Every CFTR variant counts - Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry

Simone Ahting; Lutz Nährlich; Inka Held; Constance Henn; Angelika Krill; Kerstin Landwehr; Jochen Meister; Susanne Nährig; Anna Nolde; Katharina Remke; Renate Ruppel; Annette Sauer-Heilborn; Martin Schebek; Gudrun Schopper; Bernhard Schulte-Hubbert; Carsten Schwarz; Christina Smaczny; Sabine Wege; Julia Hentschel; Registry Working Group of the German CF Registry

doi:10.1016/j.jcf.2023.10.009

Every CFTR variant counts - Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry

J Cyst Fibros. 2023 Oct 20:S1569-1993(23)00928-1. doi: 10.1016/j.jcf.2023.10.009. Online ahead of print.

Authors

Simone Ahting¹, Lutz Nährlich², Inka Held³, Constance Henn⁴, Angelika Krill⁵, Kerstin Landwehr⁶, Jochen Meister⁷, Susanne Nährig⁸, Anna Nolde⁹, Katharina Remke¹⁰, Renate Ruppel¹¹, Annette Sauer-Heilborn¹², Martin Schebek¹³, Gudrun Schopper¹⁴, Bernhard Schulte-Hubbert¹⁵, Carsten Schwarz¹⁶, Christina Smaczny¹⁷, Sabine Wege¹⁸, Julia Hentschel¹⁹; Registry Working Group of the German CF Registry

Affiliations

¹ Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany. Electronic address: simone.ahting@medizin.uni-leipzig.de.
² Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany.
³ Pediatric Practice Friesenweg, Cystic Fibrosis Center Altona, Hamburg, Germany.
⁴ Division of pediatric Pulmonology and Allergology, Hospital for children and adolescents, University Medical Center Leipzig, Leipzig, Germany.
⁵ Division of Pneumology, University Medical Center Homburg, Homburg/Saar, Germany.
⁶ Division of Allergology and Pediatric Pneumology, University Children's Hospital Bethel, University Medical Center Ostwestfalen-Lippe, Bielefeld, Germany.
⁷ Division of Pneumology, Allergology and Psychotherapy, Children's Hospital, Helios Hospital Aue, Aue, Germany.
⁸ Cystic Fibrosis Center for Adults, Med. Klinik V, University Hospital LMU, Munich, Germany.
⁹ Division of Pneumology, II. Department of Medicine and University Transplant Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
¹⁰ Department for General Paediatrics, Neonatology and Paediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany.
¹¹ University Children's Hospital, University Medical Center Erlangen, Erlangen, Germany.
¹² Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.
¹³ Division of Pediatric Pneumology, Center for Pediatric and Women's Medicine Kassel, Kassel, Germany.
¹⁴ University Children's Hospital Schwabing, Technical University of Munich, Munich, Germany.
¹⁵ Department of medical clinic I, Medical Center Carl Gustav Carus, Technical University of Dresden, Dresden, Germany.
¹⁶ Department Medicine, HMU-Health and Medical University Potsdam and Director CF Center Westbrandenburg, Division Cystic Fibrosis, Clinic Westbrandenburg, Potsdam, Germany.
¹⁷ Christiane Herzog CF-centre Frankfurt/Main, University Medical Center Frankfurt, Goethe-University Frankfurt, Frankfurt/Main, Germany.
¹⁸ Cystic Fibrosis Center, Thoraxklinik Heidelberg, University Medical Center Heidelberg, Heidelberg, Germany.
¹⁹ Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany.

PMID: 37867076
DOI: 10.1016/j.jcf.2023.10.009

Abstract

Background: In times of genotype guided therapy options, a total of 3.2 % of people with CF (pwCF) in the German CF Registry[1] only have one or no CFTR-variant detected after genetic analysis. Additionally, genetic data in the Registry can be documented as free text and can therefore be prone to error. In order to allow the greatest possible amount of pwCF access to modern therapies, we conducted a re-evaluation of free text entries and established a custom-whole-CFTR-locus NGS-approach for all pwCF who remained without genetic confirmation afterwards.

Methods: To this end, we assembled 731 free text variants of 655 pwCF in the German CF Registry. All variants were evaluated using ClinVar, HGMD and CFTR1/2, corrected in the Registries' database and uploaded to ClinVar. PwCF whose diagnosis remained uncertain as well as additional pwCF or pwCFTR-RD that were assembled through a nationwide call for testing of unclear cases were offered genetic analysis. Samples were analysed using a target-capture based NGS-custom-design-panel covering the entire CFTR-locus.

Results: Evaluation of free text variants led to the discovery of 43 variants not formerly reported in the context of CF. The Registries' dropdown list was extended by 497 variants and over 500 pwCF were provided with their most up-to-date genotype. Samples of 47 pwCF/pwCFTR-RD were sequenced via NGS with an overall success rate of 61.7 %, resulting in implementation of entire CFTR-genotyping into routine diagnostics.

Conclusion: Entire CFTR-genotyping can greatly increase the genetic diagnostic rate of pwCF/pwCFTR-RD and should be considered after inconspicuous CFTR screening panels in CFTR-diagnostics.

Keywords: Cystic fibrosis; Diagnostics; Genetics; Genotyping; Next-generation-sequencing.