Pathogenic cryptic variants detectable through exome data reanalysis significantly increase the diagnostic yield in Joubert syndrome
Joubert syndrome (JS) is a genetically heterogeneous neurodevelopmental ciliopathy. Despite exome sequencing (ES), several patients remain undiagnosed. This study aims to increase the diagnostic yield by uncovering cryptic variants through targeted ES reanalysis. We first focused on 26 patients in whom ES only disclosed heterozygous pathogenic coding variants in a JS gene. We reanalyzed raw ES data searching for copy number variants (CNVs) and intronic variants affecting splicing. We validated CNVs through real-time PCR or chromosomal microarray, and splicing variants through RT-PCR or minigenes. Cryptic variants were then searched in additional 44 ES-negative JS individuals. We identified cryptic "second hits" in 14 of 26 children (54%) and biallelic cryptic variants in 3 of 44 (7%), reaching a definite diagnosis in 17 of 70 (overall diagnostic gain 24%). We show that CNVs and intronic splicing variants are a common mutational mechanism in JS; more importantly, we demonstrate that a significant proportion of such variants can be disclosed simply through a focused reanalysis of available ES data, with a significantly increase of the diagnostic yield especially among patients previously found to carry heterozygous coding variants in the KIAA0586, CC2D2A and CPLANE1 genes.
Authors
- Federica Morelli (ORCID: https://orcid.org/0000-0003-1239-9904)
- Ginevra Zanni (ORCID: https://orcid.org/0000-0002-6367-1843)
- Simone Gana (ORCID: https://orcid.org/0000-0001-6544-7135)
- Danijela Petković Ramadža (ORCID: https://orcid.org/0000-0002-8562-153X)
- Fulvio D’Abrusco (ORCID: https://orcid.org/0000-0003-2470-665X)
- Filippo Manti (ORCID: https://orcid.org/0000-0002-2012-8410)
- Renato Borgatti (ORCID: https://orcid.org/0000-0001-8165-4994)
- Sabrina Signorini (ORCID: https://orcid.org/0000-0002-3808-4372)
- Caterina Caputi (ORCID: https://orcid.org/0000-0001-5972-1185)
- Roberta Battini (ORCID: https://orcid.org/0000-0002-7889-1355)
- Fabio Sirchia (ORCID: https://orcid.org/0000-0002-4598-2023)
- Claudio Graziano (ORCID: https://orcid.org/0000-0003-3875-6869)
- Johannes R. Lemke (ORCID: https://orcid.org/0000-0002-4435-6610)
- Jessica Garau (ORCID: https://orcid.org/0000-0002-9885-1369)
- Enrico Bertini (ORCID: https://orcid.org/0000-0001-9276-4590)
- Valentina Serpieri (ORCID: https://orcid.org/0000-0002-3553-0066)
- Stefano D’Arrigo (ORCID: https://orcid.org/0000-0001-5188-9418)
- Elisa Giorgio (ORCID: https://orcid.org/0000-0003-4076-4649)
- Eugen Boltshauser
- Enza Maria Valente (ORCID: https://orcid.org/0000-0002-0600-6820)
- Romina Romaniello (ORCID: https://orcid.org/0000-0002-8709-6732)
- Arianna De Laurentiis (ORCID: https://orcid.org/0009-0001-9520-7666)
- Luca Cattaneo
- Cecilia Maria Taccagni
- Monica Boggioni
- Vincenzo Leuzzi
Institutions
- University of Pisa (IT)
- University Hospital Centre Zagreb (HR)
- University of Zagreb (HR)
- University of Pavia (IT)
- Foundation Center (US)
- Fondazione Istituto Neurologico Nazionale Casimiro Mondino (IT)
- Urology Foundation (GB)
- Bambino Gesù Children's Hospital (IT)
- Fondazione Stella Maris (IT)
- University Children's Hospital Zurich (CH)
- Istituti di Ricovero e Cura a Carattere Scientifico (IT)
- Fondazione IRCCS Istituto Neurologico Carlo Besta (IT)
- Sapienza University of Rome (IT)
- Leipzig University (DE)
- University of Lausanne (CH)
Publication Details
- Journal
- European Journal of Human Genetics
- Published
- 2024-10-11
- DOI
- https://doi.org/10.1038/s41431-024-01703-x
- Citations
- 6
- Primary Topic
- Genetic and Kidney Cyst Diseases
- Type
- article
- Field-Weighted Citation Impact
- 3.30
Funders
- Fondazione Telethon
- Ministero della Salute
- Ministero dell’Istruzione, dell’Università e della Ricerca