Saudi Cultural Missions Theses & Dissertations
Permanent URI for this communityhttps://drepo.sdl.edu.sa/handle/20.500.14154/10
Browse
4 results
Search Results
Item Restricted Investigation of The Genetic Basis of Polycystic Ovarian Syndrome Through Exome Sequencing Studies in The Saudi Women(ARABIAN GULF UNIVERSITY, 2024) Alfifi, Yasmin Ahmad; Bakhiet, Moiz; Taha, Safa; Khan, Imran AliPolycystic ovarian syndrome (PCOS) is one of the raising endocrine and metabolic disorders in the reproductive-aged women. Rotterdam criteria is used in this study to screen the PCOS women based on hyperandrogenism, oligo-anovulation, and polycystic ovaries. Obesity is considered as a major factor for the development of PCOS along with the exacerbations of PCOS. Different formats of studies have been conducted in the PCOS women from Saudi Arabia, but none of them accurately recorded genetic basis of PCOS in Saudi women. This has led to a lack of focus on the PCOS disease in Saudi Arabia, which is now a common condition among Saudi women. Moreover, there are no exome sequencing studies were documented in the Saudi women with PCOS. Therefore, the aim of this study was to investigate the whole exome sequencing (WES) analysis in the Saudi women diagnosed with PCOS. This study selected 18 PCOS women based on the Rotterdam criteria and 8 healthy controls for the WES analysis. Additionally, we have enrolled anthropometric, biochemical, clinical details and measurements in all the 18 PCOS women and 8 control. A total of 5ml of peripheral blood was collected, 3ml was used for serum analysis, and 2 mL was used for molecular analysis. Genomic DNA was isolated, nanodrop was quantified, and then WES analysis was studied. The result in this study, altogether 96 missense variants in several genes were documented in 18 patients, which are related to PCOS. The study concludes that women with PCOS have primarily documented the rs141382822, rs747554207, rs74575904, rs56216806, and rs61752535 variants. These variants are associated with both endocrine and metabolic disorders associated with PCOS, and they play a significant role in the Saudi population.10 0Item Restricted Taxonomy and Diversification of Cyclamen L. Using Next-Generation Sequencing Approaches(University of Reading, 2023-10-27) Hubini, Ahmed; Culham, AlastairThere are 24 species of Cyclamen, which found predominantly in the Mediterranean region and its surrounding areas in Europe, Asia, and North Africa. Over the years, scientists have studied the genus morphologically, cytologically, and more recent, systematically to unravel the mystery surrounding its evolutionary past. Using Next-Generation Sequencing (NGS) techniques, we assembled complete chloroplast, nuclear ribosomal DNA, and 20 mitochondrial coding genes using multiple assemblers. Comparative analysis revealed that the chloroplast genomes in Cyclamen were largely similar to those of other angiosperms, with C. somalense being a unique case, displaying the loss of four ndh genes. Notably, ycf15 emerged as a pseudogene across the genus, similar to certain Primulaceae family members, suggesting its potential as a molecular marker for future investigations. Phylogenetic trees constructed based on the assembled genetic data displayed strong congruence, except for certain species that showed variations in their placement within the trees. The phylogenetic trees in this thesis showed the Cyclamen is monophyletic in the family Primulaceae. The mitochondrial-based tree was well-supported but remained unresolved, particularly in the Cilicium group, where a polytomy was observed. However, based on the trees, the results suggest that C. alpinum should belong to the Cilicium group instead of Coum. Additionally, C. africanum should be treated as a subspecies of hederifolium rather than a separate species. Furthermore, network approach was used to investigate the relationship in the Hederifolium group collected from Greece with different ploidy levels. Based on complete chloroplast sequences there are 17 distinct haplotypes and ten haplotypes based on nuclear ribosomal DNA. The results demonstrate a poor correlation between ploidy level and locations and current C. hederifolium subspecies classifications, due to limited genetic variation. The agreement between this thesis and the previous findings provides further support for the complex cytological characteristics exhibited by Cyclamen species within this group.11 0Item Restricted Monitoring Exceptional Responses in Patients with B-cell Malignancies(Saudi Digital Library, 2023-09-20) Alqahtani, Abdullah N M; Alqahtani, AbdullahResponse to cancer treatments can be highly variable; with some patients entering durable remissions, and others either failing to respond or relapsing early. Predicting which patients may derive long term responses and enter deep remissions remains a significant challenge. “Exceptional responders”, ie patients with prolonged and deep responses, where the majority fail to respond, represent a group of patients that could help us understand the mechanisms of treatment sensitivity and enable us to study the depth of minimal residual disease (MRD) required to sustain a durable response. I examined two cohorts of “exceptional responders” to two precision medicines to understand the molecular features, that could explain their durable response: a cohort of ten relapsed/refractory (R/R) patients with Mantle Cell Lymphoma (MCL) treated with Bruton’s Tyrosine Kinase (BTK) inhibitors and a small case series of two patients with Chronic Lymphocytic Leukaemia (CLL) treated with a CD52 antibody (alemtuzumab). Molecular features included mutational profiling, IGHV gene rearrangement, copy number variation and for the MCL cases t(11;14)(q13;q32) translocation. Interestingly, all but two MCL patients had truly unmutated IGHV and three patients had TP53 mutations, features otherwise associated with poor outcomes. The depth of response was assessed using patient-specific ddPCR assays or Lymphotrack. In two MCL cases, there was evidence of disease recurrence using ddPCR before clinical and radiological relapse. In a further two MCL cases, MRD remains undetectable. In one CLL patient, still in remission twenty years post-treatment, re- emergence of polyclonal B cells with absence of the original B-cell clone was observed. A MYD88 mutation from original tumour was undetectable by ddPCR. NGS and ddPCR methods may provide precision tools for monitoring exceptional responders and for early prediction of relapse. However, further validation will be required prior to implementation within the clinic.37 0Item Restricted The Causes of Retinal Dystrophy and The Development of More Comprehensive Screening Approach(2023) Yahya, Samar; Inglehearn, ChrisInherited retinal diseases (IRDs) are a group of genetically and phenotypically heterogenous disorders caused by variants in around 280 genes. Additional loci have also been localised to chromosomal regions, though the causative genes remain unknown. Recent improvements in screening technologies have increased the detection of pathogenic variants in IRD. This thesis describes the use of next generation sequencing (second (short-read) and third (long-read) generation sequencing) to find missing or hard to find pathogenic variants in IRD patients. The first results chapter describes use of whole exome sequencing to screen 24 individuals with syndromic and non-syndromic IRDs. This identified pathogenic variants in known genes in eight cases; CDHR1 (c.1527T>G, p.Y509*), RHO (c.284T>C, p.L95P), PRPF31 (c.797delC, p.S266*), CNGA3 (c.1088T>C, p.L363P), BBS10 (c.728- 731delAAGA, p. K243Ifs*15), USH2A (c.252T>G, p.C84W), ABCA4 (c.2588G>C, p.G863A and c.6089G>A, p.R2030Q), and SLC25A46 (c.670A>G, p.T224A). In addition, several candidate variants were highlighted for further investigation. In the second results chapter, seven patients with late onset macular dystrophy and one with age related macular degeneration were found to carry the same heterozygous ~126 kb deletion encompassing CRX, TPRX1 and SULT2A1. This phenotype has already been documented in patients with heterozygous variants in the gene encoding retinal transcription factor CRX, while there is no known functional or phenotypic link with variants in TPRX1 or SULT2A1. This therefore confirms that CRX haploinsufficiency is pathogenic, a finding that had previously been debated in the ophthalmic literature. The deletion was characterized using a PCR assay followed by cloning and Sanger sequencing or direct Sanger sequencing. Haplotype analysis was done by microsatellite genotyping. The third results chapter describes use of SMRT PacBio and nanopore long-read sequencing to screen the hard-to-sequence mutation hotspot RPGR-ORF15. Both approaches were effective in reading throughout ORF15 and allowed sequencing indexed pooled samples, and 218 IRD patients were screened, detecting known and new variants. Nanopore sequencing on the smaller Flongle flowcell allowed low-cost optimisation, but pores rapidly blocked, probably due to ORF15 secondary structures. Repeated DNase I washes reopened the pores but required use of the more expensive MinION flowcells. Ultimately, the PacBio sequencer proved simpler to use, cheaper, and more scalable.16 0