Targeted long-read sequencing identified a causal structural variant in X-linked nephrogenic diabetes insipidus

• Published in: BMC medical genomics Vol. 17; no. 1; pp. 29 - 7
• Main Authors: Strych, Lukáš, Černá, Monika, Hejnalová, Markéta, Zavoral, Tomáš, Komrsková, Pavla, Tejcová, Jitka, Bitar, Ibrahim, Sládková, Eva, Sýkora, Josef, Šubrt, Ivan
• Format: Journal Article
• Language: English
• Published: London BioMed Central 22.01.2024; BioMed Central Ltd; BMC
• Subjects: Analysis; AVPR2 deletion; AVPR2 gene; Biomedical and Life Sciences; Biomedicine; Breakpoint analysis; Breakpoints; Care and treatment; Development and progression; Diabetes; Diabetes insipidus; Diabetes Insipidus, Nephrogenic - genetics; Diabetes Mellitus; DNA sequencing; Dosage and administration; Failure to thrive; Female; Gene Deletion; Gene Expression; Gene mapping; Genetic aspects; Genetic counseling; Genetic screening; Genetic Testing; Heterozygote; Human Genetics; Humans; Hydrochlorothiazide; Kidney; Long-read sequencing; Male; Methods; Microarrays; Nephrogenic diabetes insipidus; Nucleotide sequencing; PacBio; Pediatrics; Polyuria; Rare Diseases; Urine; Czech Republic; Long-read sequencing; AVPR2 deletion; Breakpoint analysis; Nephrogenic diabetes insipidus; PacBio
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/s12920-024-01801-1

Background X-linked nephrogenic diabetes insipidus (NDI) is a rare genetic renal disease caused by pathogenic variants in the AVPR2 gene. Single nucleotide variants and small insertions/deletions in AVPR2 are reliably detected by routine clinical sequencing. Nevertheless, structural variants involving AVPR2 are challenging to identify accurately by conventional genetic testing. Here, we report a novel deletion of AVPR2 in a Czech family identified for the first time by targeted long-read sequencing (T-LRS). Methods A male proband with X-linked NDI underwent clinical sequencing of the AVPR2 gene that failed and thus indicated possible whole-gene deletion. Therefore, PCR mapping and subsequent targeted long-read sequencing (T-LRS) using a Pacific Biosciences sequencer were applied to search for the suspected deletion. To validate the deletion breakpoints and prove variant segregation in the family with X-linked NDI, Sanger sequencing of the deletion junction was performed. Quantitative real-time PCR was further carried out to confirm the carrier status of heterozygous females. Results By T-LRS, a novel 7.5 kb deletion of AVPR2 causing X-linked NDI in the proband was precisely identified. Sanger sequencing of the deletion junction confirmed the variant breakpoints and detected the deletion in the probands´ mother, maternal aunt, and maternal cousin with X-linked NDI. The carrier status in heterozygous females was further validated by quantitative real-time PCR. Conclusions Identifying the 7.5 kb deletion gave a precise molecular diagnosis for the proband, enabled genetic counselling and genetic testing for the family, and further expanded the spectrum of structural variants causing X-linked NDI. Our results also show that T-LRS has significant potential for accurately identifying putative structural variants.