ESPN 50th Annual Meeting

ESPN 2017


 
Clinical genetic testing using next generation sequencing in steroid-resistant nephrotic syndrome and Alport syndrome
ETHAN SEN 1 PHILIP DEAN 2 LAURA YARRAM-SMITH 2 AGNIESZKA BIERZYNSKA 1 GEOFF WOODWARD 2 CHRIS BUXTON 2 GEMMA DENNIS 2 GAVIN WELSH 1 MAGGIE WILLIAMS 2 MOIN SALEEM 1

1- BRISTOL RENAL, SCHOOL OF CLINICAL SCIENCES, UNIVERSITY OF BRISTOL, BRISTOL, UK
2- BRISTOL GENETICS LABORATORY, SOUTHMEAD HOSPITAL, BRISTOL, UK
 
Introduction:

Steroid-resistant nephrotic syndrome (SRNS) and Alport syndrome (AS) are rare diseases in children but may lead to end-stage renal failure requiring transplantation.  This study reports on the findings and utility of the first clinically-approved gene panel test for SRNS/AS using next generation sequencing (NGS).

Material and methods:

A customised gene panel test was developed using NGS of 37 genes associated with SRNS and AS.  Copy number variation (CNV) analysis to look for exon deletion and duplications was performed. Clinical data were collected from genetic referral forms and a bespoke proforma.  

Results:

A total of 240 patients (137 male) with disease onset ≤ 18 years were referred for diagnostic genetic testing from 12 countries.  The presentation was nephrotic syndrome (NS) in 220 and haematuria/AS in 20 patients.  The genetic diagnostic rate (GDR) for SRNS patients was 21.1% with pathogenic variants in 11 different genes, most commonly NPHS1, NPHS2 and WT1 (Table 1).  In two patients, CNV analysis revealed heterozygous novel deletions: exon 23-29 deletion in NPHS1 and exon 2 deletion in NPHS2 respectively.  In the haematuria/AS group, causative variants were found in COL4A3 and COL4A5 representing a GDR of 40%.  Importantly, COL4 likely-pathogenic variants were also found in patients unsuspected for AS.  Clinicians reported that genetic testing results assisted decisions about immunosuppression, biopsy and whether to use a close relative as a renal donor, and informed about risk of recurrence after transplant in SRNS patients.

 

Table 1: Genes with likely-pathogenic variants in patients ≤ 18 years with SRNS or haematuria / AS identified by NGS gene panel testing

 

Gene with likely-pathogenic variant

Steroid-resistant nephrotic syndrome (number of patients) (n=209)*

Haematuria / Alport syndrome (number of patients) (n=20)

NPHS1

12

0

WT1

9

0

NPHS2

7

0

LMX1B

4

0

LAMB2

3

0

MYH9

2

0

PLCE1

2

0

ACTN4

1

0

SMARCAL1

1

0

COL4A3

0

3

COL4A4

1

0

COL4A5

2

5

Total

44

8

 *None of the 11 patients with steroid-sensitive nephrotic syndrome had likely-pathogenic variants and so are not shown in this table.

 

Conclusions:

This study demonstrates that gene panel testing in routine clinical practice provides a genetic diagnosis in a significant number of patients presenting with SRNS or suspected AS.  The use of CNV analysis identified large deletions in two patients supporting the use of routine copy number analysis.  Use of clinical genetic testing after diagnosis of SRNS has the potential to stratify patients and assist decision-making regarding management.