Promises and pitfalls of whole-exome sequencing exemplified by a nephrotic syndrome family

  • Mara Sanches GuaragnaEmail author
  • Anna Cristina Gervásio de Brito Lutaif
  • Marcela Lopes de Souza
  • Andréa Trevas Maciel-Guerra
  • Vera Maria Santoro Belangero
  • Gil Guerra-Júnior
  • Maricilda Palandi de Mello
Original Article


High-throughput techniques such as whole-exome sequencing (WES) show promise for the identification of candidate genes that underlie Mendelian diseases such as nephrotic syndrome (NS). These techniques have enabled the identification of a proportion of the approximately 54 genes associated with NS. However, the main pitfall of using WES in clinical and research practice is the identification of multiple variants, which hampers interpretation during downstream analysis. One useful strategy is to evaluate the co-inheritance of rare variants in affected family members. Here, we performed WES of a patient with steroid-resistant NS (SRNS) and intermittent microhematuria. Currently, 15 years after kidney transplantation, this patient presents normal kidney function. The patient was found to be homozygous for a rare MYO1E stop-gain variant, and was heterozygous for rare variants in NS-associated genes, COL4A4, KANK1, LAMB2, ANLN, E2F3, and APOL1. We evaluated the presence or absence of these variants in both parents and 11 siblings, three of whom exhibited a milder phenotype of the kidney disease. Analysis of variant segregation in the family, indicated the MYO1E stop-gain variant as the putative causal variant underlying the kidney disease in the patient and two of her affected sisters. Two secondary variants in COL4A4—identified in some other affected family members—require further functional studies to determine whether they play a role in the development of microhematuria in affected family members. Our data illustrate the difficulties in distinguishing the causal pathogenic variants from incidental findings after WES-based variant analysis, especially in heterogenous genetic conditions, such as NS.


MYO1E Stop-gain variant Steroid-resistant nephrotic syndrome Whole-exome sequencing Incidental findings Kidney disease 



This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP—2015/20502-6 to MPdeM, FAPESP—2013/24088-4 to MSG) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq—441506/2014-3 to GG-J).

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Ethical statement

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Supplementary material

438_2019_1609_MOESM1_ESM.docx (5.7 mb)
Supplementary material 1 (DOCX 5805 kb)


  1. Al-Hamed MH, Al-Sabban E, Al-Mojalli H et al (2013) A molecular genetic analysis of childhood nephrotic syndrome in a cohort of Saudi Arabian families. J Hum Genet 58:480–489CrossRefGoogle Scholar
  2. Barker D, Hostikka S, Zhou J, Chow L, Oliphant A, Gerken S, Gregory M, Skolnick M, Atkin C, Tryggvason K (1990) Identification of mutations in the COL4A5 collagen gene in Alport syndrome. Science 248(4960):1224–1227CrossRefGoogle Scholar
  3. Benoit G, Machuca E, Antignac C (2010) Hereditary nephrotic syndrome: a systematic approach for genetic testing and a review of associated podocyte gene mutations. Pediatr Nephrol 25:1621–1632. CrossRefGoogle Scholar
  4. Bierzynska A, McCarthy HJ, Soderquest K et al (2017a) Genomic and clinical profiling of a national nephrotic syndrome cohort advocates a precision medicine approach to disease management. Kidney Int 91:937–947. CrossRefGoogle Scholar
  5. Bierzynska A, Soderquest K, Dean P et al (2017b) MAGI2 mutations cause congenital nephrotic syndrome. J Am Soc Nephrol 28:1614–1621. CrossRefGoogle Scholar
  6. Bullich G, Trujillano D, Santín S et al (2015) Targeted next-generation sequencing in steroid-resistant nephrotic syndrome: mutations in multiple glomerular genes may influence disease severity. Eur J Hum Genet 23:1192–1199. CrossRefGoogle Scholar
  7. Cheong HI, Han HW, Park HW et al (2000) Early recurrent nephrotic syndrome after renal transplantation in children with focal segmental glomerulosclerosis. Nephrol Dial Transplant 15:78–81CrossRefGoogle Scholar
  8. Chew C, Lennon R (2018) Basement membrane defects in genetic kidney diseases. Front Pediatr 6:11. CrossRefGoogle Scholar
  9. Feltran LS, Varela P, Silva ED et al (2017) Targeted Next-generation sequencing in brazilian children with nephrotic syndrome submitted to renal transplant. Transplantation 101:2905–2912. CrossRefGoogle Scholar
  10. Guaragna MS, Lutaif ACGB, Piveta CSC et al (2013) Two distinct WT1 mutations identified in patients and relatives with isolated nephrotic proteinuria. Biochem Biophys Res Commun. Google Scholar
  11. Guaragna MS, Lutaif ACGB, Piveta CSC et al (2015) NPHS2 mutations account for only 15% of nephrotic syndrome cases. BMC Med Genet 16:88. CrossRefGoogle Scholar
  12. Guaragna MS, Cleto TL, Souza ML et al (2016) NPHS1 gene mutations confirm congenital nephrotic syndrome in four Brazilian cases: a novel mutation is described. Nephrology 21:753–757. CrossRefGoogle Scholar
  13. Guenther RA, Kemp WL (2018) Delayed death due to saddle pulmonary thromboembolus in child with nephrotic syndrome induced by focal segmental glomerulosclerosis. Am J Forensic Med Pathol 39:370–374. Google Scholar
  14. ISKDC (1981) Primary nephrotic syndrome in children: clinical significance of histopathologic variants of minimal change and of diffuse mesangial hypercellularity. A report of the international study of kidney disease in children. Kidney Int 20:765–771CrossRefGoogle Scholar
  15. Lennon R, Stuart HM, Bierzynska A et al (2015) Coinheritance of COL4A5 and MYO1E mutations accentuate the severity of kidney disease. Pediatr Nephrol 30:1459–1465. CrossRefGoogle Scholar
  16. Malone AF, Phelan PJ, Hall G et al (2014) Rare hereditary COL4A3/COL4A4 variants may be mistaken for familial focal segmental glomerulosclerosis. Kidney Int 86:1253–1259. CrossRefGoogle Scholar
  17. Mele C, Iatropoulos P, Donadelli R et al (2011) MYO1E mutations and childhood familial focal segmental glomerulosclerosis. N Engl J Med 365:295–306. CrossRefGoogle Scholar
  18. Miner JH (2014) Pathology vs. molecular genetics: (re)defining the spectrum of Alport syndrome. Kidney Int 86:1081–1083. CrossRefGoogle Scholar
  19. Papazachariou L, Papagregoriou G, Hadjipanagi D et al (2017) Frequent COL4 mutations in familial microhematuria accompanied by later-onset Alport nephropathy due to focal segmental glomerulosclerosis. Clin Genet 92:517–527. CrossRefGoogle Scholar
  20. Richards S, Aziz N, Bale S et al (2015) 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. Genet Med 17:405–424. CrossRefGoogle Scholar
  21. Sadowski CE, Lovric S, Ashraf S et al (2014) A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome. J Am Soc Nephrol 26:1279–1289. CrossRefGoogle Scholar
  22. Sampson MG, Pollak MR (2015) Opportunities and challenges of genotyping patients with nephrotic syndrome in the genomic era. Semin Nephrol 35:212–221. CrossRefGoogle Scholar
  23. Sampson MG, Hodgin JB, Kretzler M (2015) Defining nephrotic syndrome from an integrative genomics perspective. Pediatr Nephrol 30:51–63. (quiz 59) CrossRefGoogle Scholar
  24. Sanna-Cherchi S, Burgess KE, Nees SN et al (2011) Exome sequencing identified MYO1E and NEIL1 as candidate genes for human autosomal recessive steroid-resistant nephrotic syndrome. Kidney Int 80:389–396. CrossRefGoogle Scholar
  25. Savige J, Ariani F, Mari F et al (2018) Expert consensus guidelines for the genetic diagnosis of Alport syndrome. Pediatr Nephrol. Google Scholar
  26. Schäffer AA (2013) Digenic inheritance in medical genetics. J Med Genet 50:641–652. CrossRefGoogle Scholar
  27. Smith JM, Stablein DM, Munoz R et al (2007) Contributions of the transplant registry: the 2006 annual report of the north american pediatric renal trials and collaborative studies (NAPRTCS). Pediatr Transplant 11:366–373. CrossRefGoogle Scholar
  28. Wakasugi M, Kazama JJ, Narita I (2018) Premature mortality due to nephrotic syndrome and the trend in nephrotic syndrome mortality in Japan, 1995–2014. Clin Exp Nephrol 22:55–60. CrossRefGoogle Scholar
  29. Wang M, Chun J, Genovese G et al (2019) Contributions of rare gene variants to familial and sporadic FSGS. J Am Soc Nephrol. (ASN.2019020152) Google Scholar
  30. Weber S, Büscher AK, Hagmann H et al (2016) Dealing with the incidental finding of secondary variants by the example of SRNS patients undergoing targeted next-generation sequencing. Pediatr Nephrol 31:73–81. CrossRefGoogle Scholar
  31. Wiggins RC (2007) The spectrum of podocytopathies: a unifying view of glomerular diseases. Kidney Int 71:1205–1214. CrossRefGoogle Scholar
  32. Wong CJ, Moxey-Mims M, Jerry-Fluker J et al (2012) CKiD (CKD in Children) prospective cohort study: a review of current findings. Am J Kidney Dis 60:1002–1011. CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Laboratory of Human Molecular Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG)State University of Campinas, UNICAMPCampinasBrazil
  2. 2.Integrated Center of Pediatric Nephrology (CIN), Department of Pediatrics, School of Medical Sciences (FCM)State University of Campinas, UNICAMPCampinasBrazil
  3. 3.Department of Medical Genetics, School of Medical Sciences (FCM)UNICAMPCampinasBrazil
  4. 4.Department of Pediatrics, School of Medical Sciences (FCM)UNICAMPCampinasBrazil
  5. 5.Growth and Development Laboratory, Center for Investigation in Pediatrics (CIPED), School of Medical Sciences (FCM)UNICAMPCampinasBrazil

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