β-Thalassemia pathogenic variants in a cohort of children from the East African coast

BACKGROUND: β-Thalassemia is rare in sub-Saharan Africa. Previous studies have suggested that it is limited to specific parts of West Africa. Based on hemoglobin A2 (HbA2 ) concentrations measured by HPLC, we recently speculated that β-thalassemia might also be present on the East African coast of Kenya. Here, we follow this up using molecular methods. METHODS: We used raised hemoglobin A2 (HbA2 ) values (> 4.0% of total Hb) to target all HbAA members of a cohort study in Kilifi, Kenya, for HBB sequencing for β-thalassemia (n = 99) together with a sample of HbAA subjects with lower HbA2 levels. Because HbA2 values are artifactually raised in subjects carrying sickle hemoglobin (HbS) we sequenced all participants with an HPLC pattern showing HbS without HbA (n = 116) and a sample with a pattern showing both HbA and HbS. RESULTS: Overall, we identified 83 carriers of four separate β-thalassemia pathogenic variants: three β0 -thalassemia [CD22 (GAA→TAA), initiation codon (ATG→ACG), and IVS1-3' end del 25bp] and one β+ -thalassemia pathogenic variants (IVS-I-110 (G→A)). We estimated the minimum allele frequency of all variants combined within the study population at 0.3%. CONCLUSIONS: β-Thalassemia is present in Kilifi, Kenya, an observation that has implications for the diagnosis and clinical care of children from the East Africa region

The epidemiology of sickle cell disease in children recruited in infancy in Kilifi, Kenya: a prospective cohort study.

BACKGROUND: Sickle cell disease is the most common severe monogenic disorder in humans. In Africa, 50-90% of children born with sickle cell disease die before they reach their fifth birthday. In this study, we aimed to describe the comparative incidence of specific clinical outcomes among children aged between birth and 5 years with and without sickle cell disease, who were resident within the Kilifi area of Kenya. METHODS: This prospective cohort study was done on members of the Kilifi Genetic Birth Cohort Study (KGBCS) on the Indian Ocean coast of Kenya. Recruitment to the study was facilitated through the Kilifi Health and Demographic Surveillance System (KHDSS), which covers a resident population of 260 000 people, and was undertaken between Jan 1, 2006, and April 30, 2011. All children who were born within the KHDSS area and who were aged 3-12 months during the recruitment period were eligible for inclusion. Participants were tested for sickle cell disease and followed up for survival status and disease-specific admission to Kilifi County Hospital by passive surveillance until their fifth birthday. Children with sickle cell disease were offered confirmatory testing and care at a dedicated outpatient clinic. FINDINGS: 15 737 infants were recruited successfully to the KGBCS, and 128 (0·8%) of these infants had sickle cell disease, of whom 70 (54·7%) enrolled at the outpatient clinic within 12 months of recruitment. Mortality was higher in children with sickle cell disease (58 per 1000 person-years of observation, 95% CI 40-86) than in those without sickle cell disease (2·4 per 1000 person-years of observation, 2·0-2·8; adjusted incidence rate ratio [IRR] 23·1, 95% CI 15·1-35·3). Among children with sickle cell disease, mortality was lower in those who enrolled at the clinic (adjusted IRR 0·26, 95% CI 0·11-0·62) and in those with higher levels of haemoglobin F (HbF; adjusted IRR 0·40, 0·17-0·94). The incidence of admission to hospital was also higher in children with sickle cell disease than in children without sickle cell disease (210 per 1000 person-years of observation, 95% CI 174-253, vs 43 per 1000 person-years of observation, 42-45; adjusted IRR 4·80, 95% CI 3·84-6·15). The most common reason for admission to hospital among those with sickle cell disease was severe anaemia (incidence 48 per 1000 person-years of observation, 95% CI 32-71). Admission to hospital was lower in those with a recruitment HbF level above the median (IRR 0·43, 95% CI 0·24-0·78; p=0·005) and those who were homozygous for α-thalassaemia (0·07, 0·01-0·83; p=0·035). INTERPRETATION: Although morbidity and mortality were high in young children with sickle cell disease in this Kenyan cohort, both were reduced by early diagnosis and supportive care. The emphasis must now move towards early detection and prevention of long-term complications of sickle cell disease. FUNDING: Wellcome Trust

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

Integration of resource oriented sanitation in informal settlements: the case of Arusha Municipality

More than 75% of Arusha population lives in unplanned settlements which are characterized by poor sanitation. This paper aimed at exploring opportunities and challenges of implementing resource oriented sanitation in informal settlements of Arusha. The study aims at developing mechanism for integrating resource oriented sanitation in informal settlements. The study revealed that, housing or land ownership is among of the challenges in implementing resource oriented sanitation in these settlements. It was also observed that 35% of households do not own land; as such do not see the need of improving sanitation system. Also limited space to extent that becomes difficult to construct another toilet or empty when one is full, lack of awareness and the adoption of supply driven approach which do not consider peoples demand. The paper assessed ability and willingness to pay for resource oriented sanitation selected case studies

β-Thalassemia pathogenic variants in a cohort of children from the East African coast

Background β-Thalassemia is rare in sub-Saharan Africa. Previous studies have suggested that it is limited to specific parts of West Africa. Based on hemoglobin A2 (HbA2) concentrations measured by HPLC, we recently speculated that β-thalassemia might also be present on the East African coast of Kenya. Here, we follow this up using molecular methods. Methods We used raised hemoglobin A2 (HbA2) values (> 4.0% of total Hb) to target all HbAA members of a cohort study in Kilifi, Kenya, for HBB sequencing for β-thalassemia (n = 99) together with a sample of HbAA subjects with lower HbA2 levels. Because HbA2 values are artifactually raised in subjects carrying sickle hemoglobin (HbS) we sequenced all participants with an HPLC pattern showing HbS without HbA (n = 116) and a sample with a pattern showing both HbA and HbS. Results Overall, we identified 83 carriers of four separate β-thalassemia pathogenic variants: three β0-thalassemia [CD22 (GAA→TAA), initiation codon (ATG→ACG), and IVS1-3ʹ end del 25bp] and one β+-thalassemia pathogenic variants (IVS-I-110 (G→A)). We estimated the minimum allele frequency of all variants combined within the study population at 0.3%. Conclusions β-Thalassemia is present in Kilifi, Kenya, an observation that has implications for the diagnosis and clinical care of children from the East Africa region

The population dynamics of haemoglobins A, A2, F and S in the context of the haemoglobinopathies HbS and α+thalassaemia in Kenyan infants

Few studies have described the dynamics of haemoglobin production in African populations with a high prevalence of haemoglobinopathies. We have used the BioRad Variant ClassicTM HPLC method to document the production patterns of the common haemoglobin variants HbA, HbA2, HbF and HbS, stratified by a+thalassaemia genotype, among 15,301 infants recruited to a study on the Coast of Kenya. Notably, we confirm that HbA2 measurements determined using this instrument are unreliable in HbAS and HbSS subjects. Further, we showed that HbA2 exceeded 4.0%, a level consistent with the presence of a-thalassaemia, in 0.8% of infants of HbAA phenotype who participated in our study. a-thalassaemia, has not been widely reported in the East Africa region and, as such, this finding merits further study

The population dynamics of haemoglobins A, A2, F and S in the context of the haemoglobinopathies HbS and α+thalassaemia in Kenyan infants

Few studies have described the dynamics of haemoglobin production in African populations with a high prevalence of haemoglobinopathies. We have used the BioRad Variant ClassicTM HPLC method to document the production patterns of the common haemoglobin variants HbA, HbA2, HbF and HbS, stratified by a+thalassaemia genotype, among 15,301 infants recruited to a study on the Coast of Kenya. Notably, we confirm that HbA2 measurements determined using this instrument are unreliable in HbAS and HbSS subjects. Further, we showed that HbA2 exceeded 4.0%, a level consistent with the presence of a-thalassaemia, in 0.8% of infants of HbAA phenotype who participated in our study. a-thalassaemia, has not been widely reported in the East Africa region and, as such, this finding merits further study

ß-thalassemia pathogenic variants in a cohort of children from the East African coast.

BACKGROUND: β-Thalassemia is rare in sub-Saharan Africa. Previous studies have suggested that it is limited to specific parts of West Africa. Based on hemoglobin A2 (HbA2 ) concentrations measured by HPLC, we recently speculated that β-thalassemia might also be present on the East African coast of Kenya. Here, we follow this up using molecular methods. METHODS: We used raised hemoglobin A2 (HbA2 ) values (> 4.0% of total Hb) to target all HbAA members of a cohort study in Kilifi, Kenya, for HBB sequencing for β-thalassemia (n = 99) together with a sample of HbAA subjects with lower HbA2 levels. Because HbA2 values are artifactually raised in subjects carrying sickle hemoglobin (HbS) we sequenced all participants with an HPLC pattern showing HbS without HbA (n = 116) and a sample with a pattern showing both HbA and HbS. RESULTS: Overall, we identified 83 carriers of four separate β-thalassemia pathogenic variants: three β0 -thalassemia [CD22 (GAA→TAA), initiation codon (ATG→ACG), and IVS1-3' end del 25bp] and one β+ -thalassemia pathogenic variants (IVS-I-110 (G→A)). We estimated the minimum allele frequency of all variants combined within the study population at 0.3%. CONCLUSIONS: β-Thalassemia is present in Kilifi, Kenya, an observation that has implications for the diagnosis and clinical care of children from the East Africa region