Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome

Svjetlana Lovric, Humphrey Fang, Virginia Vega-Warner, Carolin E. Sadowski, Heon Yung Gee, Jan Halbritter, Shazia Ashraf, Pawaree Saisawat, Neveen A. Soliman, Jameela A. Kari, Edgar A. Otto, Friedhelm Hildebrandt

Research output: Contribution to journalArticle

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Abstract

Background and objectives In steroid-resistant nephrotic syndrome (SRNS), >21 single-gene causes are known. However,mutation analysis of all known SRNS genes is time and cost intensive. This report describes a newhighthroughput method of mutation analysis using a PCR-based microfluidic technology that allows rapid simultaneous mutation analysis of 21 single-gene causes of SRNS in a large number of individuals. Design, setting, participants, & measurements This study screened individuals with SRNS; samples were submitted for mutation analysis from international sources between 1996 and 2012. For proof of principle, a pilot cohort of 48 individuals who harbored known mutations in known SRNS genes was evaluated. After improvements to the method, 48 individuals with an unknown cause of SRNS were then examined in a subsequent diagnostic study. The analysis included 16 recessive SRNS genes and 5 dominant SRNS genes. A 10- fold primer multiplexing was applied, allowing PCR-based amplification of 474 amplicons in 21 genes for 48 DNA samples simultaneously. Forty-eight individuals were indexed in a barcode PCR, and high-throughput sequencing was performed. All disease-causing variants were confirmed via Sanger sequencing. Results The pilot study identified the genetic cause of disease in 42 of 48 (87.5%) of the affected individuals. The diagnostic study detected the genetic cause of disease in 16 of 48 (33%) of the affected individuals with a previously unknown cause of SRNS. Seven novel disease-causing mutations in PLCE1 (n=5), NPHS1 (n=1), and LAMB2 (n=1) were identified in <3 weeks. Use of this method could reduce costs to 1/29th of the cost of Sanger sequencing. Conclusion This highly parallel approach allows rapid (<3weeks)mutation analysis of 21 genes known to cause SRNS at a greatly reduced cost (1/29th) compared with traditional mutation analysis techniques. It detects mutations in about 33% of childhood-onset SRNS cases.

Original languageEnglish
Pages (from-to)1109-1116
Number of pages8
JournalClinical Journal of the American Society of Nephrology
Volume9
Issue number6
DOIs
Publication statusPublished - 2014 Jan 1

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Nephrotic Syndrome
Steroids
Mutation
Genes
Costs and Cost Analysis
Inborn Genetic Diseases
Polymerase Chain Reaction
Dominant Genes
Microfluidics
Technology

All Science Journal Classification (ASJC) codes

  • Epidemiology
  • Critical Care and Intensive Care Medicine
  • Nephrology
  • Transplantation

Cite this

Lovric, Svjetlana ; Fang, Humphrey ; Vega-Warner, Virginia ; Sadowski, Carolin E. ; Gee, Heon Yung ; Halbritter, Jan ; Ashraf, Shazia ; Saisawat, Pawaree ; Soliman, Neveen A. ; Kari, Jameela A. ; Otto, Edgar A. ; Hildebrandt, Friedhelm. / Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome. In: Clinical Journal of the American Society of Nephrology. 2014 ; Vol. 9, No. 6. pp. 1109-1116.
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title = "Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome",
abstract = "Background and objectives In steroid-resistant nephrotic syndrome (SRNS), >21 single-gene causes are known. However,mutation analysis of all known SRNS genes is time and cost intensive. This report describes a newhighthroughput method of mutation analysis using a PCR-based microfluidic technology that allows rapid simultaneous mutation analysis of 21 single-gene causes of SRNS in a large number of individuals. Design, setting, participants, & measurements This study screened individuals with SRNS; samples were submitted for mutation analysis from international sources between 1996 and 2012. For proof of principle, a pilot cohort of 48 individuals who harbored known mutations in known SRNS genes was evaluated. After improvements to the method, 48 individuals with an unknown cause of SRNS were then examined in a subsequent diagnostic study. The analysis included 16 recessive SRNS genes and 5 dominant SRNS genes. A 10- fold primer multiplexing was applied, allowing PCR-based amplification of 474 amplicons in 21 genes for 48 DNA samples simultaneously. Forty-eight individuals were indexed in a barcode PCR, and high-throughput sequencing was performed. All disease-causing variants were confirmed via Sanger sequencing. Results The pilot study identified the genetic cause of disease in 42 of 48 (87.5{\%}) of the affected individuals. The diagnostic study detected the genetic cause of disease in 16 of 48 (33{\%}) of the affected individuals with a previously unknown cause of SRNS. Seven novel disease-causing mutations in PLCE1 (n=5), NPHS1 (n=1), and LAMB2 (n=1) were identified in <3 weeks. Use of this method could reduce costs to 1/29th of the cost of Sanger sequencing. Conclusion This highly parallel approach allows rapid (<3weeks)mutation analysis of 21 genes known to cause SRNS at a greatly reduced cost (1/29th) compared with traditional mutation analysis techniques. It detects mutations in about 33{\%} of childhood-onset SRNS cases.",
author = "Svjetlana Lovric and Humphrey Fang and Virginia Vega-Warner and Sadowski, {Carolin E.} and Gee, {Heon Yung} and Jan Halbritter and Shazia Ashraf and Pawaree Saisawat and Soliman, {Neveen A.} and Kari, {Jameela A.} and Otto, {Edgar A.} and Friedhelm Hildebrandt",
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Lovric, S, Fang, H, Vega-Warner, V, Sadowski, CE, Gee, HY, Halbritter, J, Ashraf, S, Saisawat, P, Soliman, NA, Kari, JA, Otto, EA & Hildebrandt, F 2014, 'Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome', Clinical Journal of the American Society of Nephrology, vol. 9, no. 6, pp. 1109-1116. https://doi.org/10.2215/CJN.09010813

Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome. / Lovric, Svjetlana; Fang, Humphrey; Vega-Warner, Virginia; Sadowski, Carolin E.; Gee, Heon Yung; Halbritter, Jan; Ashraf, Shazia; Saisawat, Pawaree; Soliman, Neveen A.; Kari, Jameela A.; Otto, Edgar A.; Hildebrandt, Friedhelm.

In: Clinical Journal of the American Society of Nephrology, Vol. 9, No. 6, 01.01.2014, p. 1109-1116.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome

AU - Lovric, Svjetlana

AU - Fang, Humphrey

AU - Vega-Warner, Virginia

AU - Sadowski, Carolin E.

AU - Gee, Heon Yung

AU - Halbritter, Jan

AU - Ashraf, Shazia

AU - Saisawat, Pawaree

AU - Soliman, Neveen A.

AU - Kari, Jameela A.

AU - Otto, Edgar A.

AU - Hildebrandt, Friedhelm

PY - 2014/1/1

Y1 - 2014/1/1

N2 - Background and objectives In steroid-resistant nephrotic syndrome (SRNS), >21 single-gene causes are known. However,mutation analysis of all known SRNS genes is time and cost intensive. This report describes a newhighthroughput method of mutation analysis using a PCR-based microfluidic technology that allows rapid simultaneous mutation analysis of 21 single-gene causes of SRNS in a large number of individuals. Design, setting, participants, & measurements This study screened individuals with SRNS; samples were submitted for mutation analysis from international sources between 1996 and 2012. For proof of principle, a pilot cohort of 48 individuals who harbored known mutations in known SRNS genes was evaluated. After improvements to the method, 48 individuals with an unknown cause of SRNS were then examined in a subsequent diagnostic study. The analysis included 16 recessive SRNS genes and 5 dominant SRNS genes. A 10- fold primer multiplexing was applied, allowing PCR-based amplification of 474 amplicons in 21 genes for 48 DNA samples simultaneously. Forty-eight individuals were indexed in a barcode PCR, and high-throughput sequencing was performed. All disease-causing variants were confirmed via Sanger sequencing. Results The pilot study identified the genetic cause of disease in 42 of 48 (87.5%) of the affected individuals. The diagnostic study detected the genetic cause of disease in 16 of 48 (33%) of the affected individuals with a previously unknown cause of SRNS. Seven novel disease-causing mutations in PLCE1 (n=5), NPHS1 (n=1), and LAMB2 (n=1) were identified in <3 weeks. Use of this method could reduce costs to 1/29th of the cost of Sanger sequencing. Conclusion This highly parallel approach allows rapid (<3weeks)mutation analysis of 21 genes known to cause SRNS at a greatly reduced cost (1/29th) compared with traditional mutation analysis techniques. It detects mutations in about 33% of childhood-onset SRNS cases.

AB - Background and objectives In steroid-resistant nephrotic syndrome (SRNS), >21 single-gene causes are known. However,mutation analysis of all known SRNS genes is time and cost intensive. This report describes a newhighthroughput method of mutation analysis using a PCR-based microfluidic technology that allows rapid simultaneous mutation analysis of 21 single-gene causes of SRNS in a large number of individuals. Design, setting, participants, & measurements This study screened individuals with SRNS; samples were submitted for mutation analysis from international sources between 1996 and 2012. For proof of principle, a pilot cohort of 48 individuals who harbored known mutations in known SRNS genes was evaluated. After improvements to the method, 48 individuals with an unknown cause of SRNS were then examined in a subsequent diagnostic study. The analysis included 16 recessive SRNS genes and 5 dominant SRNS genes. A 10- fold primer multiplexing was applied, allowing PCR-based amplification of 474 amplicons in 21 genes for 48 DNA samples simultaneously. Forty-eight individuals were indexed in a barcode PCR, and high-throughput sequencing was performed. All disease-causing variants were confirmed via Sanger sequencing. Results The pilot study identified the genetic cause of disease in 42 of 48 (87.5%) of the affected individuals. The diagnostic study detected the genetic cause of disease in 16 of 48 (33%) of the affected individuals with a previously unknown cause of SRNS. Seven novel disease-causing mutations in PLCE1 (n=5), NPHS1 (n=1), and LAMB2 (n=1) were identified in <3 weeks. Use of this method could reduce costs to 1/29th of the cost of Sanger sequencing. Conclusion This highly parallel approach allows rapid (<3weeks)mutation analysis of 21 genes known to cause SRNS at a greatly reduced cost (1/29th) compared with traditional mutation analysis techniques. It detects mutations in about 33% of childhood-onset SRNS cases.

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