Abstract
Background and Aims
Autosomal Polycystic kidney Disease (ADPKD; ORPHA 730), Alport Syndrome (AS; ORPHA 63) and Familial Haematuria (FH) are the most frequent inherited kidney diseases. Next-generation Sequencing (NGS) has facilitated their molecular identification. A multidisciplinary team from four hospitals, with nephrologists, pediatricians, and clinical and molecular geneticists, has been formed in the Spanish region of Murcia (1.5 million inhabitants) with the lab implementation of NGS. Our aim is to evaluate the genetic spectrum in AS, FH and ADPKD and the clinical utility of this comprehensive approach.
Method
During 1-year activity, 114 individuals with diagnostic suspicion of ADPKD, AS or FH have been evaluated by a coordinated clinical protocol with periodic cases discussions. A customized Agilent panel was designed to capture 113 genes associated with several genetic diseases, including some related to PKD, AS or Familial Haematuria (FH): PKD1, PKD2, PKHD1, HNF1β, COL4A1, COL4A3, COL4A4 and COL4A5. Interpretation of sequence variants was performed according to the American College of Medical Genetics and Genomics (ACMG) Guidelines. Sanger sequencing was performed to confirm variants identified by NGS and to segregate them in the families. Exon 1 of PKD1 gene was also sequenced by Sanger method, due to the suboptimal capture of this region by NGS.
Results
We detected genetic variants in 63 patients (55.3%), pathogenic or probably pathogenic variants in 54 (47.8%). 31 patients had a variant in AS associated genes: 10 in COL4A3, 18 in COL4A4, 2 in COL4A1 and 1 in COL4A5. There were 13 pathogenic variants, 12 probably pathogenic variants and 6 variants of uncertain clinical significance (VUCS). Among them, 27 had an AD inheritance, 1 AR and 3 were sporadic. All the patients with any variant had microhaematuria, a 68% had also proteinuria, and mean eGFR at diagnostic was 63.79±21 ml/min/1.73m2. 61% had auditory disturbances and 11% ophthalmologic alterations. 4 of them had underwent kidney biopsy previously, but 3 were not adequately diagnosed, so they were reclassified after the molecular diagnosis. In total, 16 kidney biopsies were avoided by the genetic diagnosis. On the other hand, 29 patients had a variant in the ADPKD associated genes: 24 in PKD1 and 5 in PKD2. There were 20 pathogenic variants and 4 probably pathogenic variants, and their inheritance was confirmed AD in 27 patients, whereas new sporadic mutations were identified in 2 patients. 22 patients had big or enormous kidneys on sonography, although 7 had normal size. Hepatic cysts were present on 5%. 19 patients had hypertension, with a mean age of diagnosis of 47±14 years. Additionally, 1 patient was diagnosed on AR polycystic disease with homozygosity PKHD1 pathogenic variant. Among all the scope, familial history was clearly present in 43 patients, uncertain in 11, and not present in 9 patients.
Conclusion
The multidisciplinary approach to hereditary kidney diseases, with the active participation of nephrologists and clinical geneticists, has allowed a molecular diagnostic yield of 48% among patients with AS and ADPKD, employing NGS technology. This has led to a quicker diagnostic result in our region, the reclassification of some patient’s diagnosis, a decrease in invasive diagnostic procedures (such as kidney biopsy) and the correspondent adverse events and cost savings. Additionally, the AD inheritance pattern in AS has been confirmed as the most frequent in the region. The active participation of nephrologists in genomic medicine teams results in a better characterization of the hereditary kidney diseases, helping in the genetic variant interpretation and management of these patients and their families.
Clinical utility of PKD2 mutation testing in a polycystic kidney disease cohort attending a specialist nephrology out-patient clinic
