Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions

Genome Medicine

Research

Malte P. Bartram¹  Janine Altmüller²  Holger Thiele³  Marek Franitza³  Christian Becker³  Peter Nürnberg⁴  Nikolai Tschernoster⁵  Markus M Rinschen⁶  Karl P. Schlingmann⁷  Jan H. Driller⁸  Bjørn P. Pedersen⁸  Stefan Kohl⁹  Martin Kömhoff^1,10  Stephen Walsh^1,11  Detlef Bockenhauer^1,12  Christian Kukat^1,13  Lena Schumacher^1,13  Andrea Wenzel^1,14  Florian Erger^1,14  Björn Reusch^1,14  Bodo Beck^1,14  Tatiana Borodina^1,15  Claudia Quedenau^1,15  Bruno Hüttel^1,16 

[1] Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Department II of Internal Medicine, University of Cologne, Cologne, Germany;Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Straße 28, 10115, Berlin, Germany;Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany;Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany;Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Department of Biomedicine, Aarhus University, Aarhus, Denmark;Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark;Department III of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;Department of General Pediatrics, University Children’s Hospital, Münster, Germany;Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark;Department of Pediatrics, Cologne Children’s Hospital, Cologne, Germany;Department of Pediatrics, University Marburg, Marburg, Germany;Department of Renal Medicine, UCL, University College London, London, UK;Department of Renal Medicine, UCL, University College London, London, UK;Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK;FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany;Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany;Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Straße 28, 10115, Berlin, Germany;Max Planck Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany;

关键词: Bartter syndrome type 3;    Salt-wasting tubulopathy;    Long-read sequencing;    Target enrichment;    CLCNKA;    CLCNKB;    Structural variant;    Risk haplotype;    Next-generation sequencing;    HiFi-sequencing;   

DOI  :  10.1186/s13073-023-01215-1

 received in 2023-03-15, accepted in 2023-07-27,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundLong-read sequencing is increasingly used to uncover structural variants in the human genome, both functionally neutral and deleterious. Structural variants occur more frequently in regions with a high homology or repetitive segments, and one rearrangement may predispose to additional events. Bartter syndrome type 3 (BS 3) is a monogenic tubulopathy caused by deleterious variants in the chloride channel gene CLCNKB, a high proportion of these being large gene deletions. Multiplex ligation-dependent probe amplification, the current diagnostic gold standard for this type of mutation, will indicate a simple homozygous gene deletion in biallelic deletion carriers. However, since the phenotypic spectrum of BS 3 is broad even among biallelic deletion carriers, we undertook a more detailed analysis of precise breakpoint regions and genomic structure.MethodsStructural variants in 32 BS 3 patients from 29 families and one BS4b patient with CLCNKB deletions were investigated using long-read and synthetic long-read sequencing, as well as targeted long-read sequencing approaches.ResultsWe report a ~3 kb duplication of 3′-UTR CLCNKB material transposed to the corresponding locus of the neighbouring CLCNKA gene, also found on ~50 % of alleles in healthy control individuals. This previously unknown common haplotype is significantly enriched in our cohort of patients with CLCNKB deletions (45 of 51 alleles with haplotype information, 2.2 kb and 3.0 kb transposition taken together, p=9.16×10−9). Breakpoint coordinates for the CLCNKB deletion were identifiable in 28 patients, with three being compound heterozygous. In total, eight different alleles were found, one of them a complex rearrangement with three breakpoint regions. Two patients had different CLCNKA/CLCNKB hybrid genes encoding a predicted CLCNKA/CLCNKB hybrid protein with likely residual function.ConclusionsThe presence of multiple different deletion alleles in our cohort suggests that large CLCNKB gene deletions originated from many independently recurring genomic events clustered in a few hot spots. The uncovered associated sequence transposition haplotype apparently predisposes to these additional events.The spectrum of CLCNKB deletion alleles is broader than expected and likely still incomplete, but represents an obvious candidate for future genotype/phenotype association studies.We suggest a sensitive and cost-efficient approach, consisting of indirect sequence capture and long-read sequencing, to analyse disease-relevant structural variant hotspots in general.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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