Document Details
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Document Type |
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Thesis |
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Document Title |
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IDENTIFYING GENETIC VARIATION UNDERLYING VOGT-KOYANAGI-HARADA (VKH) IN SAUDI PATIENTS USING EXOME SEQUENCING تحديد التباين الوراثي لمتلازمة هارادا في المرضى السعوديين باستخدام تسلسل الاكسوم |
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Subject |
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Faculty of Science |
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Document Language |
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Arabic |
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Abstract |
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Vogt-Koyanagi-Harada (VKH) is an autoimmune disease of the pigment-producing cells. The disease is considered rare in the population and predominantly affects people with darker skin. VKH is a multifactorial disease, and the precise cause of the VKH disease is unknown. All previous studies had used an association study design to decipher the role of genetic elements in the etiology of VKH. However, the genetics underlying VKH is still unclear. In this study, an in-depth sequencing approach was used to completely sequence all coding genes of the human genome in VKH patients. For this, 17 VKH patients were collected from the Madinah region of Saudi Arabia. The consultant ophthalmologist clinically examined the patients. Genomic DNA was extracted using the commercially available kit, and the DNA was quantified using a spectrophotometer. Out of 17 patients, 5 DNA samples were subjected to WES using the SureSelectXT library preparation kit followed by cluster generation and paired-end sequencing on an Illumina NextSeq500 instrument. A high-quality reads were generated which were aligned to the human reference genome assembly (GRCh38/hg38). Alignment and variant calling were performed using BWA (Burrows-Wheeler Alignment) and GATK (genome analysis toolkit) softwares. A list of approximately 90,000 variants on average was obtained across each sample. These variants were annotated using standard tools followed by filtration using population frequency databases. Only rare variants with a population frequency of less than 0.005 (<0.005) and non-synonymous variants such as nonsense, frameshift, missense, and splice site variants were retained. This analysis yielded approximately 124 variants on an average per sample. Detecting shared variants across all samples yielded 55 variants in 22 genes. These genes were prioritized further based on their expression, and functional data available in the UCSC (University of California, Santa Cruz) genome browser, and only those genes with known expression in skin, eye, brain, and ear were selected. Also, uncharacterized genes were considered. This led to the identification of 15 variants in 6 candidate genes. The six VKH candidate genes identified in this study are FLJ22184, ANKRD20A1, PRIM2, ZNF717, FAM86B2, and RFPL4A. The variants in these genes include insertions, deletion, nonsense, and missense variants. FLJ22184 encodes a long noncoding RNA, and ZNF717 encodes a transcription factor. Different studies have already described the role of lncRNAs and transcription factors in VKH. PRIM2 encodes a primase subunit and variants in this gene have been associated with a depigmentation disorder. ANKRD20A1, FAM86B2, and RFPL4A are uncharacterized genes, and functional studies are needed to establish their precise role in human health and disease. |
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Supervisor |
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Dr. Najla Ali Alburae |
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Thesis Type |
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Master Thesis |
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Publishing Year |
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1441 AH
2020 AD |
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Added Date |
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Friday, June 26, 2020 |
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Researchers
| علياء محمود البلوي | Albalawi, Alia Mahmoud | Researcher | Master | |
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