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1. mlr3summary: Concise and interpretable summaries for machine learning models

Author

Dandl, Susanne, Becker, Marc, Bischl, Bernd, Casalicchio, Giuseppe, and Bothmann, Ludwig

Subjects
Computer Science - Machine Learning
Abstract

This work introduces a novel R package for concise, informative summaries of machine learning models. We take inspiration from the summary function for (generalized) linear models in R, but extend it in several directions: First, our summary function is model-agnostic and provides a unified summary output also for non-parametric machine learning models; Second, the summary output is more extensive and customizable -- it comprises information on the dataset, model performance, model complexity, model's estimated feature importances, feature effects, and fairness metrics; Third, models are evaluated based on resampling strategies for unbiased estimates of model performances, feature importances, etc. Overall, the clear, structured output should help to enhance and expedite the model selection process, making it a helpful tool for practitioners and researchers alike., Comment: 9 pages

Published
2024

5. Automated Benchmark-Driven Design and Explanation of Hyperparameter Optimizers

Author

Moosbauer, Julia, Binder, Martin, Schneider, Lennart, Pfisterer, Florian, Becker, Marc, Lang, Michel, Kotthoff, Lars, and Bischl, Bernd

Subjects
Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Automated hyperparameter optimization (HPO) has gained great popularity and is an important ingredient of most automated machine learning frameworks. The process of designing HPO algorithms, however, is still an unsystematic and manual process: Limitations of prior work are identified and the improvements proposed are -- even though guided by expert knowledge -- still somewhat arbitrary. This rarely allows for gaining a holistic understanding of which algorithmic components are driving performance, and carries the risk of overlooking good algorithmic design choices. We present a principled approach to automated benchmark-driven algorithm design applied to multifidelity HPO (MF-HPO): First, we formalize a rich space of MF-HPO candidates that includes, but is not limited to common HPO algorithms, and then present a configurable framework covering this space. To find the best candidate automatically and systematically, we follow a programming-by-optimization approach and search over the space of algorithm candidates via Bayesian optimization. We challenge whether the found design choices are necessary or could be replaced by more naive and simpler ones by performing an ablation analysis. We observe that using a relatively simple configuration, in some ways simpler than established methods, performs very well as long as some critical configuration parameters have the right value., Comment: * Equal Contributions

Published
2021

6. mlr3spatiotempcv: Spatiotemporal resampling methods for machine learning in R

Author

Schratz, Patrick, Becker, Marc, Lang, Michel, and Brenning, Alexander

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning, Statistics - Methodology
Abstract

Spatial and spatiotemporal machine-learning models require a suitable framework for their model assessment, model selection, and hyperparameter tuning, in order to avoid error estimation bias and over-fitting. This contribution reviews the state-of-the-art in spatial and spatiotemporal cross-validation, and introduces the {R} package {mlr3spatiotempcv} as an extension package of the machine-learning framework {mlr3}. Currently various {R} packages implementing different spatiotemporal partitioning strategies exist: {blockCV}, {CAST}, {skmeans} and {sperrorest}. The goal of {mlr3spatiotempcv} is to gather the available spatiotemporal resampling methods in {R} and make them available to users through a simple and common interface. This is made possible by integrating the package directly into the {mlr3} machine-learning framework, which already has support for generic non-spatiotemporal resampling methods such as random partitioning. One advantage is the use of a consistent nomenclature in an overarching machine-learning toolkit instead of a varying package-specific syntax, making it easier for users to choose from a variety of spatiotemporal resampling methods. This package avoids giving recommendations which method to use in practice as this decision depends on the predictive task at hand, the autocorrelation within the data, and the spatial structure of the sampling design or geographic objects being studied., Comment: 35 pages, 15 Figures, 1 Table

Published
2021

7. Hyperparameter Optimization: Foundations, Algorithms, Best Practices and Open Challenges

Author

Bischl, Bernd, Binder, Martin, Lang, Michel, Pielok, Tobias, Richter, Jakob, Coors, Stefan, Thomas, Janek, Ullmann, Theresa, Becker, Marc, Boulesteix, Anne-Laure, Deng, Difan, and Lindauer, Marius

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning
Abstract

Most machine learning algorithms are configured by one or several hyperparameters that must be carefully chosen and often considerably impact performance. To avoid a time consuming and unreproducible manual trial-and-error process to find well-performing hyperparameter configurations, various automatic hyperparameter optimization (HPO) methods, e.g., based on resampling error estimation for supervised machine learning, can be employed. After introducing HPO from a general perspective, this paper reviews important HPO methods such as grid or random search, evolutionary algorithms, Bayesian optimization, Hyperband and racing. It gives practical recommendations regarding important choices to be made when conducting HPO, including the HPO algorithms themselves, performance evaluation, how to combine HPO with ML pipelines, runtime improvements, and parallelization. This work is accompanied by an appendix that contains information on specific software packages in R and Python, as well as information and recommended hyperparameter search spaces for specific learning algorithms. We also provide notebooks that demonstrate concepts from this work as supplementary files.

Published
2021

9. A Modular Genetic Approach to Newborn Screening from Spinal Muscular Atrophy to Sickle Cell Disease—Results from Six Years of Genetic Newborn Screening.

Author

Bzdok, Jessica, Czibere, Ludwig, Burggraf, Siegfried, Pauly, Natalie, Maier, Esther M., Röschinger, Wulf, Becker, Marc, and Durner, Jürgen

Subjects
SPINAL muscular atrophy, SEVERE combined immunodeficiency, SICKLE cell anemia, GENETIC testing, NEWBORN screening
Abstract

Background/Objectives: Genetic newborn screening (NBS) has already entered the phase of common practice in many countries. In Germany, spinal muscular atrophy (SMA), severe combined immunodeficiency (SCID) and sickle cell disease (SCD) are currently a mandatory part of NBS. Here, we describe the experience of six years of genetic NBS including the prevalence of those three diseases in Germany. Methods: Samples and nucleic acids were extracted from dried blood spot cards, commonly used for NBS. A qPCR assay was used to detect disease-causing variants for SMA and SCD, and the detection of T-cell receptor excision circles (TRECs) was performed for SCID screening. Results: The results of the NBS of over 1 million newborns for SMA, approximately 770,000 for SCID and over 410,000 for SCD are discussed in detail. In these newborns, we have identified 121 cases of SMA, 15 cases of SCID and syndrome-based immunodeficiencies and 77 cases of SCD or β-thalassemia. Conclusions: The flexibility of multiplex qPCR is assessed as an effective tool for incorporating different molecular genetic markers for screening. The processing of dried blood spot (DBS) filter cards for molecular genetic assays and the assays are described in detail; turn-around times and cost estimations are included to give an insight into the processes and discuss further options for optimization. The identified cases are in the range expected for the total number of screened newborns, but present a more exact view on the actual prevalences for Germany. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Telemedical management of symptomatic Covid-19 outpatients

Author

von Falkenhausen, Aenne S, primary, Geipel, Scott, additional, Gail, Antonia, additional, Scherer, Clemens, additional, Stockhausen, Sven, additional, Sams, Lauren E, additional, Becker, Finn, additional, Doldi, Philipp M, additional, Lemmermöhle, Eric, additional, de Villèle, Paul, additional, Schleef, Michael, additional, Becker, Marc, additional, Lauterbach, Moritz, additional, Massberg, Steffen, additional, Kääb, Stefan, additional, and Sinner, Moritz F, additional

Published
2024
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11. Non-sequential Pipelines and Tuning

Author

Bischl, Bernd, Sonabend, Raphael, Kotthoff, Lars, Lang, Michel, Binder, Martin, Pfisterer, Florian, Becker, Marc, Wright, Marvin N., Bischl, Bernd, Sonabend, Raphael, Kotthoff, Lars, Lang, Michel, Binder, Martin, Pfisterer, Florian, Becker, Marc, and Wright, Marvin N.

Abstract

Real-world applications often require complicated pipeline that do not progress sequentially. For example, many experiments have demonstrated that bagging is a powerful method to improve model performance. Bagging can be thought of as a non-sequential pipeline where a learner is replicated, each separate learner is trained and makes predictions, and their results are combined. This is non-sequential as data is not flowing sequentially through the pipeline but is instead passed to all learners (who may then subsample the data) and then recombined, thus creating a pipeline where operations have multiple inputs and outputs. Pipeline operations also have hyperparameters that can be set and tuned to improve model performance. Moreover the choice of operations to include in a pipeline can also be tuned, known as combined algorithm selection and hyperparameter optimization (CASH). This chapter looks at more advanced uses of mlr3pipelines. This is put into practice by demonstrating how to build a bagging and stacking pipeline from scratch, as well as how to access common pipelines that are readily available in mlr3pipelines. The chapter then looks at tuning pipelines and CASH.

Published
2024

18. Tumorgrafts as In Vivo Surrogates for Women with Ovarian Cancer

Author

Weroha, S John, Becker, Marc A, Enderica-Gonzalez, Sergio, Harrington, Sean C, Oberg, Ann L, Maurer, Matthew J, Perkins, Sarah E, AlHilli, Mariam, Butler, Kristina A, McKinstry, Sarah, Fink, Stephanie, Jenkins, Robert B, Hou, Xiaonan, Kalli, Kimberly R, Goodman, Karin M, Sarkaria, Jann N, Karlan, Beth Y, Kumar, Amanika, Kaufmann, Scott H, Hartmann, Lynn C, and Haluska, Paul

Subjects
Rare Diseases, Ovarian Cancer, Orphan Drug, Cancer, Good Health and Well Being, Adult, Aged, Aged, 80 and over, Animals, Biomarkers, Tumor, Chromosome Aberrations, Cluster Analysis, Comparative Genomic Hybridization, Disease Models, Animal, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Graft Survival, Heterografts, Humans, Mice, Middle Aged, Neoplasm Grading, Neoplasm Metastasis, Neoplasm Staging, Ovarian Neoplasms, Ultrasonography, Xenograft Model Antitumor Assays, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeOvarian cancer has a high recurrence and mortality rate. A barrier to improved outcomes includes a lack of accurate models for preclinical testing of novel therapeutics.Experimental designClinically relevant, patient-derived tumorgraft models were generated from sequential patients and the first 168 engrafted models are described. Fresh ovarian, primary peritoneal, and fallopian tube carcinomas were collected at the time of debulking surgery and injected intraperitoneally into severe combined immunodeficient mice.ResultsTumorgrafts demonstrated a 74% engraftment rate with microscopic fidelity of primary tumor characteristics. Low-passage tumorgrafts also showed comparable genomic aberrations with the corresponding primary tumor and exhibit gene set enrichment of multiple ovarian cancer molecular subtypes, similar to patient tumors. Importantly, each of these tumorgraft models is annotated with clinical data and for those that have been tested, response to platinum chemotherapy correlates with the source patient.ConclusionsPresented herein is the largest known living tumor bank of patient-derived, ovarian tumorgraft models that can be applied to the development of personalized cancer treatment.

Published
2014

19. Quality considerations and major pitfalls for high throughput DNA-based newborn screening for severe combined immunodeficiency and spinal muscular atrophy.

Author

Bzdok, Jessica, Czibere, Ludwig, Burggraf, Siegfried, Landt, Olfert, Maier, Esther M., Röschinger, Wulf, Albert, Michael H., Hegert, Sebastian, Janzen, Nils, Becker, Marc, and Durner, Jürgen

Subjects
SEVERE combined immunodeficiency, SPINAL muscular atrophy, NEWBORN screening, T cell receptors, AUDIOMETRY, SICKLE cell anemia, T cells
Abstract

Background: Many newborn screening programs worldwide have introduced screening for diseases using DNA extracted from dried blood spots (DBS). In Germany, DNA-based assays are currently used to screen for severe combined immunodeficiency (SCID), spinal muscular atrophy (SMA), and sickle cell disease (SCD). Methods: This study analysed the impact of pre-analytic DNA carry-over in sample preparation on the outcome of DNA-based newborn screening for SCID and SMA and compared the efficacy of rapid extraction versus automated protocols. Additionally, the distribution of T cell receptor excision circles (TREC) on DBS cards, commonly used for routine newborn screening, was determined. Results: Contaminations from the punching procedure were detected in the SCID and SMA assays in all experimental setups tested. However, a careful evaluation of a cut-off allowed for a clear separation of true positive polymerase chain reaction (PCR) amplifications. Our rapid in-house extraction protocol produced similar amounts compared to automated commercial systems. Therefore, it can be used for reliable DNA-based screening. Additionally, the amount of extracted DNA significantly differs depending on the location of punching within a DBS. Conclusions: Newborn screening for SMA and SCID can be performed reliably. It is crucial to ensure that affected newborns are not overlooked. Therefore a carefully consideration of potential contaminating factors and the definition of appropriate cut-offs to minimise the risk of false results are of special concern. It is also important to note that the location of punching plays a pivotal role, and therefore an exact quantification of TREC numbers per μl may not be reliable and should therefore be avoided. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Indigenous Movements in Ecuador.

Author

Becker, Marc

Abstract

The article discusses the author's experiences in Ecuador in 1990, where they witnessed Indigenous movements inspired by Marxist theory and José Carlos Mariátegui's ideas. The author's research shifted towards studying Indigenous movements in Ecuador, challenging common narratives and highlighting the intersectionality of race, class, and gender within leftist movements. The author also delves into the history of leftist movements in Latin America, focusing on the role of the CIA and FBI in the region. [Extracted from the article]

Published
2024
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26. Politicized Identities and Social Movements

Author

Becker, Marc

Subjects
Politicized Ethnicity: A Comparative Perspective (Nonfiction work) -- Weber, Anke -- Hiers, Wesley -- Flesken, Anaid -- Book reviews, Earth Politics: Religion, Decolonization, and Bolivia's Indigenous Intellectuals (Nonfiction work) -- Ari, Waskar -- Book reviews, Governing Indigenous Territories: Enacting Sovereignty in the Ecuadorian Amazon (Nonfiction work) -- Erazo, Juliet S. -- Book reviews, Multiple Injustices: Indigenous Women, Law, and Political Struggle in Latin America (Nonfiction work) -- Hernandez Castillo, R. Aida -- Book reviews, Singing for the Dead: The Politics of Indigenous Revival in Mexico (Nonfiction work) -- Faudree, Paja -- Book reviews, Earth Beings: Ecologies of Practice across Andean Worlds (Nonfiction work) -- De la Cadena, Marisol -- Book reviews, We Are the Face of Oaxaca: Testimony and Social Movements (Nonfiction work) -- Stephen, Lynn -- Book reviews, Humanities, Regional focus/area studies
Abstract

This essay reviews the following works: Earth Politics: Religion, Decolonization, and Bolivia's Indigenous Intellectuals. By Waskar Ari. Durham, NC: Duke University Press, 2014. Pp. ix + 262. $25.95 paper. ISBN: [...]

Published
2018
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27. Hyperparameter optimization: Foundations, algorithms, best practices, and open challenges

Author

Bischl, Bernd, Binder, Martin, Lang, Michel, Pielok, Tobias, Richter, Jakob, Coors, Stefan, Thomas, Janek, Ullmann, Theresa, Becker, Marc, Boulesteix, Anne‐Laure, Deng, Difan, Lindauer, Marius, Bischl, Bernd, Binder, Martin, Lang, Michel, Pielok, Tobias, Richter, Jakob, Coors, Stefan, Thomas, Janek, Ullmann, Theresa, Becker, Marc, Boulesteix, Anne‐Laure, Deng, Difan, and Lindauer, Marius

Abstract

Most machine learning algorithms are configured by a set of hyperparameters whose values must be carefully chosen and which often considerably impact performance. To avoid a time-consuming and irreproducible manual process of trial-and-error to find well-performing hyperparameter configurations, various automatic hyperparameter optimization (HPO) methods—for example, based on resampling error estimation for supervised machine learning—can be employed. After introducing HPO from a general perspective, this paper reviews important HPO methods, from simple techniques such as grid or random search to more advanced methods like evolution strategies, Bayesian optimization, Hyperband, and racing. This work gives practical recommendations regarding important choices to be made when conducting HPO, including the HPO algorithms themselves, performance evaluation, how to combine HPO with machine learning pipelines, runtime improvements, and parallelization. This article is categorized under: Algorithmic Development > Statistics Technologies > Machine Learning Technologies > Prediction.

Published
2023

36. Testimonials

Author

Béjar, Alejandro Álvarez, Angotti, Tom, Antunes, Ricardo, Austin, Robert, Babb, Florence E., Barkin, David, Becker, Marc, Beserra, Bernadete, Boito, Armando, Carranza, Julio, Cockcroft, James D., Wise, Raúl Delgado, Alfonso, Haroldo Dilla, Dore, Elizabeth, Dosh, Paul, Dupuy, Alex, Ellner, Steve, Gandásegui, Marco A., Green, James N., Johnson, Dale, Jonas, Susanne, Landau, Saul, Levy, Jim, Segrera, Francisco López, Löwy, Michael, Martins, Mônica Dias, Morton, Adam David, Motta, Sara C., Munck, Ronaldo, Olivera, Mercedes, Oppenheim, Lois Hecht, Oyarzún, Kemy, Pereira, Anthony W., Petras, James, Zedong, Mao, Pino, Julio César, Pozzi, Pablo, Ricupero, Bernardo, Robinson, William I., Rus, Jan, Sader, Emir, Safa, Helen, de Sousa Santos, Boaventura, Spalding, Hobart, Salazar, Luis Suárez, Torres-Rivas, Edelberto, Vanden, Harry, Vilas, Carlos M., Webber, Jeffery R., White, Russell, and Wilson, Tamar Diana

Published
2013

38. The benefits of counting butterflies - recommendations for a successful citizen science project

Author

Kühn, Elisabeth, Becker, Marc, Harpke, Alexander, Kühn, Ingolf, Kuhlicke, Christian, Schmitt, T., Settele, Josef, Musche, Martin, Kühn, Elisabeth, Becker, Marc, Harpke, Alexander, Kühn, Ingolf, Kuhlicke, Christian, Schmitt, T., Settele, Josef, and Musche, Martin

Abstract

Citizen science (CS) projects, being popular across many fields of science, have recently also become a popular tool to collect biodiversity data. Although the benefits of such projects for science and policy making are well understood, relatively little is known about the benefits participants get from these projects as well as their personal backgrounds and motivations. Furthermore, very little is known about their expectations. We here examine these aspects, with the citizen science project “German Butterfly Monitoring” as an example. A questionnaire was sent to all participants of the project and the responses to the questionnaire indicated the following: • Most transect walkers do not have a professional background in this field, though they do have a high educational level, and are close to retirement, with a high number of females; • An important motivation to join the project is to preserve the natural environment and to contribute to scientific knowledge; • Participants benefit by enhancing their knowledge about butterflies and especially their ability to identify different species (taxonomic knowledge); • Participants do not have specific expectations regarding the project beyond proper management and coordination, but have an intrinsic sense of working for a greater good. The willingness to join a project is higher if the project contributes to the solution of a problem discussed in the media (here, insect decline). Based on our findings from the analysis of the questionnaire we can derive a set of recommendations for establishing a successful CS project. These include the importance of good communication, e.g., by explaining what the (scientific) purpose of the project is and what problems are to be solved with the help of the data collected in the project. The motivation to join a CS project is mostly intrinsic and CS is a good tool to engage people during difficult times such as the COVID-19 pandemic, giving participants the feeling of doing something

Published
2022

44. The interplay of viral loads, clinical presentation, and serological responses in SARS-CoV-2 – Results from a prospective cohort of outpatient COVID-19 cases

Author

Puchinger, Kerstin, primary, Castelletti, Noemi, additional, Rubio-Acero, Raquel, additional, Geldmacher, Christof, additional, Eser, Tabea M., additional, Deák, Flora, additional, Paunovic, Ivana, additional, Bakuli, Abhishek, additional, Saathoff, Elmar, additional, von Meyer, Alexander, additional, Markgraf, Alisa, additional, Falk, Philine, additional, Reich, Jakob, additional, Riess, Friedrich, additional, Girl, Philipp, additional, Müller, Katharina, additional, Radon, Katja, additional, Guggenbuehl Noller, Jessica Michelle, additional, Wölfel, Roman, additional, Hoelscher, Michael, additional, Kroidl, Inge, additional, Wieser, Andreas, additional, Olbrich, Laura, additional, Alamoudi, Emad, additional, Anderson, Jared, additional, Baumann, Maximilian, additional, Behlen, Marieke, additional, Beyerl, Jessica, additional, Böhnlein, Rebecca, additional, Brauer, Anna, additional, Britz, Vera, additional, Bruger, Jan, additional, Caroli, Friedrich, additional, Contento, Lorenzo, additional, Diekmannshemke, Jana, additional, Do, Anna, additional, Dobler, Gerhard, additional, Eberle, Ute, additional, Eckstein, Judith, additional, Frese, Jonathan, additional, Forster, Felix, additional, Frahnow, Turid, additional, Fröschl, Günter, additional, Geisenberger, Otto, additional, Gillig, Kristina, additional, Heiber, Arlett, additional, Hinske, Christian, additional, Hoefflin, Janna, additional, Hofberger, Tim, additional, Höfinger, Michael, additional, Hofmann, Larissa, additional, Horn, Sacha, additional, Huber, Kristina, additional, Janke, Christian, additional, Kappl, Ursula, additional, Kiani, Charlotte, additional, Kroidl, Arne, additional, Laxy, Michael, additional, Leidl, Reiner, additional, Lindner, Felix, additional, Mayrhofer, Rebecca, additional, Mekota, Anna-Maria, additional, Müller, Hannah, additional, Metaxa, Dafni, additional, Pattard, Leonie, additional, Pletschette, Michel, additional, Prückner, Stephan, additional, Pusl, Konstantin, additional, Raimúndez, Elba, additional, Rothe, Camila, additional, Schäfer, Nicole, additional, Schandelmaier, Paul, additional, Schneider, Lara, additional, Schultz, Sophie, additional, Schunk, Mirjam, additional, Schwettmann, Lars, additional, Seibold, Heidi, additional, Sothmann, Peter, additional, Stapor, Paul, additional, Theis, Fabian, additional, Thiel, Verena, additional, Thiesbrummel, Sophie, additional, Thur, Niklas, additional, Waibel, Julia, additional, Wallrauch, Claudia, additional, Winter, Simon, additional, Wolff, Julia, additional, Wullinger, Pia, additional, Yaqine, Houda, additional, Zange, Sabine, additional, Zeggini, Eleftheria, additional, Zimmermann, Thomas, additional, Zielke, Anna, additional, Ibraheem, Mohamed, additional, Ahmed, Mohamed, additional, Becker, Marc, additional, Diepers, Paulina, additional, Schälte, Yannik, additional, Garí, Mercè, additional, Pütz, Peter, additional, Pritsch, Michael, additional, Fingerle, Volker, additional, Le Gleut, Ronan, additional, Gilberg, Leonard, additional, Brand, Isabel, additional, Diefenbach, Max, additional, Eser, Tabea, additional, Weinauer, Franz, additional, Martin, Silke, additional, Quenzel, Ernst-Markus, additional, Durner, Jürgen, additional, Fuchs, Christiane, additional, and Hasenauer, Jan, additional

Published
2022
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47. Infants Diagnosed with Spinal Muscular Atrophy and 4 SMN2 Copies through Newborn Screening – Opportunity or Burden?

Author

Müller-Felber, Wolfgang, Vill, Katharina, Schwartz, Oliver, Gläser, Dieter, Nennstiel, Uta, Wirth, Brunhilde, Burggraf, Siegfried, Röschinger, Wulf, Becker, Marc, Durner, Jürgen, Eggermann, Katja, Müller, Christine, Hannibal, Iris, Olgemöller, Bernd, Schara, Ulrike, Blaschek, Astrid, and Kölbel, Heike

Subjects
Male, Research Report, newborn screening, Medizin, Infant, Newborn, Infant, Pilot Projects, Spinal muscular atrophy, Survival of Motor Neuron 1 Protein, Pedigree, nervous system diseases, Muscular Atrophy, Spinal, Survival of Motor Neuron 2 Protein, Neonatal Screening, survival motor neuron gene, Germany, Humans, Female, Erratum, Follow-Up Studies, SMN2
Abstract

Although the value of newborn screening (NBS) for early detection and treatment opportunity in SMA patients is generally accepted, there is still an ongoing discussion about the best strategy in children with 4 and more copies of the SMN2 gene. This gene is known to be the most important but not the only disease modifier. In our SMA-NBS pilot project in Germany comprising 278,970 infants screened between January 2018 and November 2019 were 38 positive cases with a homozygous SMN1 deletion. 40% of them had 4 or more SMN2 copies. The incidence for homozygous SMN1 deletion was 1 : 7350, which is within the known range of SMA incidence in Germany. Of the 15 SMA children with 4 SMN2 copies, one child developed physical signs of SMA by the age of 8 months. Reanalysis of the SMN2 copy number by a different test method revealed 3 copies. Two children had affected siblings with SMA Type III, who were diagnosed only after detection of the index patient in the NBS. One had a positive family history with an affected aunt (onset of disease at the age of 3 years). Three families were lost to medical follow up; two because of socioeconomic reasons and one to avoid the psychological stress associated with the appointments. Decisions on how to handle patients with 4 SMN2 copies are discussed in the light of the experience gathered from our NBS pilot SMA program.

Published
2020

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