Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions
Abstract Background Long-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 addit...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | Genome Medicine |
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| Online Access: | https://doi.org/10.1186/s13073-023-01215-1 |
| _version_ | 1797451888901226496 |
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| author | Nikolai Tschernoster Florian Erger Stefan Kohl Björn Reusch Andrea Wenzel Stephen Walsh Holger Thiele Christian Becker Marek Franitza Malte P. Bartram Martin Kömhoff Lena Schumacher Christian Kukat Tatiana Borodina Claudia Quedenau Peter Nürnberg Markus M Rinschen Jan H. Driller Bjørn P. Pedersen Karl P. Schlingmann Bruno Hüttel Detlef Bockenhauer Bodo Beck Janine Altmüller |
| author_facet | Nikolai Tschernoster Florian Erger Stefan Kohl Björn Reusch Andrea Wenzel Stephen Walsh Holger Thiele Christian Becker Marek Franitza Malte P. Bartram Martin Kömhoff Lena Schumacher Christian Kukat Tatiana Borodina Claudia Quedenau Peter Nürnberg Markus M Rinschen Jan H. Driller Bjørn P. Pedersen Karl P. Schlingmann Bruno Hüttel Detlef Bockenhauer Bodo Beck Janine Altmüller |
| author_sort | Nikolai Tschernoster |
| collection | DOAJ |
| description | Abstract Background Long-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. Methods Structural 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. Results We 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. Conclusions The 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. |
| first_indexed | 2024-03-09T15:00:56Z |
| format | Article |
| id | doaj.art-562f2d8f33f64894b552c46d64c66672 |
| institution | Directory Open Access Journal |
| issn | 1756-994X |
| language | English |
| last_indexed | 2024-03-09T15:00:56Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj.art-562f2d8f33f64894b552c46d64c666722023-11-26T13:54:20ZengBMCGenome Medicine1756-994X2023-08-0115111710.1186/s13073-023-01215-1Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletionsNikolai Tschernoster0Florian Erger1Stefan Kohl2Björn Reusch3Andrea Wenzel4Stephen Walsh5Holger Thiele6Christian Becker7Marek Franitza8Malte P. Bartram9Martin Kömhoff10Lena Schumacher11Christian Kukat12Tatiana Borodina13Claudia Quedenau14Peter Nürnberg15Markus M Rinschen16Jan H. Driller17Bjørn P. Pedersen18Karl P. Schlingmann19Bruno Hüttel20Detlef Bockenhauer21Bodo Beck22Janine Altmüller23Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital CologneInstitute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of CologneDepartment of Pediatrics, Cologne Children’s HospitalInstitute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of CologneInstitute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of CologneDepartment of Renal Medicine, UCL, University College LondonCologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital CologneCologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital CologneCologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital CologneCenter for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital CologneDepartment of Pediatrics, University MarburgFACS & Imaging Core Facility, Max Planck Institute for Biology of AgeingFACS & Imaging Core Facility, Max Planck Institute for Biology of AgeingMax Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital CologneDepartment of Biomedicine, Aarhus UniversityDepartment of Molecular Biology and Genetics, Aarhus UniversityDepartment of Molecular Biology and Genetics, Aarhus UniversityDepartment of General Pediatrics, University Children’s HospitalMax Planck Genome-Centre Cologne, Max Planck Institute for Plant Breeding ResearchDepartment of Renal Medicine, UCL, University College LondonInstitute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of CologneCenter for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital CologneAbstract Background Long-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. Methods Structural 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. Results We 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. Conclusions The 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.https://doi.org/10.1186/s13073-023-01215-1Bartter syndrome type 3Salt-wasting tubulopathyLong-read sequencingTarget enrichmentCLCNKACLCNKB |
| spellingShingle | Nikolai Tschernoster Florian Erger Stefan Kohl Björn Reusch Andrea Wenzel Stephen Walsh Holger Thiele Christian Becker Marek Franitza Malte P. Bartram Martin Kömhoff Lena Schumacher Christian Kukat Tatiana Borodina Claudia Quedenau Peter Nürnberg Markus M Rinschen Jan H. Driller Bjørn P. Pedersen Karl P. Schlingmann Bruno Hüttel Detlef Bockenhauer Bodo Beck Janine Altmüller Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions Genome Medicine Bartter syndrome type 3 Salt-wasting tubulopathy Long-read sequencing Target enrichment CLCNKA CLCNKB |
| title | Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions |
| title_full | Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions |
| title_fullStr | Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions |
| title_full_unstemmed | Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions |
| title_short | Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions |
| title_sort | long read sequencing identifies a common transposition haplotype predisposing for clcnkb deletions |
| topic | Bartter syndrome type 3 Salt-wasting tubulopathy Long-read sequencing Target enrichment CLCNKA CLCNKB |
| url | https://doi.org/10.1186/s13073-023-01215-1 |
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