Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations
| dc.contributor.advisor | Wonkam, Ambroise | |
| dc.contributor.advisor | Mnika, Khuthala | |
| dc.contributor.advisor | Esoh, Kevin | |
| dc.contributor.advisor | Nembaware, Victoria | |
| dc.contributor.author | Samie, Nabeelah | |
| dc.date.accessioned | 2026-07-20T08:05:19Z | |
| dc.date.available | 2026-07-20T08:05:19Z | |
| dc.date.issued | 2026 | |
| dc.date.updated | 2026-07-20T08:03:54Z | |
| dc.description.abstract | Introduction Sickle cell disease (SCD) is mostly caused, in homozygous state, by a single point mutation (c.20A>T, p.Glu7Val), which results in the formation of mutant haemoglobin S (HbS) instead of haemoglobin A. It is a life-long inherited recessive disorder that predominantly affects people of African, Indian, and Mediterranean descent. The polymerisation of HbS within red blood cells (RBCs) is the primary pathophysiological alteration in SCD, which results in the sickle shape of RBCs. Sickle-shaped RBCs are more prone to haemolysis and they block blood flow, resulting in anaemia, hypoxia painful episodes, and multiple organ damage. Haematological indices include haematocrit (HTC), haemoglobin concentration (HGB), mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC), RBC width, RBC count, white blood cell (WBC) count, lymphocyte count, monocyte count, platelet count, HbA2 and HbF percentage. Haematological indices indicate the size, development, and haemoglobin content of RBCs. Consequently, haematological indices are routinely measured as a means of monitoring SCD. Because these indices are potentially associated with genomic variation, extensive genome-wide association studies have been performed to determine variants associated with haematological indices. Many common variants were identified, however, non-European populations such as African and Asian populations are underrepresented in these studies. Whole genome sequencing, a method used for detecting novel variants, recently resulted in the identification of 14 novel variants associated with haematological indices in 62,653 ethnically diverse participants from the Trans-Omics for Precision Medicine (TOPMed) program, in the United States of America (USA). Namely: HBB (rs11549407 and rs34598529), RPN1 (rs112097551), ELL2 (rs116635225), 10q26 (rs986415672), MIDN (rs73494666), G6PD (rs76723693), SHANK2 (rs535577177), TMPRSS6 (rs228914), HBA1/2 (rs868351380 and rs372755452), EIF5/MARK3 (rs370308370), PIEZO1 (rs763477215) and 19q12 (rs1368500441). The association between these variants and haematological indices have not yet been investigated in African SCD patients. Aim This study aims to investigate 13 novel haematological indices associated variants, previously found in the TOPMed project, among SCD patients from Cameroon and Senegal. Methods Study participants: This study included individuals with SCD recruited from various regions of Cameroon and Senegal and ethnically matched non-SCD individuals recruited from various regions of Cameroon. Molecular methods: Genetic characterisation was performed using polymerase chain reaction (PCR) and TaqMan SNP genotyping. Capillary electrophoresis and Sanger sequencing were also performed on a subset of samples for genotype validations. Statistical analysis: Descriptive analysis was performed using IBM SPSS Statistics for Windows (version 25) on data collected from 804 SCD patients from Cameroon. The statistics performed included an analysis of sociodemographic factors, anthropometric variables and haematological indices. Association tests of SNPs were run using PLINK1.9 with the maximum permutation test procedure used to correct for multiple testing and to determine empirical significance levels. The logistic command of PLINK was used with 100,000 maximum permutations to test for significant SNPs while adjusting for sex and age. Results Both Cameroon and Senegal SCD patients had a higher percentage of females than males (53.9% and 54.1%, respectively). The median age was 16 (range: 1-66) and 21 (range: 5-45) for the Cameroon and Senegal SCD patients respectively. Among the Cameroon SCD patients, the majority did not have overt stroke (97%), kidney disease (91.2%) and pulmonary hypertension (93.4%), and 92.2% were not using hydroxyurea. Association analysis using Spearman's rank correlation test found age to be significantly negatively associated with the number of vaso-occlusive crises/year (pvalue: <0.001) and the number of hospitalisations/year (p-value: <0.001). Further analysis using Spearman's rank correlation test found a significantly positive association between the number of vaso-occlusive crises/year and MCHC (p-value: 0.039). Additionally, MCHC and HbA2 were found to be significantly positively associated with the number of hospitalisations/year (p-value: <0.001 and 0.015, respectively), while monocytes were found to be significantly negatively associated with the number of hospitalisations/year (p-value: 0.005). and Logistic regression analysis yielded five statistically significant associations between variants haematological indices. Namely, G6PD variant (NC_000023.11:g.154533025A>G) was associated with HGB, MCV and HCT; HBA1/2 variant (NC_000016.10:g.199622del) was associated with platelet count, and HBB variant (NC_000011.10:g.5227100T>C) was associated with HbF level. Eight of the 13 variants (ELL2 (rs116635225), HBB (rs11549407 and rs34598529), SHANK2 (rs535577177), HBA1/2 (rs372755452), PIEZO1 (rs763477215), MIDN (rs73494666) and 19q12 (rs1368500441)) minor allele frequencies (MAF) were found more commonly in individuals with SCD from Cameroon compared to all other populations, suggesting an enrichment among people living with SCD. Conclusions This study has revealed three variants in G6PD, alpha-thalassemia (HBA1/2), and beta-globin (HBB) genes significantly associated with various haematological indices in African SCD patients, which could have implications in SCD risk stratification models for anticipatory guidance in clinical practice. Most variants that were investigated (8/13) displayed a higher MAF in individuals with SCD, compared to other unselected global populations, in whom some variants were monomorphic i.e., European and Asian populations, probably due to the higher African genetic diversity. Alternatively, these differences in MAF, particularly when compared to control populations with the same ethnolinguistic background are suggesting an enrichment of targeted variants in people living with SCD, which are potentially due to the impact of the related genes on the pathobiology of SCD. Additional studies including specific GWAS on haematological indices in larger samples of people living with SCD from multiple African populations from diverse ethnolinguistic background, and geographical locations, will be needed to gain more insight in these SNPs, and new ones to be discovered. The outcomes of such studies will be beneficial for developing accurate predictive modelling tools to guide follow-up and treatment practices of SCD, as well as to unravelling new therapeutic targets. | |
| dc.identifier.apacitation | Samie, N. (2026). <i>Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations</i>. (). University of Cape Town. Retrieved from http://hdl.handle.net/11427/43605 | en_ZA |
| dc.identifier.chicagocitation | Samie, Nabeelah. <i>"Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations."</i> ., University of Cape Town, 2026. http://hdl.handle.net/11427/43605 | en_ZA |
| dc.identifier.citation | Samie, N. 2026. Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations. . University of Cape Town. http://hdl.handle.net/11427/43605 | en_ZA |
| dc.identifier.ris | TY - Thesis / Dissertation AU - Samie, Nabeelah AB - Introduction Sickle cell disease (SCD) is mostly caused, in homozygous state, by a single point mutation (c.20A>T, p.Glu7Val), which results in the formation of mutant haemoglobin S (HbS) instead of haemoglobin A. It is a life-long inherited recessive disorder that predominantly affects people of African, Indian, and Mediterranean descent. The polymerisation of HbS within red blood cells (RBCs) is the primary pathophysiological alteration in SCD, which results in the sickle shape of RBCs. Sickle-shaped RBCs are more prone to haemolysis and they block blood flow, resulting in anaemia, hypoxia painful episodes, and multiple organ damage. Haematological indices include haematocrit (HTC), haemoglobin concentration (HGB), mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC), RBC width, RBC count, white blood cell (WBC) count, lymphocyte count, monocyte count, platelet count, HbA2 and HbF percentage. Haematological indices indicate the size, development, and haemoglobin content of RBCs. Consequently, haematological indices are routinely measured as a means of monitoring SCD. Because these indices are potentially associated with genomic variation, extensive genome-wide association studies have been performed to determine variants associated with haematological indices. Many common variants were identified, however, non-European populations such as African and Asian populations are underrepresented in these studies. Whole genome sequencing, a method used for detecting novel variants, recently resulted in the identification of 14 novel variants associated with haematological indices in 62,653 ethnically diverse participants from the Trans-Omics for Precision Medicine (TOPMed) program, in the United States of America (USA). Namely: HBB (rs11549407 and rs34598529), RPN1 (rs112097551), ELL2 (rs116635225), 10q26 (rs986415672), MIDN (rs73494666), G6PD (rs76723693), SHANK2 (rs535577177), TMPRSS6 (rs228914), HBA1/2 (rs868351380 and rs372755452), EIF5/MARK3 (rs370308370), PIEZO1 (rs763477215) and 19q12 (rs1368500441). The association between these variants and haematological indices have not yet been investigated in African SCD patients. Aim This study aims to investigate 13 novel haematological indices associated variants, previously found in the TOPMed project, among SCD patients from Cameroon and Senegal. Methods Study participants: This study included individuals with SCD recruited from various regions of Cameroon and Senegal and ethnically matched non-SCD individuals recruited from various regions of Cameroon. Molecular methods: Genetic characterisation was performed using polymerase chain reaction (PCR) and TaqMan SNP genotyping. Capillary electrophoresis and Sanger sequencing were also performed on a subset of samples for genotype validations. Statistical analysis: Descriptive analysis was performed using IBM SPSS Statistics for Windows (version 25) on data collected from 804 SCD patients from Cameroon. The statistics performed included an analysis of sociodemographic factors, anthropometric variables and haematological indices. Association tests of SNPs were run using PLINK1.9 with the maximum permutation test procedure used to correct for multiple testing and to determine empirical significance levels. The logistic command of PLINK was used with 100,000 maximum permutations to test for significant SNPs while adjusting for sex and age. Results Both Cameroon and Senegal SCD patients had a higher percentage of females than males (53.9% and 54.1%, respectively). The median age was 16 (range: 1-66) and 21 (range: 5-45) for the Cameroon and Senegal SCD patients respectively. Among the Cameroon SCD patients, the majority did not have overt stroke (97%), kidney disease (91.2%) and pulmonary hypertension (93.4%), and 92.2% were not using hydroxyurea. Association analysis using Spearman's rank correlation test found age to be significantly negatively associated with the number of vaso-occlusive crises/year (pvalue: <0.001) and the number of hospitalisations/year (p-value: <0.001). Further analysis using Spearman's rank correlation test found a significantly positive association between the number of vaso-occlusive crises/year and MCHC (p-value: 0.039). Additionally, MCHC and HbA2 were found to be significantly positively associated with the number of hospitalisations/year (p-value: <0.001 and 0.015, respectively), while monocytes were found to be significantly negatively associated with the number of hospitalisations/year (p-value: 0.005). and Logistic regression analysis yielded five statistically significant associations between variants haematological indices. Namely, G6PD variant (NC_000023.11:g.154533025A>G) was associated with HGB, MCV and HCT; HBA1/2 variant (NC_000016.10:g.199622del) was associated with platelet count, and HBB variant (NC_000011.10:g.5227100T>C) was associated with HbF level. Eight of the 13 variants (ELL2 (rs116635225), HBB (rs11549407 and rs34598529), SHANK2 (rs535577177), HBA1/2 (rs372755452), PIEZO1 (rs763477215), MIDN (rs73494666) and 19q12 (rs1368500441)) minor allele frequencies (MAF) were found more commonly in individuals with SCD from Cameroon compared to all other populations, suggesting an enrichment among people living with SCD. Conclusions This study has revealed three variants in G6PD, alpha-thalassemia (HBA1/2), and beta-globin (HBB) genes significantly associated with various haematological indices in African SCD patients, which could have implications in SCD risk stratification models for anticipatory guidance in clinical practice. Most variants that were investigated (8/13) displayed a higher MAF in individuals with SCD, compared to other unselected global populations, in whom some variants were monomorphic i.e., European and Asian populations, probably due to the higher African genetic diversity. Alternatively, these differences in MAF, particularly when compared to control populations with the same ethnolinguistic background are suggesting an enrichment of targeted variants in people living with SCD, which are potentially due to the impact of the related genes on the pathobiology of SCD. Additional studies including specific GWAS on haematological indices in larger samples of people living with SCD from multiple African populations from diverse ethnolinguistic background, and geographical locations, will be needed to gain more insight in these SNPs, and new ones to be discovered. The outcomes of such studies will be beneficial for developing accurate predictive modelling tools to guide follow-up and treatment practices of SCD, as well as to unravelling new therapeutic targets. DA - 2026 DB - OpenUCT DP - University of Cape Town KW - sickle cell disease KW - TOPMed LK - https://open.uct.ac.za PB - University of Cape Town PY - 2026 T1 - Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations TI - Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations UR - http://hdl.handle.net/11427/43605 ER - | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/11427/43605 | |
| dc.identifier.vancouvercitation | Samie N. Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations. []. University of Cape Town, 2026 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/43605 | en_ZA |
| dc.language.iso | en | |
| dc.language.rfc3066 | eng | |
| dc.publisher | University of Cape Town | |
| dc.publisher.department | Department of Pathology | |
| dc.publisher.faculty | Faculty of Health Sciences | |
| dc.publisher.institution | University of Cape Town | |
| dc.subject | sickle cell disease | |
| dc.subject | TOPMed | |
| dc.title | Investigating variants associated with quantitative red blood cell indices from TOPMed predictions in African Sickle Cell Disease populations | |
| dc.type | Thesis / Dissertation | |
| dc.type.qualificationlevel | Masters | |
| dc.type.qualificationlevel | MScMed |