Reverse Phenotyping after Whole-Exome Sequencing in Steroid-Resistant Nephrotic Syndrome.

Landini S1,2,3, Mazzinghi B4, Becherucci F4, Allinovi M2,3, Provenzano A1,3, Palazzo V1, Ravaglia F4, Artuso R1, Bosi E2, Stagi S5, Sansavini G4, Guzzi F2,3,4, Cirillo L4, Vaglio A2,3,4, Murer L6, Peruzzi L7, Pasini A8, Materassi M4, Roperto RM4, Anders HJ9, Rotondi M10, Giglio SR1,2,3, Romagnani P11,3,4.

Author information

1: Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy.
2: Department of Clinical and Experimental Biomedical Sciences "Mario Serio,".
3: Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), and.
4: Nephrology and Dialysis Unit, Meyer Children's University Hospital, Florence, Italy.
5: Department of Health Sciences, University of Florence, Florence, Italy.
6: Pediatric Nephrology Dialysis and Transplant Unit, Department of Pediatrics, University of Padua, Padua, Italy.
7: Pediatric Nephrology Unit, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Turin, Italy.
8: Nephrology and Dialysis Unit, Department of Pediatrics, Azienda Ospedaliero Universitaria, Policlinico Sant'Orsola-Malpighi, Bologna, Italy.
9: Medizinische Klinik and Poliklinik IV, Klinikum der Ludwig Maximilians University (LMU) München, München, Germany; and.
10: Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), University of Pavia, Pavia, Italy.
11: Department of Clinical and Experimental Biomedical Sciences "Mario Serio," paola.romagnani@unifi.it sabrina.giglio@meyer.it.

Abstract

BACKGROUND AND OBJECTIVES:

Nephrotic syndrome is a typical presentation of genetic podocytopathies but occasionally other genetic nephropathies can present as clinically indistinguishable phenocopies. We hypothesized that extended genetic testing followed by reverse phenotyping would increase the diagnostic rate for these patients.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS:

All patients diagnosed with nephrotic syndrome and referred to our center between 2000 and 2018 were assessed in this retrospective study. When indicated, whole-exome sequencing and in silico filtering of 298 genes related to CKD were combined with subsequent reverse phenotyping in patients and families. Pathogenic variants were defined according to current guidelines of the American College of Medical Genetics.

RESULTS:

A total of 111 patients (64 steroid-resistant and 47 steroid-sensitive) were included in the study. Not a single pathogenic variant was detected in the steroid-sensitive group. Overall, 30% (19 out of 64) of steroid-resistant patients had pathogenic variants in podocytopathy genes, whereas a substantial number of variants were identified in other genes, not commonly associated with isolated nephrotic syndrome. Reverse phenotyping, on the basis of a personalized diagnostic workflow, permitted to identify previously unrecognized clinical signs of an unexpected underlying genetic nephropathy in a further 28% (18 out of 64) of patients. These patients showed similar multidrug resistance, but different long-term outcome, when compared with genetic podocytopathies.

CONCLUSIONS:

Reverse phenotyping increased the diagnostic accuracy in patients referred with the diagnosis of steroid-resistant nephrotic syndrome.

KEYWORDS:

United States; chronic kidney disease; chronic renal insufficiency; genetic testing; humans; medical genetics; multiple drug resistance; nephrotic syndrome; phenotype; retrospective studies; steroids; whole exome sequencing; whole-exome sequencing; workflow