DOI QR코드

DOI QR Code

Clinical Genetic Testing in Children with Kidney Disease

  • Kang, Eungu (Department of Pediatrics, Korea University Ansan Hospital, Korea University College of Medicine) ;
  • Lee, Beom Hee (Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine)
  • 투고 : 2021.03.18
  • 심사 : 2021.05.10
  • 발행 : 2021.06.30

초록

Chronic kidney disease, the presence of structural and functional abnormalities in the kidneys, is associated with a lower quality of life and increased morbidity and mortality in children. Genetic etiologies account for a substantial proportion of pediatric chronic kidney disease. With recent advances in genetic testing techniques, an increasing number of genetic causes of kidney disease continue to be found. Genetic testing is recommended in children with steroid-resistant nephrotic syndrome, congenital malformations of the kidney and urinary tract, cystic disease, or kidney disease with extrarenal manifestations. Diagnostic yields differ according to the category of clinical diagnosis and the choice of test. Here, we review the characteristics of genetic testing modalities and the implications of genetic testing in clinical genetic diagnostics.

키워드

과제정보

This research was supported in part by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (NRF-2018M3A9H1078335).

참고문헌

  1. Andrassy KM. Comments on 'KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease'. Kidney Int 2013;84:622-3. https://doi.org/10.1038/ki.2013.243
  2. Mong Hiep TT, Ismaili K, Collart F, Van Damme-Lombaerts R, Godefroid N, Ghuysen MS, et al. Clinical characteristics and outcomes of children with stage 3-5 chronic kidney disease. Pediatr Nephrol 2010;25:935-40. https://doi.org/10.1007/s00467-009-1424-2
  3. Weaver DJ, Mitsnefes M. Cardiovascular Disease in Children and Adolescents With Chronic Kidney Disease. Semin Nephrol 2018; 38:559-69. https://doi.org/10.1016/j.semnephrol.2018.08.002
  4. Ruidiaz-Gomez KS, Higuita-Gutierrez LF. Impact of chronic kidney disease on health-related quality of life in the pediatric population: meta-analysis. J Pediatr (Rio J) 2020:S0021-7557(20)30243-6.
  5. Vivante A, Hildebrandt F. Exploring the genetic basis of early-onset chronic kidney disease. Nat Rev Nephrol 2016;12:133-46. https://doi.org/10.1038/nrneph.2015.205
  6. Harambat J, van Stralen KJ, Kim JJ, Tizard EJ. Epidemiology of chronic kidney disease in children. Pediatr Nephrol 2012;27:363-73. https://doi.org/10.1007/s00467-011-1939-1
  7. Smith JM, Stablein DM, Munoz R, Hebert D, McDonald RA. Contributions of the Transplant Registry: The 2006 Annual Report of the North American Pediatric Renal Trials and Collaborative Studies (NAPRTCS). Pediatr Transplant 2007;11:366-73. https://doi.org/10.1111/j.1399-3046.2007.00704.x
  8. McClellan WM, Satko SG, Gladstone E, Krisher JO, Narva AS, Freedman BI. Individuals with a family history of ESRD are a high-risk population for CKD: implications for targeted surveillance and intervention activities. Am J Kidney Dis 2009;53:S100-6. https://doi.org/10.1053/j.ajkd.2008.07.059
  9. Connaughton DM, Bukhari S, Conlon P, Cassidy E, O'Toole M, Mohamad M, et al. The Irish Kidney Gene Project-Prevalence of Family History in Patients with Kidney Disease in Ireland. Nephron 2015;130:293-301. https://doi.org/10.1159/000436983
  10. Connaughton DM, Hildebrandt F. Personalized medicine in chronic kidney disease by detection of monogenic mutations. Nephrology Dialysis Transplantation 2019;35:390-7. https://doi.org/10.1093/ndt/gfz028
  11. Rasouly HM, Groopman EE, Heyman-Kantor R, Fasel DA, Mitrotti A, Westland R, et al. The Burden of Candidate Pathogenic Variants for Kidney and Genitourinary Disorders Emerging From Exome Sequencing. Ann Intern Med 2019;170:11-21. https://doi.org/10.7326/M18-1241
  12. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The Sequence of the Human Genome. Science 2001;291:1304-51. https://doi.org/10.1126/science.1058040
  13. Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med 2010;61:437-55. https://doi.org/10.1146/annurev-med-100708-204735
  14. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010;86:749-64. https://doi.org/10.1016/j.ajhg.2010.04.006
  15. Hays T, Groopman EE, Gharavi AG. Genetic testing for kidney disease of unknown etiology. Kidney Int 2020;98:590-600. https://doi.org/10.1016/j.kint.2020.03.031
  16. Verbitsky M, Westland R, Perez A, Kiryluk K, Liu Q, Krithivasan P, et al. The copy number variation landscape of congenital anomalies of the kidney and urinary tract. Nat Genet 2019;51:117-27. https://doi.org/10.1038/s41588-018-0281-y
  17. Sanna-Cherchi S, Kiryluk K, Burgess KE, Bodria M, Sampson MG, Hadley D, et al. Copy-number disorders are a common cause of congenital kidney malformations. Am J Hum Genet 2012;91:987-97. https://doi.org/10.1016/j.ajhg.2012.10.007
  18. Caruana G, Wong MN, Walker A, Heloury Y, Webb N, Johnstone L, et al. Copy-number variation associated with congenital anomalies of the kidney and urinary tract. Pediatr Nephrol 2015;30:487-95. https://doi.org/10.1007/s00467-014-2962-9
  19. Wang XV, Blades N, Ding J, Sultana R, Parmigiani G. Estimation of sequencing error rates in short reads. BMC Bioinformatics 2012;13:185. https://doi.org/10.1186/1471-2105-13-185
  20. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 2016;17:333-51. https://doi.org/10.1038/nrg.2016.49
  21. Artuso R, Fallerini C, Dosa L, Scionti F, Clementi M, Garosi G, et al. Advances in Alport syndrome diagnosis using next-generation sequencing. Eur J Hum Genet 2012;20:50-7. https://doi.org/10.1038/ejhg.2011.164
  22. McCarthy HJ, Bierzynska A, Wherlock M, Ognjanovic M, Kerecuk L, Hegde S, et al. Simultaneous sequencing of 24 genes associated with steroid-resistant nephrotic syndrome. Clin J Am Soc Nephrol 2013;8:637-48. https://doi.org/10.2215/CJN.07200712
  23. Otto EA, Ramaswami G, Janssen S, Chaki M, Allen SJ, Zhou W, et al. Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy. J Med Genet 2011;48:105-16. https://doi.org/10.1136/jmg.2010.082552
  24. Murray SL, Fennelly NK, Doyle B, Lynch SA, Conlon PJ. Integration of genetic and histopathology data in interpretation of kidney disease. Nephrol Dial Transplant 2020;35:1113-32. https://doi.org/10.1093/ndt/gfaa176
  25. Ahn YH, Lee C, Kim NKD, Park E, Kang HG, Ha I-S, et al. Targeted Exome Sequencing Provided Comprehensive Genetic Diagnosis of Congenital Anomalies of the Kidney and Urinary Tract. Journal of Clinical Medicine 2020;9:751. https://doi.org/10.3390/jcm9030751
  26. Sen ES, Dean P, Yarram-Smith L, Bierzynska A, Woodward G, Buxton C, et al. Clinical genetic testing using a custom-designed steroid-resistant nephrotic syndrome gene panel: analysis and recommendations. J Med Genet 2017;54:795-804. https://doi.org/10.1136/jmedgenet-2017-104811
  27. Park E, Lee C, Kim NKD, Ahn YH, Park YS, Lee JH, et al. Genetic Study in Korean Pediatric Patients with Steroid-Resistant Nephrotic Syndrome or Focal Segmental Glomerulosclerosis. Journal of Clinical Medicine 2020;9:2013. https://doi.org/10.3390/jcm9062013
  28. Bullich G, Domingo-Gallego A, Vargas I, Ruiz P, Lorente-Grandoso L, Furlano M, et al. A kidney-disease gene panel allows a comprehensive genetic diagnosis of cystic and glomerular inherited kidney diseases. Kidney Int 2018;94:363-71. https://doi.org/10.1016/j.kint.2018.02.027
  29. Landini S, Mazzinghi B, Becherucci F, Allinovi M, Provenzano A, Palazzo V, et al. Reverse Phenotyping after Whole-Exome Sequencing in Steroid-Resistant Nephrotic Syndrome. Clin J Am Soc Nephrol 2020;15:89-100. https://doi.org/10.2215/CJN.06060519
  30. Warejko JK, Tan W, Daga A, Schapiro D, Lawson JA, Shril S, et al. Whole Exome Sequencing of Patients with Steroid-Resistant Nephrotic Syndrome. Clin J Am Soc Nephrol 2018;13:53-62. https://doi.org/10.2215/CJN.04120417
  31. Zhou B, Ho SS, Zhang X, Pattni R, Haraksingh RR, Urban AE. Wholegenome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis. J Med Genet 2018;55:735-43. https://doi.org/10.1136/jmedgenet-2018-105272
  32. Meienberg J, Bruggmann R, Oexle K, Matyas G. Clinical sequencing: is WGS the better WES? Hum Genet 2016;135:359-62. https://doi.org/10.1007/s00439-015-1631-9
  33. Baker SW, Murrell JR, Nesbitt AI, Pechter KB, Balciuniene J, Zhao X, et al. Automated Clinical Exome Reanalysis Reveals Novel Diagnoses. J Mol Diagn 2019;21:38-48. https://doi.org/10.1016/j.jmoldx.2018.07.008
  34. Rao J, Liu X, Mao J, Tang X, Shen Q, Li G, et al. Genetic spectrum of renal disease for 1001 Chinese children based on a multicenter registration system. Clin Genet 2019;96:402-10. https://doi.org/10.1111/cge.13606
  35. Mann N, Braun DA, Amann K, Tan W, Shril S, Connaughton DM, et al. Whole-Exome Sequencing Enables a Precision Medicine Approach for Kidney Transplant Recipients. J Am Soc Nephrol 2019;30:201-15. https://doi.org/10.1681/ASN.2018060575
  36. Groopman EE, Marasa M, Cameron-Christie S, Petrovski S, Aggarwal VS, Milo-Rasouly H, et al. Diagnostic Utility of Exome Sequencing for Kidney Disease. N Engl J Med 2019;380:142-51. https://doi.org/10.1056/NEJMoa1806891
  37. Lionel AC, Costain G, Monfared N, Walker S, Reuter MS, Hosseini SM, et al. Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Genet Med 2018;20:435-43. https://doi.org/10.1038/gim.2017.119
  38. Sadowski CE, Lovric S, Ashraf S, Pabst WL, Gee HY, Kohl S, et al. A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome. J Am Soc Nephrol 2015;26:1279-89. https://doi.org/10.1681/ASN.2014050489
  39. Ali H, Al-Mulla F, Hussain N, Naim M, Asbeutah AM, AlSahow A, et al. PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease. Scientific Reports 2019;9:4141. https://doi.org/10.1038/s41598-019-40761-w
  40. Kingsmore SF, Cakici JA, Clark MM, Gaughran M, Feddock M, Batalov S, et al. A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants. Am J Hum Genet 2019;105:719-33. https://doi.org/10.1016/j.ajhg.2019.08.009
  41. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in medicine : official journal of the American College of Medical Genetics 2015;17:405-24. https://doi.org/10.1038/gim.2015.30
  42. Deignan JL, Chung WK, Kearney HM, Monaghan KG, Rehder CW, Chao EC. Points to consider in the reevaluation and reanalysis of genomic test results: a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2019;21:1267-70. https://doi.org/10.1038/s41436-019-0478-1
  43. SoRelle JA, Thodeson DM, Arnold S, Gotway G, Park JY. Clinical Utility of Reinterpreting Previously Reported Genomic Epilepsy Test Results for Pediatric Patients. JAMA Pediatr 2019;173:e182302. https://doi.org/10.1001/jamapediatrics.2018.2302
  44. Kalia SS, Adelman K, Bale SJ, Chung WK, Eng C, Evans JP, et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genet Med 2017;19:249-55. https://doi.org/10.1038/gim.2016.190
  45. Ethical and policy issues in genetic testing and screening of children. Pediatrics 2013;131:620-2. https://doi.org/10.1542/peds.2012-3680
  46. Tan W, Airik R. Primary coenzyme Q10 nephropathy, a potentially treatable form of steroid-resistant nephrotic syndrome. Pediatr Nephrol 2021. doi: 10.1007/s00467-020-04914-8.
  47. Madariaga L, Garcia-Castano A, Ariceta G, Martinez-Salazar R, Aguayo A, Castano L. Variable phenotype in HNF1B mutations: extrarenal manifestations distinguish affected individuals from the population with congenital anomalies of the kidney and urinary tract. Clin Kidney J 2019;12:373-9. https://doi.org/10.1093/ckj/sfy102
  48. Sanyanusin P, McNoe LA, Sullivan MJ, Weaver RG, Eccles MR. Mutation of PAX2 in two siblings with renal-coloboma syndrome. Hum Mol Genet 1995;4:2183-4. https://doi.org/10.1093/hmg/4.11.2183
  49. Ruf RG, Xu PX, Silvius D, Otto EA, Beekmann F, Muerb UT, et al. SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes. Proc Natl Acad Sci U S A 2004;101:8090-5. https://doi.org/10.1073/pnas.0308475101
  50. Kohlhase J, Wischermann A, Reichenbach H, Froster U, Engel W. Mutations in the SALL1 putative transcription factor gene cause Townes-Brocks syndrome. Nat Genet 1998;18:81-3. https://doi.org/10.1038/ng0198-81
  51. Van Esch H, Groenen P, Nesbit MA, Schuffenhauer S, Lichtner P, Vanderlinden G, et al. GATA3 haplo-insufficiency causes human HDR syndrome. Nature 2000;406:419-22. https://doi.org/10.1038/35019088
  52. Chernin G, Vega-Warner V, Schoeb DS, Heeringa SF, Ovunc B, Saisawat P, et al. Genotype/phenotype correlation in nephrotic syndrome caused by WT1 mutations. Clin J Am Soc Nephrol 2010;5:1655-62. https://doi.org/10.2215/CJN.09351209
  53. ACMG Board of Directors. Points to consider for informed consent for genome/exome sequencing. Genet Med 2013;15:748-9. https://doi.org/10.1038/gim.2013.94
  54. Connaughton DM, Kennedy C, Shril S, Mann N, Murray SL, Williams PA, et al. Monogenic causes of chronic kidney disease in adults. Kidney Int 2019;95:914-28. https://doi.org/10.1016/j.kint.2018.10.031
  55. Cheong HI. Genetic tests in children with steroid-resistant nephrotic syndrome. Kidney Res Clin Pract 2020;39:7-16. https://doi.org/10.23876/j.krcp.20.001
  56. Ayme S, Bockenhauer D, Day S, Devuyst O, Guay-Woodford LM, Ingelfinger JR, et al. Common Elements in Rare Kidney Diseases: Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney Int 2017;92:796-808. https://doi.org/10.1016/j.kint.2017.06.018