., PEDIA: Prioritization of Exome Data by Image Analysis, Genetics in Medicine, June 5, 2019. https://doi.org/10.1038/s41436-019-0566-2

Commercial entities interested in software applications and customization of pipelines please contact info@gene-talk.de