An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  Eisenberger, Tobias ^a   Decker, Christian ^a   Hiersche, Milan ^a   Hamann, Ruben C ^a   Decker, Eva ^a   Neuber, Steffen ^a   Frank, Valeska ^a   Bolz, Hanno J ^a   Fehrenbach, Henry ^b   Pape, Lars ^c   Toenshoff, Burkhard ^d   Mache, Christoph ^e   Latta, Kay ^f   Bergmann, Carsten ^a,g  

^a Bioscientia Center for Human Genetics   (Germany)

^b Klinikum Memmingen   (Germany)

^c HANNOVER MEDICAL SCHOOL   (Germany)

^d UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^e MEDICAL UNIVERSITY OF GRAZ   (Austria)

^f Clementine Kinderhospital   (Germany)

^g UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

POLYCYSTIN 1; PROTEIN SERINE THREONINE KINASE; PYRUVATE DEHYDROGENASE (ACETYL-TRANSFERRING) KINASE;

ALGORITHM; ARTICLE; AUTOSOMAL DOMINANT DISORDER; BIOINFORMATICS; CLINICAL FEATURE; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE AMPLIFICATION; GENE MUTATION; GENETIC HETEROGENEITY; GENETIC SCREENING; HUMAN; KIDNEY POLYCYSTIC DISEASE; MAJOR CLINICAL STUDY; MOLECULAR GENETICS; NEXT GENERATION SEQUENCING; PSEUDOGENE; FALSE NEGATIVE RESULT; GENE DUPLICATION; GENE LOCUS; GENETICS; HIGH THROUGHPUT SEQUENCING; KIDNEY; METABOLISM; MOLECULAR DIAGNOSIS; POLYCYSTIC KIDNEY DISEASES; PROCEDURES;

DNA COPY NUMBER VARIATIONS; FALSE NEGATIVE REACTIONS; GENE DUPLICATION; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KIDNEY; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYCYSTIC KIDNEY DISEASES; PROTEIN-SERINE-THREONINE KINASES; PSEUDOGENES;

EID: 84922353943     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116680     Document Type: Article

References (36)

1. Gerdes JM, Davis EE, Katsanis N (2009) The vertebrate primary cilium in development, homeostasis, and disease. Cell 137: 32-45. doi: 10.1016/j.cell.2009.03.023 PMID: 19345185
2. Goetz SC, Anderson KV (2010) The primary cilium: a signalling centre during vertebrate development. Nat Rev Genet 11: 331-344. doi: 10.1038/nrg2774 PMID: 20395968
3. Bergmann C (2014) Autosomal recessive polycystic kidney disease: Oxford University Press.
4. Harris PC, Torres VE (2009) Polycystic kidney disease. Annu Rev Med: 321-337. doi: 10.1146/ annurev.med.60.101707.125712 PMID: 18947299
5. Salomon R, Saunier S, Niaudet P (2009) Nephronophthisis. Pediatr Nephrol 24: 2333-2344. doi: 10.1007/s00467-008-0840-z PMID: 18607645
6. Bogdanova N, Markoff A, Gerke V, McCluskey M, Horst J, et al. (2001) Homologues to the first gene for autosomal dominant polycystic kidney disease are pseudogenes. Genomics 74: 333-341. PMID: 11414761
7. Symmons O, Varadi A, Aranyi T (2008) How segmental duplications shape our genome: recent evolution of ABCC6 and PKD1 Mendelian disease genes. Mol Biol Evol 25: 2601-2613. doi: 10.1093/ molbev/msn202 PMID: 18791038
8. Rossetti S, Chauveau D, Walker D, Saggar-Malik A, Winearls CG, et al. (2002) A complete mutation screen of the ADPKD genes by DHPLC. Kidney international 61: 1588-1599. PMID: 11967008
9. Rossetti S, Hopp K, Sikkink RA, Sundsbak JL, Lee YK, et al. (2012) Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing. J Am Soc Nephrol 23: 915-933. doi: 10.1681/ASN.2011101032 PMID: 22383692
10. Turner EH, Ng SB, Nickerson DA, Shendure J (2009) Methods for genomic partitioning. Annu Rev Genomics Hum Genet 10: 263-284. doi: 10.1146/annurev-genom-082908-150112 PMID: 19630561
11. Eisenberger T, Neuhaus C, Khan AO, Decker C, Preising MN, et al. (2013) Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: the example of retinal dystrophies. PLoS One 8: e78496. doi: 10.1371/journal.pone.0078496 PMID: 24265693
12. Bergmann C (2014) ARPKD and early manifestations of ADPKD: the original polycystic kidney disease and phenocopies. Pediatr Nephrol. PMID: 25543194
13. Bergmann C, Bruchle NO, Frank V, Rehder H, Zerres K (2008) Perinatal deaths in a family with autosomal dominant polycystic kidney disease and a PKD2 mutation. N Engl J Med 359: 318-319. doi: 10.1056/NEJMc0801868 PMID: 18635443
14. Hoff S, Halbritter J, Epting D, Frank V, Nguyen TM, et al. (2013) ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3. Nat Genet 45: 951-956. doi: 10.1038/ng. 2681 PMID: 23793029
15. Fehrenbach H, Decker C, Eisenberger T, Frank V, Hampel T, et al. (2014) Mutations in WDR19 encoding the intraflagellar transport component IFT144 cause a broad spectrum of ciliopathies. Pediatr Nephrol. PMID: 25543194
16. Schmidts M, Frank V, Eisenberger T, Al Turki S, Bizet AA, et al. (2013) Combined NGS approaches identify mutations in the intraflagellar transport gene IFT140 in skeletal ciliopathies with early progressive kidney Disease. Hum Mutat 34: 714-724. doi: 10.1002/humu.22294 PMID: 23418020
17. Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55: 641-658. doi: 10.1373/clinchem.2008.112789 PMID: 19246620
18. de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, et al. (2012) Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 367: 1921-1929. doi: 10.1056/ NEJMoa1206524 PMID: 23033978
19. Audrezet MP, Cornec-Le Gall E, Chen JM, Redon S, Quere I, et al. (2012) Autosomal dominant polycystic kidney disease: comprehensive mutation analysis of PKD1 and PKD2 in 700 unrelated patients. Hum Mutat 33: 1239-1250. doi: 10.1002/humu.22103 PMID: 22508176
20. Landsverk ML, Douglas GV, Tang S, Zhang VW, Wang GL, et al. (2012) Diagnostic approaches to apparent homozygosity. Genet Med 14: 877-882. doi: 10.1038/gim.2012.58 PMID: 22595940
21. Rossetti S, Consugar MB, Chapman AB, Torres VE, Guay-Woodford LM, et al. (2007) Comprehensive molecular diagnostics in autosomal dominant polycystic kidney disease. Journal of the American Society of Nephrology: JASN 18: 2143-2160. PMID: 17582161
22. Rossetti S, Harris PC (2007) Genotype-phenotype correlations in autosomal dominant and autosomal recessive polycystic kidney disease. Journal of the American Society of Nephrology: JASN 18: 1374-1380. PMID: 17429049
23. Consugar MB, Wong WC, Lundquist PA, Rossetti S, Kubly VJ, et al. (2008) Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome. Kidney Int 74: 1468-1479. doi: 10.1038/ki.2008.485 PMID: 18818683
24. Bergmann C, von Bothmer J, Ortiz Brüchle N, Venghaus A, Frank V, et al. (2011) Mutations in multiple PKD genes may explain early and severe polycystic kidney disease. Journal of the American Society of Nephrology: JASN 22: 2047-2056. doi: 10.1681/ASN.2010101080 PMID: 22034641
25. Arts HH, Knoers NV (2013) Current insights into renal ciliopathies: what can genetics teach us? Pediatr Nephrol 28: 863-874. doi: 10.1007/s00467-012-2259-9 PMID: 22829176
26. Ott E, Decker E, Kramer C, Eisenberger T, Frank V, et al. (2014) Definining new genes and disease mechanisms for cystic kidney disease and related disorders. Journal of Medical Genetics W4-04:91.
27. Frank V, Habbig S, Bartram MP, Eisenberger T, Veenstra-Knol HE, et al. (2013) Mutations in NEK8 link multiple organ dysplasia with altered Hippo signalling and increased c-MYC expression. Hum Mol Genet 22: 2177-2185. doi: 10.1093/hmg/ddt070 PMID: 23418306
28. Trujillano D, Bullich G, Ossowski S, Ballarin J, Torra R, et al. (2014) Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing. Molecuar Genetics & Genetic Medicine 5. doi: 10.1093/brain/awq331 PMID: 21126992
29. Eisenberger T, Di Donato N, Baig SM, Neuhaus C, Beyer A, et al. (2014) Targeted and genomewide NGS data disqualify mutations in MYO1A, the "DFNA48 gene", as a cause of deafness. Hum Mutat 35: 565-570. doi: 10.1002/humu.22532 PMID: 24616153
30. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi: 10.1093/bioinformatics/btp324 PMID: 19451168
31. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
32. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303. doi: 10.1101/gr.107524.110 PMID: 20644199
33. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, et al. (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568-576. doi: 10.1101/gr.129684.111 PMID: 22300766
34. Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M (2011) ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics 12 Suppl 14: S7. doi: 10.1186/1471-2105-12-S14-S7 PMID: 22373054
35. Nix DA, Eisen MB (2005) GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics 6:9. PMID: 15655071
36. Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, et al. (2010) GeneCards Version 3: the human gene integrator. Database (Oxford) 2010: baq020.