Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions.
Bartter syndrome type 3
CLCNKA
CLCNKB
HiFi-sequencing
Long-read sequencing
Next-generation sequencing
Risk haplotype
Salt-wasting tubulopathy
Structural variant
Target enrichment
Journal
Genome medicine
ISSN: 1756-994X
Titre abrégé: Genome Med
Pays: England
ID NLM: 101475844
Informations de publication
Date de publication:
23 08 2023
23 08 2023
Historique:
received:
15
03
2023
accepted:
27
07
2023
medline:
25
8
2023
pubmed:
24
8
2023
entrez:
23
8
2023
Statut:
epublish
Résumé
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. 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. 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 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.
Sections du résumé
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
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.
Identifiants
pubmed: 37612755
doi: 10.1186/s13073-023-01215-1
pii: 10.1186/s13073-023-01215-1
pmc: PMC10464140
doi:
Substances chimiques
CLCNKB protein, human
0
Chloride Channels
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
62Informations de copyright
© 2023. BioMed Central Ltd., part of Springer Nature.
Références
Endocrine. 2020 Apr;68(1):192-202
pubmed: 31834604
Genome Res. 2019 Apr;29(4):635-645
pubmed: 30894395
Oncotarget. 2017 Sep 27;8(60):101614-101622
pubmed: 29254190
Clin J Am Soc Nephrol. 2018 Feb 7;13(2):242-250
pubmed: 29146702
N Engl J Med. 2004 Mar 25;350(13):1314-9
pubmed: 15044642
Nat Genet. 1996 Jun;13(2):183-8
pubmed: 8640224
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Genome Med. 2023 Aug 23;15(1):62
pubmed: 37612755
Nature. 2017 Jan 26;541(7638):500-505
pubmed: 28002411
Biochim Biophys Acta. 2010 Aug;1798(8):1457-64
pubmed: 20188062
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Pediatr Res. 2007 Sep;62(3):364-9
pubmed: 17622951
Trans Assoc Am Physicians. 1966;79:221-35
pubmed: 5929460
Hum Mutat. 2020 Sep;41(9):1671-1679
pubmed: 32516842
Nat Genet. 2008 May;40(5):592-599
pubmed: 18391953
Science. 2022 Apr;376(6588):44-53
pubmed: 35357919
J Am Soc Nephrol. 2021 Mar;32(3):756-765
pubmed: 33542107
Nephrol Dial Transplant. 2009 May;24(5):1455-64
pubmed: 19096086
BMC Bioinformatics. 2020 Dec 28;21(Suppl 21):562
pubmed: 33371881
Genet Med. 2016 Feb;18(2):180-8
pubmed: 25880437
J Pediatr. 2001 Jul;139(1):105-10
pubmed: 11445802
J Med Genet. 2008 Mar;45(3):182-6
pubmed: 18310267
Nat Genet. 1997 Oct;17(2):171-8
pubmed: 9326936
Nature. 1992 Jan 16;355(6357):262-5
pubmed: 1731223
Mol Genet Genomic Med. 2022 Oct;10(10):e2027
pubmed: 35913199
Am J Med. 1962 Dec;33:811-28
pubmed: 13969763
Pediatr Res. 2000 Dec;48(6):754-8
pubmed: 11102542
N Engl J Med. 2016 May 12;374(19):1853-63
pubmed: 27120771
Front Pharmacol. 2020 Mar 17;11:327
pubmed: 32256370
Nat Genet. 1996 Oct;14(2):152-6
pubmed: 8841184
J Am Soc Nephrol. 2017 Aug;28(8):2540-2552
pubmed: 28381550
Horm Res Paediatr. 2020;93(2):137-142
pubmed: 32506065
J Pediatr. 1985 Nov;107(5):694-701
pubmed: 3863906
Sci Rep. 2021 Aug 9;11(1):16099
pubmed: 34373523
Pediatr Nephrol. 1998 May;12(4):315-27
pubmed: 9655365
Nat Genet. 2001 Nov;29(3):310-4
pubmed: 11687798
Orphanet J Rare Dis. 2019 Feb 13;14(1):41
pubmed: 30760291
Nat Genet. 1996 Jan;12(1):24-30
pubmed: 8528245
Elife. 2020 Aug 04;9:
pubmed: 32749217
Science. 2021 Apr 2;372(6537):
pubmed: 33632895
Cell. 2018 Apr 5;173(2):291-304.e6
pubmed: 29625048
Hum Mutat. 2003 Jun;21(6):577-81
pubmed: 12754702
J Am Soc Nephrol. 2018 Mar;29(3):727-739
pubmed: 29237739
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Cell. 2022 May 26;185(11):1986-2005.e26
pubmed: 35525246
J Am Soc Nephrol. 2000 Aug;11(8):1449-1459
pubmed: 10906158
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242