Prioritization and burden analysis of rare variants in 208 candidate genes suggest they do not play a major role in CAKUT

Kidney International

Volumn 89, Issue 2, 2016, Pages 476-486

  Nicolaou, Nayia ^a   Pulit, Sara L ^a   Nijman, Isaac J ^a   Monroe, Glen R ^a   Feitz, Wout F J ^b   Schreuder, Michiel F ^b   Van Eerde, Albertien M ^a   De Jong, Tom P V M ^a   Giltay, Jacques C ^a   Van Der Zwaag, Bert ^a   Havenith, Marlies R ^a   Zwakenberg, Susan ^a   Van Der Zanden, Loes F M ^b   Poelmans, Geert ^b,c,d   Cornelissen, Elisabeth A M ^b   Lilien, Marc R ^e   Franke, Barbara ^b,d   Roeleveld, Nel ^b   Van Rooij, Iris A L M ^b   Cuppen, Edwin ^a   Bongers, Ernie M H F ^b   Giles, Rachel H ^a   Knoers, Nine V A M ^a   Renkema, Kirsten Y ^a   more..

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d RADBOUD UNIVERSITY   (Netherlands)

^e UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

CAKUT; kidney development; pediatric nephrology

Indexed keywords

FIBROCYSTIN; HEPATOCYTE NUCLEAR FACTOR 1BETA; SEMAPHORIN 3A; TRANSCRIPTION FACTOR PAX2;

ADULT; AGT GENE; AGTR1 GENE; ALTERNATIVE RNA SPLICING; ARTICLE; CHD1L GENE; COHORT ANALYSIS; CONGENITAL ANOMALY OF THE KIDNEY AND URINARY TRACT; CONTROLLED STUDY; DACH1 GENE; DISEASE ASSOCIATION; EXON; FEMALE; FGF8 GENE; FMN1 GENE; FOLLOW UP; FREM1 GENE; GENE; GENE DELETION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC RISK; GENETIC SCREENING; GENETIC VARIABILITY; HNF1B GENE; HUMAN; IN VITRO STUDY; IN VIVO STUDY; INVS GENE; KIDNEY MALFORMATION; LRP4 GENE; MAJOR CLINICAL STUDY; MALE; NEXT GENERATION SEQUENCING; PAX2 GENE; PKHD1 GENE; PRIORITY JOURNAL; RARE DISEASE; REN GENE; RISK FACTOR; SEMA3A GENE; SIX5 GENE; UMOD GENE; UPK3A GENE; DNA SEQUENCE; GENETICS; UROGENITAL TRACT MALFORMATION;

EXONS; GENE DELETION; HUMANS; SEQUENCE ANALYSIS, DNA; UROGENITAL ABNORMALITIES;

EID: 84944929508     PISSN: 00852538     EISSN: 15231755     Source Type: Journal    
DOI: 10.1038/ki.2015.319     Document Type: Article

References (73)

1. J. Harambat, K.J. van Stralen, and J.J. Kim Epidemiology of chronic kidney disease in children Pediatr Nephrol 27 2012 363 373
2. E. Wuhl, K.J. van Stralen, C. Wanner, and et al. Renal replacement therapy for rare diseases affecting the kidney: an analysis of the ERA-EDTA Registry Nephrol Dial Transplant 29 2014 iv1 iv8
3. F. Hildebrandt Genetic kidney diseases Lancet 375 2010 1287 1295
4. S. Sanna-Cherchi, P. Ravani, V. Corbani, and et al. Renal outcome in patients with congenital anomalies of the kidney and urinary tract Kidney Int 76 2009 528 533
5. B. Bulum, Z.B. Ozcakar, E. Ustuner, and et al. High frequency of kidney and urinary tract anomalies in asymptomatic first-degree relatives of patients with CAKUT Pediatr Nephrol 28 2013 2143 2147
6. K.Y. Renkema, P.J. Winyard, I.N. Skovorodkin, and et al. Novel perspectives for investigating congenital anomalies of the kidney and urinary tract (CAKUT) Nephrol Dial Transplant 26 2011 3843 3851
7. S. Weber Novel genetic aspects of congenital anomalies of kidney and urinary tract Curr Opin Pediatr 24 2012 212 218
8. E. Monn, and T. Nordshus Hereditary renal adysplasia Acta Paediatr Scand 73 1984 278 280
9. E. McPherson, J. Carey, A. Kramer, and et al. Dominantly inherited renal adysplasia Am J Med Genet 26 1987 863 872
10. B.S. Kaplan, L.S. Milner, S. Jequier, and et al. Autosomal dominant inheritance of small kidneys Am J Med Genet 32 1989 120 126
11. B. Doray, B. Gasser, I. Reinartz, and et al. Hereditary renal adysplasia in a three generations family Genet Couns 10 1999 251 257
12. P. Saisawat, V. Tasic, V. Vega-Warner, and et al. Identification of two novel CAKUT-causing genes by massively parallel exon resequencing of candidate genes in patients with unilateral renal agenesis Kidney Int 81 2012 196 200
13. S. Kohl, D.Y. Hwang, G.C. Dworschak, and et al. Mild recessive mutations in six Fraser syndrome-related genes cause isolated congenital anomalies of the kidney and urinary tract J Am Soc Nephrol 25 2014 1917 1922
14. P. Saisawat, S. Kohl, A.C. Hilger, and et al. Whole-exome resequencing reveals recessive mutations in TRAP1 in individuals with CAKUT and VACTERL association Kidney Int 85 2014 1310 1317
15. I. Ichikawa, F. Kuwayama, JCt Pope, and et al. Paradigm shift from classic anatomic theories to contemporary cell biological views of CAKUT Kidney Int 61 2002 889 898
16. N. Uetani, and M. Bouchard Plumbing in the embryo: developmental defects of the urinary tracts Clin Genet 75 2009 307 317
17. M. Little, K. Georgas, D. Pennisi, and et al. Kidney development: two tales of tubulogenesis Curr Top Dev Biol 90 2010 193 229
18. I.V. Yosypiv Congenital anomalies of the kidney and urinary tract: a genetic disorder? Int J Nephrol 2012 2012 909083
19. A. Vivante, S. Kohl, D.Y. Hwang, and et al. Single-gene causes of congenital anomalies of the kidney and urinary tract (CAKUT) in humans Pediatr Nephrol 29 2014 695 704
20. S. Weber, V. Moriniere, T. Knuppel, and et al. Prevalence of mutations in renal developmental genes in children with renal hypodysplasia: results of the ESCAPE study J Am Soc Nephrol 17 2006 2864 2870
21. R. Thomas, S. Sanna-Cherchi, B.A. Warady, and et al. HNF1B and PAX2 mutations are a common cause of renal hypodysplasia in the CKiD cohort Pediatr Nephrol 26 2011 897 903
22. L. Madariaga, V. Moriniere, C. Jeanpierre, and et al. Severe prenatal renal anomalies associated with mutations in HNF1B or PAX2 genes Clin J Am Soc Nephrol 8 2013 1179 1187
23. R. Chatterjee, E. Ramos, M. Hoffman, and et al. Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations Hum Genet 131 2012 1725 1738
24. E.L. Edghill, C. Bingham, S. Ellard, and et al. Mutations in hepatocyte nuclear factor-1beta and their related phenotypes J Med Genet 43 2006 84 90
25. B.E. Hoskins, C.H. Cramer 2nd, V. Tasic, and et al. Missense mutations in EYA1 and TCF2 are a rare cause of urinary tract malformations Nephrol Dial Transplant 23 2008 777 779
26. T. Ulinski, S. Lescure, S. Beaufils, and et al. Renal phenotypes related to hepatocyte nuclear factor-1beta (TCF2) mutations in a pediatric cohort J Am Soc Nephrol 17 2006 497 503
27. F. Bu, T. Maga, N.C. Meyer, and et al. Comprehensive genetic analysis of complement and coagulation genes in atypical hemolytic uremic syndrome J Am Soc Nephrol 25 2014 55 64
28. A.W. Kurian, E.E. Hare, M.A. Mills, and et al. Clinical evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment J Clin Oncol 32 2014 2001 2009
29. G.L. Carvill, S.B. Heavin, S.C. Yendle, and et al. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1 Nat Genet 45 2013 825 830
30. V. Moriniere, K. Dahan, P. Hilbert, and et al. Improving mutation screening in familial hematuric nephropathies through next generation sequencing J Am Soc Nephrol 25 2014 2740 2751
31. R. Gao, Y. Liu, A.P. Gjesing, and et al. Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model BMC Genet 15 2014 13
32. J. Vandrovcova, E.R. Thomas, S.S. Atanur, and et al. The use of next-generation sequencing in clinical diagnosis of familial hypercholesterolemia Genet Med 15 2013 948 957
33. D.Y. Hwang, G.C. Dworschak, S. Kohl, and et al. Mutations in 12 known dominant disease-causing genes clarify many congenital anomalies of the kidney and urinary tract Kidney Int 85 2014 1429 1433
34. L. Heidet, S. Decramer, A. Pawtowski, and et al. Spectrum of HNF1B mutations in a large cohort of patients who harbor renal diseases Clin J Am Soc Nephrol 5 2010 1079 1090
35. P.D. Stenson, M. Mort, E.V. Ball, and et al. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine Hum Genet 133 2014 1 9
36. J. Favor, R. Sandulache, A. Neuhauser-Klaus, and et al. The mouse Pax2(1Neu) mutation is identical to a human PAX2 mutation in a family with renal- coloboma syndrome and results in developmental defects of the brain, ear, eye, and kidney Proc Natl Acad Sci USA 93 1996 13870 13875
37. B.E. Hoskins, C.H. Cramer, D. Silvius, and et al. Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome Am J Hum Genet 80 2007 800 804
38. S. Tinschert, N. Ruf, I. Bernascone, and et al. Functional consequences of a novel uromodulin mutation in a family with familial juvenile hyperuricaemic nephropathy Nephrol Dial Transplant 19 2004 3150 3154
39. I.A. Adzhubei, S. Schmidt, L. Peshkin, and et al. A method and server for predicting damaging missense mutations Nat Methods 7 2010 248 249
40. P. Kumar, S. Henikoff, and P.C. Ng Predicting the effects of coding non- synonymous variants on protein function using the SIFT algorithm Nat Protoc 4 2009 1073 1081
41. G.M. Cooper, E.A. Stone, G. Asimenos, and et al. Distribution and intensity of constraint in mammalian genomic sequence Genome Res 15 2005 901 913
42. M. Kircher, D.M. Witten, P. Jain, and et al. A general framework for estimating the relative pathogenicity of human genetic variants Nat Genet 46 2014 310 315
43. S. Petrovski, Q. Wang, E.L. Heinzen, and et al. Genic intolerance to functional variation and the interpretation of personal genomes PLoS Genet 9 2013 e1003709
44. C. Genomes Project, G.R. Abecasis, A. Auton, and et al. An integrated map of genetic variation from 1,092 human genomes Nature 491 2012 56 65
45. D.G. MacArthur, T.A. Manolio, D.P. Dimmock, and et al. Guidelines for investigating causality of sequence variants in human disease Nature 508 2014 469 476
46. M. Bower, R. Salomon, J. Allanson, and et al. Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database Hum Mutat 33 2012 457 466
47. S. Sanna-Cherchi, R.V. Sampogna, N. Papeta, and et al. Mutations in DSTYK and dominant urinary tract malformations N Engl J Med 369 2013 621 629
48. S. Sanna-Cherchi, K. Kiryluk, K.E. Burgess, and et al. Copy-number disorders are a common cause of congenital kidney malformations Am J Hum Genet 91 2012 987 997
49. G. Caruana, M.N. Wong, A. Walker, and et al. Copy-number variation associated with congenital anomalies of the kidney and urinary tract Pediatr Nephrol 30 2015 487 495
50. A.M. van Eerde, K. Duran, E. van Riel, and et al. Genes in the ureteric budding pathway: association study on vesico-ureteral reflux patients PLoS One 7 2012 e31327
51. M. Harakalova, M. Mokry, B. Hrdlickova, and et al. Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing Nat Protoc 6 2011 1870 1886
52. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows- Wheeler transform Bioinformatics 25 2009 1754 1760
53. The Genome of the Netherlands C Whole-genome sequence variation, population structure and demographic history of the Dutch population Nat Genet 46 2014 818 825
54. I.J. Nijman, J.M. van Montfrans, M. Hoogstraat, and et al. Targeted next- generation sequencing: a novel diagnostic tool for primary immunodeficiencies J Allergy Clin Immunol 133 2014 529 534
55. B.E. Madsen, and S.R. Browning A groupwise association test for rare mutations using a weighted sum statistic PLoS Genet 5 2009 e1000384
56. M.C. Wu, S. Lee, T. Cai, and et al. Rare-variant association testing for sequencing data with the sequence kernel association test Am J Hum Genet 89 2011 82 93
57. A.L. Price, G.V. Kryukov, P.I. de Bakker, and et al. Pooled association tests for rare variants in exon-resequencing studies Am J Hum Genet 86 2010 832 838
58. A.P. Morris, and E. Zeggini An evaluation of statistical approaches to rare variant analysis in genetic association studies Genet Epidemiol 34 2010 188 193
59. P. Sanyanusin, L.A. McNoe, M.J. Sullivan, and et al. Mutation of PAX2 in two siblings with renal-coloboma syndrome Hum Mol Genet 4 1995 2183 2184
60. I. Inoue, A. Rohrwasser, C. Helin, and et al. A mutation of angiotensinogen in a patient with preeclampsia leads to altered kinetics of the renin- angiotensin system J Biol Chem 270 1995 11430 11436
61. O. Gribouval, M. Gonzales, T. Neuhaus, and et al. Mutations in genes in the renin-angiotensin system are associated with autosomal recessive renal tubular dysgenesis Nat Genet 37 2005 964 968
62. A. Brockschmidt, B. Chung, S. Weber, and et al. CHD1L: a new candidate gene for congenital anomalies of the kidneys and urinary tract (CAKUT) Nephrol Dial Transplant 27 2012 2355 2364
63. R. Schild, T. Knuppel, M. Konrad, and et al. Double homozygous missense mutations in DACH1 and BMP4 in a patient with bilateral cystic renal dysplasia Nephrol Dial Transplant 28 2013 227 232
64. J. Falardeau, W.C. Chung, A. Beenken, and et al. Decreased FGF8 signaling causes deficiency of gonadotropin-releasing hormone in humans and mice J Clin Invest 118 2008 2822 2831
65. B.I. Dimitrov, T. Voet, L. De Smet, and et al. Genomic rearrangements of the GREM1-FMN1 locus cause oligosyndactyly, radio-ulnar synostosis, hearing loss, renal defects syndrome and Cenani-Lenz-like non-syndromic oligosyndactyly J Med Genet 47 2010 569 574
66. A.M. Alazami, R. Shaheen, F. Alzahrani, and et al. FREM1 mutations cause bifid nose, renal agenesis, and anorectal malformations syndrome Am J Hum Genet 85 2009 414 418
67. E.A. Otto, B. Schermer, T. Obara, and et al. Mutations in INVS encoding inversin cause nephronophthisis type 2, linking renal cystic disease to the function of primary cilia and left-right axis determination Nat Genet 34 2003 413 420
68. Y. Li, B. Pawlik, N. Elcioglu, and et al. LRP4 mutations alter Wnt/beta-catenin signaling and cause limb and kidney malformations in Cenani-Lenz syndrome Am J Hum Genet 86 2010 696 706
69. S. Rossetti, R. Torra, E. Coto, and et al. A complete mutation screen of PKHD1 in autosomal-recessive polycystic kidney disease (ARPKD) pedigrees Kidney Int 64 2003 391 403
70. O. Gribouval, V. Moriniere, A. Pawtowski, and et al. Spectrum of mutations in the renin-angiotensin system genes in autosomal recessive renal tubular dysgenesis Hum Mutat 33 2012 316 326
71. N.K. Hanchate, P. Giacobini, P. Lhuillier, and et al. SEMA3A, a gene involved in axonal pathfinding, is mutated in patients with Kallmann syndrome PLoS Genet 8 2012 e1002896
72. S.E. Williams, A.A. Reed, J. Galvanovskis, and et al. Uromodulin mutations causing familial juvenile hyperuricaemic nephropathy lead to protein maturation defects and retention in the endoplasmic reticulum Hum Mol Genet 18 2009 2963 2974
73. D. Jenkins, M. Bitner-Glindzicz, S. Malcolm, and et al. De novo Uroplakin IIIa heterozygous mutations cause human renal adysplasia leading to severe kidney failure J Am Soc Nephrol 16 2005 2141 2149