Diagnostics of genetic disorders with whole genome and mRNA sequencing : doctoral dissertation

Bergant, Gaber (author), Peterlin, Borut (mentor)

Despite the widespread use of exome sequencing (ES), over 60% of patients with suspected genetic diseases remain undiagnosed. Additionally, the precise genetic cause of many rare diseases remains obscure. This study addresses these two challenges using genome sequencing (GS) in patients with suspected diverse genetic diseases and RNA sequencing in patients with suspected hereditary myopathies. In this study we tested two hypotheses: (1) GS and RNA sequencing improve the diagnostic yield of genetic diagnostics and (2) enable the discovery of potential new disease mechanisms and genes previously not yet associated with genetic diseases. Employing GS and RNA sequencing, we achieved a diagnostic yield of 12.5% (16/128 patients) and 18.2% (2/11 patients) in previously negative ES patients, respectively. Additionally, both methods detected variants that could not be detected by ES. We also identified five candidate genes for new genetic diseases, which we thoroughly investigated, and one genetic variant which we propose causes the disease through a novel mechanism. Our results confirm both of our initial hypotheses and contribute significantly to progress in human genetics. Furthermore, our study lays a solid foundation for future research aimed at applying comprehensive diagnostic methods to some of the most challenging cases in clinical genetics.

• Language: English
• Keywords: genetic diagnostics, genome sequencing, next-generation sequencing, rare disease, RNA sequencing
• Work type: Doctoral dissertation
• Typology: 2.08 - Doctoral Dissertation
• Organization: BF - Biotechnical Faculty
• Year: 2025
• PID: 20.500.12556/RUL-167864
• COBISS.SI-ID: 229332483
• Publication date in RUL: 18.03.2025

Secondary language

• Language: Slovenian
• Title: Diagnostika genetskih bolezni z uporabo sekvenciranja celotnega genoma in informacijske RNA : doktorska disertacija

Abstract

Kljub široki uporabi eksomskega sekvenciranja (ES) ostaja več kot 60 % bolnikov s sumom na genetske bolezni nediagnosticiranih, veliko redkih bolezni pa ima še nepoznane genetske vzroke. Ta disertacija naslavlja ta dva izziva genetske diagnostike z uporabo genomskega sekvenciranja (GS) pri bolnikih s sumom na raznovrstne genetske bolezni in sekvenciranja RNA pri bolnikih s sumom na dedne miopatije. Testirali smo dve hipotezi: (1) GS in RNA sekvenciranje izboljšata diagnostični izplen genetske diagnostike in (2) omogočata odkrivanje potencialnih novih mehanizmov bolezni in genov, ki še niso bili povezani z genetskimi boleznimi. Z GS in RNA sekvenciranjem smo dosegli 12,5 % (16/128 bolnikov) oziroma 18,2 % (2/11 bolnikov) dodatni diagnostični izplen v primerjavi z ES, z obema metodama pa smo odkrili različice, katerih ni mogoče zaznati z ES. Identificirali smo pet kandidatnih genov za nove genetske bolezni, katere smo temeljito raziskali in eno genetsko različico v znanem genu, za katero predlagamo, da povzroča bolezen preko novega mehanizma. Naši rezultati potrjujejo obe prvotno zastavljeni hipotezi, s čimer smo pokazali, da z obema pristopoma izboljšamo genetsko diagnostiko pri bolnikih z redkimi boleznimi, hkrati pa omogočata tudi odkrivanje novih genov in mehanizmov povezanih z genetskimi boleznimi pri človeku.

• Keywords: genetska diagnostika, genomsko sekvenciranje, sekvenciranje naslednje generacije, redke bolezni, RNA sekvenciranje