A Labor- and Cost-effective Non-optical Semiconductor (Ion Torrent) Next-generation Sequencing of the SLC12A3 and CLCNKA/B Genes in Gitelman's Syndrome Patients

Overview

Journal J Hum Genet

Specialty Genetics

Date 2014 May 17

PMID 24830959

Citations 8

Authors

Beatriz Tavira

Juan Gomez

Fernando Santos

Helena Gil

Victoria Alvarez

Eliecer Coto

Affiliations

Soon will be listed here.

Abstract

Gitelman's syndrome (GS) is a rare recessive disorder caused by mutations in the renal salt-handling genes SLC12A3 and CLCNKB. Our aim was to develop a next-generation sequencing (NGS) procedure for these genes based on two-tubes multiplex amplification of DNA pools and semiconductor sequencing with the Ion Torrent Personal Genome Machine (PGM). We created one pool with DNA from 20 GS patients previously Sanger sequenced for the coding exons of SLC12A3. A total of 13 mutations present in 11 of these patients were used as control variants to validate the NGS procedure. The full coding sequence of SLC12A3, CLCNKB and CLCNKA was amplified in only two Ampliseq tubes and processed and sequenced with the PGM. Large SLC12A3 and CLCNKB deletions were ascertained through multiplex ligation-dependent probe amplification in some patients. With the exception of the SLC12A3 exon 9, all the amplicons were successfully read and 12 of the 13 control variants were detected. The analysis of CLCNKB showed four putative mutations in the GS pool that were further assigned to specific patients. Two patients were heterozygous compounds for a single-nucleotide mutation and a large deletion at SLC12A3 or CLCNKB. We reported a NGS procedure that would facilitate the rapid and cost-effective large-scale screening of the three renal salt-handling genes. In addition to characterize the mutational spectrum of GS patients, the described procedure would facilitate the rapid and cost-effective screening of these genes at a population scale.

Citing Articles

Advances in Diagnosis and Treatment of Inherited Kidney Diseases in Children.

Wang G, Liao M, Tan D, Chen X, Chao R, Zhu Y Kidney Dis (Basel). 2024; 10(6):558-572.

PMID: 39664340 PMC: 11631113. DOI: 10.1159/000541564.

Molecular complexity analysis of the diagnosis of Gitelman syndrome in China.

Song W, Hu Y, Zhao L, Zhang J, Zhang Y, Wen J Open Life Sci. 2023; 18(1):20220634.

PMID: 37360783 PMC: 10290276. DOI: 10.1515/biol-2022-0634.

Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing.

Diepenbroek M, Bayer B, Anslinger K Genes (Basel). 2021; 12(9).

PMID: 34573344 PMC: 8466929. DOI: 10.3390/genes12091362.

Allele-specific RT-PCR for the rapid detection of recurrent SLC12A3 mutations for Gitelman syndrome.

Yan M, Yang S, Tseng M, Cheng C, Tsai J, Sung C NPJ Genom Med. 2021; 6(1):68.

PMID: 34389731 PMC: 8363728. DOI: 10.1038/s41525-021-00230-8.

Digenetic inheritance of SLC12A3 and CLCNKB genes in a Chinese girl with Gitelman syndrome.

Kong Y, Xu K, Yuan K, Zhu J, Gu W, Liang L BMC Pediatr. 2019; 19(1):114.

PMID: 30999883 PMC: 6471809. DOI: 10.1186/s12887-019-1498-3.

References

Mastroianni N, Bettinelli A, Bianchetti M, Colussi G, De Fusco M, Sereni F . Novel molecular variants of the Na-Cl cotransporter gene are responsible for Gitelman syndrome. Am J Hum Genet. 1996; 59(5):1019-26. PMC: 1914834. View

Lemmink H, Knoers N, Karolyi L, Van Dijk H, Niaudet P, Antignac C . Novel mutations in the thiazide-sensitive NaCl cotransporter gene in patients with Gitelman syndrome with predominant localization to the C-terminal domain. Kidney Int. 1998; 54(3):720-30. DOI: 10.1046/j.1523-1755.1998.00070.x. View

Missirian V, Comai L, Filkov V . Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments. BMC Bioinformatics. 2011; 12:287. PMC: 3150297. DOI: 10.1186/1471-2105-12-287. View

Zelikovic I, Szargel R, Hawash A, Labay V, Hatib I, Cohen N . A novel mutation in the chloride channel gene, CLCNKB, as a cause of Gitelman and Bartter syndromes. Kidney Int. 2002; 63(1):24-32. DOI: 10.1046/j.1523-1755.2003.00730.x. View

Coto E, Rodriguez J, Jeck N, Alvarez V, Stone R, Loris C . A new mutation (intron 9 +1 G>T) in the SLC12A3 gene is linked to Gitelman syndrome in Gypsies. Kidney Int. 2003; 65(1):25-9. DOI: 10.1111/j.1523-1755.2004.00388.x. View

Simon D, Bia M, Ellison D, Karet F, Molina A, Vaara I . Gitelman's variant of Bartter's syndrome, inherited hypokalaemic alkalosis, is caused by mutations in the thiazide-sensitive Na-Cl cotransporter. Nat Genet. 1996; 12(1):24-30. DOI: 10.1038/ng0196-24. View

Konrad M, Vollmer M, Lemmink H, van den Heuvel L, Jeck N, Vargas-Poussou R . Mutations in the chloride channel gene CLCNKB as a cause of classic Bartter syndrome. J Am Soc Nephrol. 2000; 11(8):1449-1459. DOI: 10.1681/ASN.V1181449. View

Rothberg J, Hinz W, Rearick T, Schultz J, Mileski W, Davey M . An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011; 475(7356):348-52. DOI: 10.1038/nature10242. View

Gomez J, Reguero J, Moris C, Alvarez V, Coto E . Non optical semi-conductor next generation sequencing of the main cardiac QT-interval duration genes in pooled DNA samples. J Cardiovasc Transl Res. 2013; 7(1):133-7. DOI: 10.1007/s12265-013-9516-6. View

10.

Li X, Buckton A, Wilkinson S, John S, Walsh R, Novotny T . Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers. PLoS One. 2013; 8(7):e67744. PMC: 3701544. DOI: 10.1371/journal.pone.0067744. View

11.

Harakalova M, Nijman I, Medic J, Mokry M, Renkens I, Blankensteijn J . Genomic DNA pooling strategy for next-generation sequencing-based rare variant discovery in abdominal aortic aneurysm regions of interest-challenges and limitations. J Cardiovasc Transl Res. 2011; 4(3):271-80. PMC: 3099005. DOI: 10.1007/s12265-011-9263-5. View

12.

Otto E, Ramaswami G, Janssen S, Chaki M, Allen S, Zhou W . Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy. J Med Genet. 2010; 48(2):105-16. PMC: 3913043. DOI: 10.1136/jmg.2010.082552. View

13.

Elliott A, Radecki J, Moghis B, Li X, Kammesheidt A . Rapid detection of the ACMG/ACOG-recommended 23 CFTR disease-causing mutations using ion torrent semiconductor sequencing. J Biomol Tech. 2012; 23(1):24-30. PMC: 3313698. DOI: 10.7171/jbt.12-2301-003. View

14.

Peters M, Jeck N, Reinalter S, Leonhardt A, Tonshoff B, Klaus G G . Clinical presentation of genetically defined patients with hypokalemic salt-losing tubulopathies. Am J Med. 2002; 112(3):183-90. DOI: 10.1016/s0002-9343(01)01086-5. View

15.

Guay-Woodford L . Bartter syndrome: unraveling the pathophysiologic enigma. Am J Med. 1998; 105(2):151-61. DOI: 10.1016/s0002-9343(98)00196-x. View

16.

Tsongalis G, Peterson J, De Abreu F, Tunkey C, Gallagher T, Strausbaugh L . Routine use of the Ion Torrent AmpliSeq™ Cancer Hotspot Panel for identification of clinically actionable somatic mutations. Clin Chem Lab Med. 2013; 52(5):707-14. DOI: 10.1515/cclm-2013-0883. View

17.

Costa J, Sousa S, Justino A, Kay T, Fernandes S, Cirnes L . Nonoptical massive parallel DNA sequencing of BRCA1 and BRCA2 genes in a diagnostic setting. Hum Mutat. 2013; 34(4):629-35. DOI: 10.1002/humu.22272. View

18.

Loman N, Misra R, Dallman T, Constantinidou C, Gharbia S, Wain J . Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012; 30(5):434-9. DOI: 10.1038/nbt.2198. View

19.

Vargas-Poussou R, Dahan K, Kahila D, Venisse A, Riveira-Munoz E, Debaix H . Spectrum of mutations in Gitelman syndrome. J Am Soc Nephrol. 2011; 22(4):693-703. PMC: 3065225. DOI: 10.1681/ASN.2010090907. View

20.

Mitsui J, Fukuda Y, Azuma K, Tozaki H, Ishiura H, Takahashi Y . Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer. J Hum Genet. 2010; 55(7):448-55. DOI: 10.1038/jhg.2010.46. View