Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing

Journal of Molecular Diagnostics

Volumn 16, Issue 2, 2014, Pages 216-228

  Tan, Adrian Y ^a   Michaeel, Alber ^a   Liu, Genyan ^a   Elemento, Olivier ^a   Blumenfeld, Jon ^a,b   Donahue, Stephanie ^b   Parker, Tom ^b   Levine, Daniel ^b   Rennert, Hanna ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b ROGOSIN INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MUTATIONAL ANALYSIS; EXONS; GENE ORDER; GENETIC TESTING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; POLYCYSTIC KIDNEY, AUTOSOMAL DOMINANT; POLYMERASE CHAIN REACTION; PROSPECTIVE STUDIES; REGISTRIES; SENSITIVITY AND SPECIFICITY; TRPP CATION CHANNELS;

EID: 84894032215     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2013.10.005     Document Type: Article

References (38)

1. D.J. Peters, and L.A. Sandkuijl Genetic heterogeneity of polycystic kidney disease in Europe Contrib Nephrol 97 1992 128 139
2. P.C. Harris 2008 Homer W. Smith Award: insights into the pathogenesis of polycystic kidney disease from gene discovery J Am Soc Nephrol 20 2009 1188 1198
3. V.E. Torres, P.C. Harris, and Y. Pirson Autosomal dominant polycystic kidney disease Lancet 369 2007 1287 1301
4. W.E. Braun Autosomal dominant polycystic kidney disease: emerging concepts of pathogenesis and new treatments Cleve Clin J Med 76 2009 97 104
5. J. Hughes, C.J. Ward, B. Peral, R. Aspinwall, K. Clark, J.L. San Millan, V. Gamble, and P.C. Harris The polycystic kidney disease 1 (PKD1) gene encodes a novel protein with multiple cell recognition domains Nat Genet 10 1995 151 160
6. T. Mochizuki, G. Wu, T. Hayashi, S.L. Xenophontos, B. Veldhuisen, J.J. Saris, D.M. Reynolds, Y. Cai, P.A. Gabow, A. Pierides, W.J. Kimberling, M.H. Breuning, C.C. Deltas, D.J. Peters, and S. Somlo PKD2, a gene for polycystic kidney disease that encodes an integral membrane protein Science 272 1996 1339 1342
7. P.C. Harris, and S. Rossetti Molecular diagnostics for autosomal dominant polycystic kidney disease Nat Rev Nephrol 6 2010 197 206
8. The International Polycystic Kidney Disease Consortium Polycystic kidney disease: the complete structure of the PKD1 gene and its protein Cell 81 1995 289 298
9. A.B. Chapman, and W. Wei Imaging approaches to patients with polycystic kidney disease Semin Nephrol 31 2011 237 244
10. J.D. Blumenfeld Pretransplant genetic testing of live kidney donors at risk for autosomal dominant polycystic kidney disease Transplantation 87 2009 6 7
11. V.E. Torres, A.B. Chapman, O. Devuyst, R.T. Gansevoort, J.J. Grantham, E. Higashihara, R.D. Perrone, H.B. Krasa, J. Ouyang, and F.S. Czerwiec Tolvaptan in patients with autosomal dominant polycystic kidney disease N Engl J Med 367 2012 2407 2418
12. S. Rossetti, L. Strmecki, V. Gamble, S. Burton, V. Sneddon, B. Peral, S. Roy, A. Bakkaloglu, R. Komel, C.G. Winearls, and P.C. Harris Mutation analysis of the entire PKD1 gene: genetic and diagnostic implications Am J Hum Genet 68 2001 46 63
13. Y.C. Tan, A. Michaeel, J. Blumenfeld, S. Donahue, T. Parker, D. Levine, and H. Rennert A novel long-range PCR sequencing method for genetic analysis of the entire PKD1 gene J Mol Diagn 14 2012 305 313
14. S. Rossetti, D. Chauveau, D. Walker, A. Saggar-Malik, C.G. Winearls, V.E. Torres, and P.C. Harris A complete mutation screen of the ADPKD genes by DHPLC Kidney Int 61 2002 1588 1599
15. G. Kuhlenbaumer, J. Hullmann, and S. Appenzeller Novel genomic techniques open new avenues in the analysis of monogenic disorders Hum Mutat 32 2011 144 151
16. M.L. Metzker Sequencing technologies: the next generation Nat Rev Genet 11 2010 31 46
17. S. Rossetti, K. Hopp, R.A. Sikkink, J.L. Sundsbak, Y.K. Lee, V. Kubly, B.W. Eckloff, C.J. Ward, C.G. Winearls, V.E. Torres, and P.C. Harris Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing J Am Soc Nephrol 23 2012 915 933
18. Y.C. Tan, J.D. Blumenfeld, R. Anghel, S. Donahue, R. Belenkaya, M. Balina, T. Parker, D. Levine, D.G. Leonard, and H. Rennert Novel method for genomic analysis of PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease Hum Mutat 30 2009 264 273
19. S. Rozen, and H. Skaletsky Primer3 on the WWW for general users and for biologist programmers Methods Mol Biol 132 2000 365 386
20. O. Harismendy, and K. Frazer Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology Biotechniques 46 2009 229 231
21. M. Meyer, and M. Kircher Illumina sequencing library preparation for highly multiplexed target capture and sequencing Cold Spring Harb Protoc 2010 2010 pdb prot5448
22. E. Aronesty Comparison of sequencing utility programs Open Bioinformatics J 2013 http://dx.doi.org/10.2174/1875036201307010001
23. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
24. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M.A. DePristo The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res 20 2010 1297 1303
25. M.A. DePristo, E. Banks, R. Poplin, K.V. Garimella, J.R. Maguire, C. Hartl, A.A. Philippakis, G. del Angel, M.A. Rivas, M. Hanna, A. McKenna, T.J. Fennell, A.M. Kernytsky, A.Y. Sivachenko, K. Cibulskis, S.B. Gabriel, D. Altshuler, and M.J. Daly A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat Genet 43 2011 491 498
26. K. Wang, M. Li, and H. Hakonarson ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Res 38 2010 e164
27. J.T. den Dunnen, and S.E. Antonarakis Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion Hum Mutat 15 2000 7 12
28. Q. Liu, Y. Guo, J. Li, J. Long, B. Zhang, and Y. Shyr Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data BMC Genomics 13 Suppl 8 2012 S8
29. P.C. Ng, and S. Henikoff Predicting deleterious amino acid substitutions Genome Res 11 2001 863 874
30. I. Adzhubei, D.M. Jordan, and S.R. Sunyaev Predicting functional effect of human missense mutations using PolyPhen-2 Curr Protoc Hum Genet 2013 Chapter 7: Unit7.20
31. J.M. Schwarz, C. Rodelsperger, M. Schuelke, and D. Seelow MutationTaster evaluates disease-causing potential of sequence alterations Nat Methods 7 2010 575 576
32. E.L. Chin, C. da Silva, and M. Hegde Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations BMC Genet 14 2013 6
33. T. Huang Next generation sequencing to characterize mitochondrial genomic DNA heteroplasmy Curr Protoc Hum Genet 2011 Chapter 19: Unit19.18
34. H.L. Rehm, S.J. Bale, P. Bayrak-Toydemir, J.S. Berg, K.K. Brown, J.L. Deignan, M.J. Friez, B.H. Funke, M.R. Hegde, and E. Lyon ACMG clinical laboratory standards for next-generation sequencing Genet Med 15 2013 733 747
35. X.P. Qi, Z.F. Du, J.M. Ma, X.L. Chen, Q. Zhang, J. Fei, X.M. Wei, D. Chen, H.P. Ke, X.Z. Liu, F. Li, Z.G. Chen, Z. Su, H.Y. Jin, W.T. Liu, Y. Zhao, H.L. Jiang, Z.Z. Lan, P.F. Li, M.Y. Fang, W. Dong, and X.N. Zhang Genetic diagnosis of autosomal dominant polycystic kidney disease by targeted capture and next-generation sequencing: utility and limitations Gene 2012 2012 01590 01599
36. D. Aird, M.G. Ross, W.S. Chen, M. Danielsson, T. Fennell, C. Russ, D.B. Jaffe, C. Nusbaum, and A. Gnirke Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Genome Biol 12 2011 R18
37. M.P. Audrezet, E. Cornec-Le Gall, J.M. Chen, S. Redon, I. Quere, J. Creff, C. Benech, S. Maestri, Y. Le Meur, and C. Ferec Autosomal dominant polycystic kidney disease: comprehensive mutation analysis of PKD1 and PKD2 in 700 unrelated patients Hum Mutat 33 2012 1239 1250
38. M.B. Consugar, W.C. Wong, P.A. Lundquist, S. Rossetti, V.J. Kubly, D.L. Walker, L.J. Rangel, R. Aspinwall, W.P. Niaudet, S. Ozen, A. David, M. Velinov, E.J. Bergstralh, K.T. Bae, A.B. Chapman, L.M. Guay-Woodford, J.J. Grantham, V.E. Torres, J.R. Sampson, B.D. Dawson, and P.C. Harris Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome Kidney Int 74 2008 1468 1479