Role of next generation sequencing (NGS) in the diagnosis of hereditary renal disease

Abstract

NGS is a new approach used to identify genetic mutations that may underline kidney disease. The advantages of NGS compared to Sanger sequencing are the ability to run multiple samples simultaneously, shorter turn-around time and lower cost. For example, compared to older methods that took weeks to complete, NGS can shorten the turn-around time for Alport syndrome diagnosis to just 6 days and the cost to 40%. In addition custom NGS can be designed to identify mutations in a selected group of genes associated with proteinuria and FSGS on renal biopsy. FSGS can be a histologic manifestation of a variety of glomerular diseases including specific podocyte gene mutations (NPHS2, PLC1E, CD2AP, TRPC6) but also glomerular basement membrane abnormalities due to COL4A3-5 mutations. Using custom designed NGS on 14 patients and 19 selected genes, we have identified novel and rare mutations in COLA3, COLA4 AND COLA5, but also mutations in LAMA5 in patients phenotyped as FSGS. Other patients with FSGS were found to have a 6p deletion in APOL1 that is known to be associated with the development of FSGS in African Americans. In this cohort, some patients had congenital hydronephrosis and VUR induced proteinuria. There was no history of familial disease. One of these patients unexpectedly was found to have a novel COLA3 mutation in addition to an expected SALL2 mutation known to be associated with urinary tract developmental anomalies. NGS results were verified using Sanger sequencing. The findings in this study suggest that NGS is a powerful method to identify specific structural changes in the genome that could not have been predicted by the histopathological phenotype. A high throughput approach for mutation analysis is more advantageous compared to single gene approaches and promises to become a clinically useful diagnostic tool.