Clinical exome sequencing is a powerful tool in the diagnostic flow of monogenic kidney diseases: an Italian experience

Abstract

Background A considerable minority of patients on waiting lists for kidney transplantation either have no diagnosis (and fall into the subset of undiagnosed cases) because kidney biopsy was not performed or histological findings were non-specific, or do not fall into any well-defined clinical category. Some of these patients might be affected by a previously unrecognised monogenic disease. Methods Through a multidisciplinary cooperative effort, we built an analytical pipeline to identify patients with chronic kidney disease (CKD) with a clinical suspicion of a monogenic condition or without a well-defined diagnosis. Following the stringent phenotypical and clinical characterization required by the flowchart, candidates meeting these criteria were further investigated by clinical exome sequencing followed by in silico analysis of 225 kidney-disease-related genes. Results By using an ad hoc web-based platform, we enrolled 160 patients from 13 different Nephrology and Genetics Units located across the Piedmont region over 15 months. A preliminary “remote” evaluation based on well-defined inclusion criteria allowed us to define eligibility for NGS analysis. Among the 138 recruited patients, 52 (37.7%) were children and 86 (62.3%) were adults. Up to 48% of them had a positive family history for kidney disease. Overall, applying this workflow led to the identification of genetic variants potentially explaining the phenotype in 78 (56.5%) cases. Conclusions These results underline the importance of clinical exome sequencing as a versatile and highly useful, non-invasive tool for genetic diagnosis of kidney diseases. Identifying patients who can benefit from targeted therapies, and improving the management of organ transplantation are further expected applications.

The role of genetic testing in the diagnostic workflow of pediatric patients with kidney diseases: the experience of a single institution

“…We previously reported on the design and set-up of a “kidney” gene panel that comprises > 400 genes all involved in different forms of kidney diseases [ 14 ]. For this study, we implemented analysis with subpanels focused on the specific clinical category of suspicion (e.g., CAKUT, glomerulopathy, tubulopathy, etc.)…”

“…Nucleic acid extraction from peripheral blood, analysis of DNA quality, library preparation and sequencing were performed as previously reported [ 14 ]. Raw data obtained from sequencing were converted in FASTQ files and then aligned with Enrichment 3.1.0 or DRAGEN Enrichment tools (Illumina) and mapped on TruSightOne Expanded v2.0 manifest using Homo Sapiens UCSC GRCh37 genome as reference to obtain single nucleotide variants, copy number variants (CNV) and structural variants vcf files.…”

Spectrum of genetic disorders and gene variants in the United Arab Emirates national population: insights from the CTGA database

“…This increase is mainly due to the enhanced ability to diagnose genetic disorders and a consequent surge in the reporting of such disorders within the past decade. With the advent and ease of access to technologies such as Whole Exome Sequencing (WES) and gene panel sequencing, diagnostic rates of genetic disorders have increased significantly ( Vaisitti et al, 2021 ; Sanchez-Luquez et al, 2022 ; Moundir et al, 2023 ). In fact, within our set of genetic disorders reported in the UAE, a significant portion comes from the utilization of such sequencing techniques on fairly large patient populations ( Al-Shamsi et al, 2016 ; Alsamri et al, 2020 ; Mahfouz et al, 2020 ; Saleh et al, 2021 ).…”

Spectrum of Genetic Disorders and Gene Variants in the United Arab Emirates National Population: Insights from the CTGA Database

“…This increase is mainly due to the enhanced ability to diagnose genetic disorders and a consequent surge in the reporting of such disorders within the past decade. With the advent and ease of access to technologies such as Whole Exome Sequencing (WES) and gene panel sequencing, diagnostic rates of genetic disorders have increased significantly (Vaisitti et al, 2021; Sanchez-Luquez et al, 2022; Moundir et al, 2023). In fact, within our set of genetic disorders reported in the UAE, a significant portion comes from the utilization of such high-throughput sequencing techniques on fairly large patient populations (Al-Shamsi et al, 2016; Alsamri et al, 2020; Mahfouz et al, 2020; Saleh et al, 2021).…”