Supervisor: TÜ MRI professor Andres Metspalu.
Opponent: Professor Aarno Palotie, Wellcome Trust Sangeri Instituut ja Soome Molekulaarse Meditsiini Instituut, Helsinki Ülikool, Helsinki, Soome Vabariik
Genetic causes of inherited diseases have been extensively studied over the past several decades and a wide variety of molecular tests have been developed for diagnosing genetic disorders. However, the successful introduction of currently available tests into routine clinical practice is limited due to different reasons, for example a large number of DNA variations per disease, a low number of samples per rare disease per laboratory, turnaround time, high cost of setup and/or maintenance. Thus, the advances in molecular diagnostic medicine depend on the development and availability of new methods with the potential to solve above-mentioned shortcomings.
The aims of this thesis were to develop and evaluate the suitability of APEX (Arrayed Primer Extension) and APEX-2 microarray-based assays for the diagnosis and carrier screening of rare genetic diseases and for rapid molecular diagnosis of Down syndrome in clinical practice. The main advantages of the APEX/APEX-2 assay include its flexibility and single-step hybridization of the template, followed by primer extension, which make the assay relatively fast, simple, and robust with fewer components, pipetting steps, and manipulations in the workflow. The main outcomes of the current thesis include: i) a novel cost-effective cystic fibrosis (CF) test with a higher mutation detection capability for CF diagnosis and carrier screening in Caucasians, non-Caucasians, and individuals of mixed ethnicity, compared to assays currently available in diagnostic laboratories; ii) a novel diagnostic APEX microarray for simultaneous multigene mutation detection in nonsyndromic sensorineural hearing loss (SNHL) patients. The SNHL test allows the detection of genetic causes of deafness in children (and adults), improving medical management for patients and genetic counseling for families; iii) a novel BBS-ALMS test which is an efficient and cost-effective first-pass diagnostic screening tool for molecular analysis of Bardet-Biedl (BBS) and Alström syndrome (ALMS) patients, and iv) a novel T21 APEX-2 assay that could be used as a rapid pre-test to reduce parental anxiety during genetic counseling before final karyotyping.