nach oben

Erschienen in:

26.02.2016 | Original Article

Comprehensive genetic testing approach for major inherited kidney diseases, using next-generation sequencing with a custom panel

verfasst von: Takayasu Mori, Kazuyoshi Hosomichi, Motoko Chiga, Shintaro Mandai, Hirofumi Nakaoka, Eisei Sohara, Tomokazu Okado, Tatemitsu Rai, Sei Sasaki, Ituro Inoue, Shinichi Uchida

Erschienen in: Clinical and Experimental Nephrology | Ausgabe 1/2017

Einloggen, um Zugang zu erhalten

Abstract

Background

Gene identification of hereditary kidney diseases by DNA sequencing is important for precise diagnosis, treatment, and genetic consultations. However, the conventional Sanger sequencing is now practically powerless in the face of ever increasing numbers of reported causative genes of various hereditary diseases. The advent of next-generation sequencing technology has enabled large-scale, genome-wide, simultaneous sequence analyses of multiple candidate genes.

Methods

We designed and verified a comprehensive diagnosis panel for approximately 100 major inherited kidney diseases, including 127 known genes. The panel was named Simple, sPEedy and Efficient Diagnosis of Inherited KIdney Diseases (SPEEDI-KID). We applied the panel to 73 individuals, clinically diagnosed with an inherited kidney disease, from 56 families.

Results

The panel efficiently covered the candidate genes and allowed a prompt and accurate genetic diagnosis. Moreover, 18 unreported mutations suspected as the disease causes were detected. All these mutations were validated by Sanger sequencing, with 100 % concordance.

Conclusion

In conclusion, we developed a powerful diagnostic method, focusing on inherited kidney diseases, using a custom panel, SPEEDI-KID, allowing a fast, easy, and comprehensive diagnosis regardless of the disease type.

Nur mit Berechtigung zugänglich

Samorodnitsky E, Jewell BM, Hagopian R, Miya J, Wing MR, Lyon E, Damodaran S, Bhatt D, Reeser JW, Datta J, Roychowdhury S. Evaluation of hybridization capture versus amplicon-based methods for whole-exome sequencing. Hum Mutat. 2015;36:903–14.CrossRefPubMedPubMedCentral

Renkema KY, Stokman MF, Giles RH, Knoers NV. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol. 2014;10:433–44.CrossRefPubMed

Schrier RW, Coffman TM, Falk RJ, et al. Schrier’s diseases of the kidney. Amsterdam: Wolters Kluwer; 2012.

Antoniadi T, Buxton C, Dennis G, Forrester N, Smith D, Lunt P, Burton-Jones S. Application of targeted multi-gene panel testing for the diagnosis of inherited peripheral neuropathy provides a high diagnostic yield with unexpected phenotype-genotype variability. BMC Med Genet. 2015;16:84.CrossRefPubMedPubMedCentral

Polla DL, Cardoso MT, Silva MC, Cardoso IC, Medina CT, Araujo R, Fernandes CC, Reis AM, de Andrade RV, Pereira RW, Pogue R. Use of targeted exome sequencing for molecular diagnosis of skeletal disorders. PLoS One. 2015;10:e0138314.CrossRefPubMedPubMedCentral

Fernandez-San Jose P, Corton M, Blanco-Kelly F, Avila-Fernandez A, Lopez-Martinez MA, Sanchez-Navarro I, Sanchez-Alcudia R, Perez-Carro R, Zurita O, Sanchez-Bolivar N, Lopez-Molina MI, Garcia-Sandoval B, Riveiro-Alvarez R, Ayuso C. Targeted next-generation sequencing improves the diagnosis of autosomal dominant retinitis pigmentosa in Spanish patients. Invest Ophthalmol Vis Sci. 2015;56:2173–82.CrossRefPubMed

Wilson FH, Disse-Nicodème S, Choate KA, Ishikawa K, Nelson-Williams C, Desitter I, Gunel M, Milford DV, Lipkin GW, Achard JM, Feely MP, Dussol B, Berland Y, Unwin RJ, Mayan H, Simon DB, Farfel Z, Jeunemaitre X, Lifton RP. Human hypertension caused by mutations in WNK kinases. Science. 2001;293:1107–12.CrossRefPubMed

Boyden LM, Choi M, Choate KA, Nelson-Williams CJ, Farhi A, Toka HR, Tikhonova IR, Bjornson R, Mane SM, Colussi G, Lebel M, Gordon RD, Semmekrot BA, Poujol A, Välimäki MJ, De Ferrari ME, Sanjad SA, Gutkin M, Karet FE, Tucci JR, Stockigt JR, Keppler-Noreuil KM, Porter CC, Anand SK, Whiteford ML, Davis ID, Dewar SB, Bettinelli A, Fadrowski JJ, Belsha CW, Hunley TE, Nelson RD, Trachtman H, Cole TR, Pinsk M, Bockenhauer D, Shenoy M, Vaidyanathan P, Foreman JW, Rasoulpour M, Thameem F, Al-Shahrouri HZ, Radhakrishnan J, Gharavi AG, Goilav B, Lifton RP. Mutations in kelch-like 3 and cullin 3 cause hypertension and electrolyte abnormalities. Nature. 2012;482:98–102.CrossRefPubMedPubMedCentral

Hashimura Y, Nozu K, Kaito H, Nakanishi K, Fu XJ, Ohtsubo H, Hashimoto F, Oka M, Ninchoji T, Ishimori S, Morisada N, Matsunoshita N, Kamiyoshi N, Yoshikawa N, Iijima K. Milder clinical aspects of X-linked Alport syndrome in men positive for the collagen IV α5 chain. Kidney Int. 2014;85:1208–13.CrossRefPubMed

10.

Baudhuin LM, Lagerstedt SA, Klee EW, Fadra N, Oglesbee D, Ferber MJ. Confirming variants in next-generation sequencing panel testing by Sanger sequencing. J Mol Diagn. 2015;17:456–61.CrossRefPubMed

11.

Tan YC, Michaeel A, Blumenfeld J, Donahue S, Parker T, Levine D, Rennert H. A novel long-range PCR sequencing method for genetic analysis of the entire PKD1 gene. J Mol Diagn. 2012;14:305–13.CrossRefPubMedPubMedCentral

12.

Tan AY, Michaeel A, Liu G, Elemento O, Blumenfeld J, Donahue S, Parker T, Levine D, Rennert H. Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing. J Mol Diagn. 2014;16:216–28.CrossRefPubMedPubMedCentral

13.

Trujillano D, Bullich G, Ossowski S, Ballarín J, Torra R, Estivill X, Ars E. Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing. Mol Genet Genomic Med. 2014;2:412–21.CrossRefPubMedPubMedCentral

14.

Harris PC, Hopp K. The mutation, a key determinant of phenotype in ADPKD. J Am Soc Nephrol. 2013;24:868–70.CrossRefPubMed

15.

Vargas-Poussou R, Dahan K, Kahila D, Venisse A, Riveira-Munoz E, Debaix H, Grisart B, Bridoux F, Unwin R, Moulin B, Haymann JP, Vantyghem MC, Rigothier C, Dussol B, Godin M, Nivet H, Dubourg L, Tack I, Gimenez-Roqueplo AP, Houillier P, Blanchard A, Devuyst O, Jeunemaitre X. Spectrum of mutations in Gitelman syndrome. J Am Soc Nephrol. 2011;22:693–703.CrossRefPubMedPubMedCentral

16.

Blackburn HL, Schroeder B, Turner C, Shriver CD, Ellsworth DL, Ellsworth RE. Management of incidental findings in the Era of next-generation sequencing. Curr Genomics. 2015;16:159–74.CrossRefPubMedPubMedCentral

17.

Abdul-Karim R, Berkman BE, Wendler D, Rid A, Khan J, Badgett T, Hull SC. Disclosure of incidental findings from next-generation sequencing in pediatric genomic research. Pediatrics. 2013;131:564–71.CrossRefPubMedPubMedCentral

18.

Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire AL, Nussbaum RL, O’Daniel JM, Ormond KE, Rehm HL, Watson MS, Williams MS, Biesecker LG. Genomics ACoMGa, ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15:565–74.CrossRefPubMedPubMedCentral

19.

Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2014;15:256–78.CrossRefPubMed

20.

Sulonen AM, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 2011;12:R94.CrossRefPubMedPubMedCentral

21.

Huentelman MJ. Targeted next-generation sequencing: microdroplet PCR approach for variant detection in research and clinical samples. Expert Rev Mol Diagn. 2011;11:347–9.CrossRefPubMed

Titel: Comprehensive genetic testing approach for major inherited kidney diseases, using next-generation sequencing with a custom panel
verfasst von: Takayasu Mori
Kazuyoshi Hosomichi
Motoko Chiga
Shintaro Mandai
Hirofumi Nakaoka
Eisei Sohara
Tomokazu Okado
Tatemitsu Rai
Sei Sasaki
Ituro Inoue
Shinichi Uchida
Publikationsdatum: 26.02.2016
Verlag: Springer Japan
Erschienen in: Clinical and Experimental Nephrology / Ausgabe 1/2017
Print ISSN: 1342-1751
Elektronische ISSN: 1437-7799
DOI: https://doi.org/10.1007/s10157-016-1252-1

Leitlinien kompakt für die Innere Medizin

Mit medbee Pocketcards sicher entscheiden.

^{Seit 2022 gehört die medbee GmbH zum Springer Medizin Verlag}

Kostenlos registrieren

Neu im Fachgebiet Innere Medizin

25.04.2024 | Hypotonie | Nachrichten

Update Innere Medizin

Bestellen Sie unseren Fach-Newsletter und bleiben Sie gut informiert.

Newsletter bestellen

Springer Medizin

Comprehensive genetic testing approach for major inherited kidney diseases, using next-generation sequencing with a custom panel

Abstract

Background

Methods

Results

Conclusion

Leitlinien kompakt für die Innere Medizin

Neu im Fachgebiet Innere Medizin

Niedriger diastolischer Blutdruck erhöht Risiko für schwere kardiovaskuläre Komplikationen

Therapiestart mit Blutdrucksenkern erhöht Frakturrisiko

Viel Bewegung in der Parkinsonforschung

Adjuvante Immuntherapie verlängert Leben bei RCC

Update Innere Medizin

Springer Medizin

Abstract

Background

Methods

Results

Conclusion

Bitte loggen Sie sich ein, um Zugang zu diesem Inhalt zu erhalten

Weitere Artikel der Ausgabe 1/2017

Bilateral nephromegaly due to isolated renal sarcoidosis

Podocyte-specific NF-κB inhibition ameliorates proteinuria in adriamycin-induced nephropathy in mice

Long-term efficacy and safety of common steroid-sparing agents in idiopathic nephrotic children

Relationship between mortality and speed of eGFR decline in the 3 months prior to dialysis initiation

Rare renal ciliopathies in non-consanguineous families that were identified by targeted resequencing

Anti-alpha-enolase antibodies in membranous nephropathy: isotype matters

Leitlinien kompakt für die Innere Medizin

Neu im Fachgebiet Innere Medizin

Niedriger diastolischer Blutdruck erhöht Risiko für schwere kardiovaskuläre Komplikationen

Therapiestart mit Blutdrucksenkern erhöht Frakturrisiko

Viel Bewegung in der Parkinsonforschung

Adjuvante Immuntherapie verlängert Leben bei RCC

Update Innere Medizin