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oai:figshare.com:article/29978956 2025-08-27T07:46:19Z category_24310 category_24208 category_27241 portal_753 item_type_3 month_year_08_2025

Analysis of the secondary African genomic data to identify allele frequencies in genetic determinants associated with varying outcomes of COVID-19 in other population groups Fatima Barmania (22118269) Genomics Bioinformatics and computational biology not elsewhere classified Other health sciences not elsewhere classified COVID-19 Bioinformatics Allele frequency SARS-CoV-2 African population Bioinformatic pipeline analysis Genetic variation Genetics and genomics/medical genetics Functional prediction SDG 10 Reduced inequalities <p dir="ltr">This dataset listed here contains supplementary data supporting Chapter 3, 4, 5 and 6 of the thesis "Analysis of variants in host genes associated with COVID-19 outcomes in the African population." The data includes raw genotype calls, processed summary tables, and supporting analyses to enable understanding of the thesis chapters.</p><p dir="ltr">Appendix B includes the following supplementary files:</p><p dir="ltr">Supplementary_File_1 (list of COVID-19 genetic articles)</p><p dir="ltr">Supplementary_File_2_T1/T2 (list of COVID-19 associated variants and genes identified in LD)</p><p dir="ltr">Pipeline_Script (pipeline code used to analyse sequencing data)</p><p dir="ltr">Gene_Transcripts (transcript identifiers used for each gene)</p><p dir="ltr">Gene_Locations (the location and gene length information used)</p><p dir="ltr">Appendix C includes the following supplementary files:</p><p dir="ltr">Supplementary data has been published under the DOI <a href="https://doi.org/10.1038/s41431-022-01089-8" target="_blank">https://doi.org/10.1038/s41431-022-01089-8</a> and includes-</p><p dir="ltr">Appendix_C_Supplementary Data A</p><p dir="ltr">Appendix_C_Supplementary Data B</p><p dir="ltr">Appendix_C_Supplementary Data C</p><p dir="ltr">Appendix_C_Supplementary Notes and Supplementary Figure 1</p><p dir="ltr">Appendix_D includes the following supplementary files:</p><p dir="ltr">Appendix_D_Supplementary_Data_A- (List of previously published COVID-19 variants assessed in the AFR population and the AF’s of each variant in the AFR, EUR, EAS, SAS and AMR population groups).</p><p dir="ltr">Appendix_D_Supplementary_Data_B- (Raw frequency data for each variant, including p-values and odds ratios).</p><p dir="ltr">Appendix E includes the following supplementary files:</p><p dir="ltr">Appendix_E_Supplementary_Data_A- (Includes 5 tables)<br>T1: Sample list for the GnomAD data</p><p dir="ltr">T2: Gene Function/ category information for 153 COVID-19 associated genes</p><p dir="ltr">T3: 39 biologically plausible candidate genes and total variants identified across all populations analysed using the pipeline</p><p dir="ltr">T4: High priority list of 20 candidate genes analysed in chapter 6</p><p dir="ltr">T5: AF and raw data for the 43 common AFR variants</p><p dir="ltr">Appendix_E_Supplementary_Data_B (Functional prediction data for variants in genes <i>ACE2</i>, <i>IL10RB</i> and <i>TMPRSS2</i>)</p><p dir="ltr">Appendix_E_Supplementary_Data_C (Functional prediction data for variants in genes <i>TYK2</i>, <i>DPP9</i>, <i>OAS1-3</i>)</p><p dir="ltr">Appendix_E_Supplementary_Data_D (Functional prediction data for variants in genes <i>MUC5B</i>, <i>ELF5</i>, <i>SFTPD</i> and <i>IFNA10</i>)</p><p dir="ltr">Appendix_E_Supplementary_Data_E (Functional prediction data for variants in genes <i>FOXP4</i>, <i>IRF1</i> and <i>PLSCR1</i>)</p><p dir="ltr">Appendix_E_Supplementary_Data_F (Functional prediction data for variants in genes <i>LZTFL1</i> and <i>JAK1</i>)</p> 2025-08-27T07:46:19Z Dataset Dataset 10.25403/UPresearchdata.29978956.v1 https://figshare.com/articles/dataset/Analysis_of_the_secondary_African_genomic_data_to_identify_allele_frequencies_in_genetic_determinants_associated_with_varying_outcomes_of_COVID-19_in_other_population_groups/29978956 CC BY 4.0