Comparison between conventional and comprehensive sequencing approaches for genetic diagnosis of Alport syndrome

Abstract

Background Alport syndrome (AS) is a hereditary disease caused by mutations in COL4A3‐5 genes. Recently, comprehensive genetic analysis has become the first‐line diagnostic tool for AS. However, no reports comparing mutation identification rates between conventional sequencing and comprehensive screening have been published. Methods In this study, 441 patients clinically suspected of having AS were divided into two groups and compared. The initial mutational analysis method involved targeted exome sequencing using next‐generation sequencing (NGS) (n = 147, NGS group) or Sanger sequencing for COL4A3/COL4A4/COL4A5 (n = 294, Sanger group). Results In the NGS group, 126 patients (86%) were diagnosed with AS by NGS, while two had pathogenic mutations in other genes, NPHS1 and EYA1. Further, 239 patients (81%) were diagnosed with AS by initial analysis in the Sanger group. Thirteen patients who were negative for mutation detection in the Sanger group were analyzed by NGS; three were diagnosed with AS. Two had mutations in CLCN5 or LAMB2. The final variant detection rate was 90%. Discussion Our results reveal that Sanger sequencing and targeted exome sequencing have high diagnostic ability. NGS also has the advantage of detecting other inherited kidney diseases and pathogenic mutations missed by Sanger sequencing.

How to resolve confusion in the clinical setting for the diagnosis of heterozygous COL4A3 or COL4A4 gene variants? Discussion and suggestions from nephrologists

“…Due to the increased availability of NGS, the number of reports of ADAS is rapidly increasing [9,10,34]. For example, Yamamura et al performed genetic analysis for 390 families with suspicion of AS and showed that XLAS represented 74% of the cases, ARAS 9%, and ADAS 17%, which was notably higher than previously reported [10]. However, some experts still question the diagnosis of ADAS [14].…”

“…Although ADAS was thought to be an extremely rare disease and its disease concept was unclear for a long time, recent studies clarified genetic, clinical, and pathological features [6]. Furthermore, due to the rapid development of comprehensive genetic analysis technique using next-generation sequencing (NGS), it has been revealed that the number of patients with chronic kidney disease (CKD) caused by these gene mutations is far higher than previously expected [9][10][11][12], resulting in ongoing discussions regarding the diagnosis of this condition [13][14][15][16][17]. Here, we review the previous publications regarding TBMN and ADAS and discuss the diagnosis of cases with heterozygous COL4A3 or COL4A4 variants.…”

Genetic background, recent advances in molecular biology, and development of novel therapy in Alport syndrome

“…NPHS1 gene variants usually lead to a more severe phenotype of congenital nephrotic syndrome; however, some missense variants lead to milder phenotypes, such as in our case [ 14 ]. The overall diagnosis rate was 90% in this study [ 13 ].…”

“…We recently published the results of genetic testing for AS in Japan [ 13 ]. We conducted Sanger sequencing for 294 suspected AS cases and next-generation sequencing (NGS) for 147 suspected AS cases.…”

IgA nephropathy suspected to be combined with Fabry disease or Alport syndrome: a case report

“…However, the results of patients with threonine mutation to methionine do not support Alport syndrome. [17][18][19] Multidrug combination is mainly used to slow progress of disease. Target therapy is expected to change the prospects of IgAN treatment strategies.…”