Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

Mulder, Nicola; Nembaware, Victoria; Adekile, Adekunle; Anie, Kofi A.; Inusa, Baba; Bj, Brown; Campbell, Andrew; Chinenere, Furahini; Chunda‐Liyoka, Catherine; Derebail, Vimal K.; Geard, Amy; Ghedira, Kaïs; Hamilton, Carol M.; Hanchard, Neil A.; Haendel, Melissa; Huggins, Wayne; Ibrahim, Muntaser E.; Jupp, Simon; Kamga, Karen Kengne; Knight‐Madden, Jennifer; Philomène, Lopez-Sall; Mbiyavanga, Mamana; Munube, Deogratias; Nirenberg, Damian; Nnodu, Obiageli; Ofori-Acquah, Solomon F.; Ohene‐Frempong, Kwaku; Opap, Kenneth; Panji, Sumir; Park, Miriam; Pule, Gift D.; Royal, Charmaine D.; Sangeda, Raphael Zozimus; Tayo, Bamidele O.; Treadwell, Marsha; Tshilolo, Léon; Wonkam, Ambroise

doi:10.1016/j.atg.2016.03.005

Cited by 16 publications

(16 citation statements)

References 25 publications

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“…This mainly results from the effect of pain and symptoms on their daily lives, and society's attitudes towards them. Cultural factors are particularly important to these problems because of beliefs and practices [54]. Furthermore, the ability of people with SCD to cope with their condition varies greatly because severity, general health, and quality of life varies greatly among individuals [55,56].…”

Section: Psychosocial Impactmentioning

confidence: 99%

Sickle Cell Disease—Genetics, Pathophysiology, Clinical Presentation and Treatment

Inusa

Hsu

Kohli

et al. 2019

IJNS

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124

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Sickle cell disease (SCD) is a monogenetic disorder due to a single base-pair point mutation in the β-globin gene resulting in the substitution of the amino acid valine for glutamic acid in the β-globin chain. Phenotypic variation in the clinical presentation and disease outcome is a characteristic feature of the disorder. Understanding the pathogenesis and pathophysiology of the disorder is central to the choice of therapeutic development and intervention. In this special edition for newborn screening for haemoglobin disorders, it is pertinent to describe the genetic, pathologic and clinical presentation of sickle cell disease as a prelude to the justification for screening. Through a systematic review of the literature using search terms relating to SCD up till 2019, we identified relevant descriptive publications for inclusion. The scope of this review is mainly an overview of the clinical features of pain, the cardinal symptom in SCD, which present following the drop in foetal haemoglobin as young as five to six months after birth. The relative impact of haemolysis and small-vessel occlusive pathology remains controversial, a combination of features probably contribute to the different pathologies. We also provide an overview of emerging therapies in SCD.

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Section: Psychosocial Impactmentioning

confidence: 99%

Sickle Cell Disease—Genetics, Pathophysiology, Clinical Presentation and Treatment

Inusa

Hsu

Kohli

et al. 2019

IJNS

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124

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“…Genetic counseling within high-risk populations has greatly reduced the burden of genetic diseases. Sickle cell disease (SCD, OMIM603903) is one of the most common genetic causes of illness and death in the world (Makani, Ofori-Acquah, Nnodu, Wonkam, & Ohene-Frempong, 2013) and up to 75% of SCD in newborns world-wide occurs in SSA (Mulder, Nembaware, et al, 2016). SCD is a heterogeneous disorder with a highly variable clinical spectrum (van der Land et al, 2013) and its genetic haplotypes are defined by restriction of fragment length polymorphisms in the β-globin locus (Makani et al, 2013).…”

Section: Genomic Counseling Services Adopted By National Healthcarementioning

confidence: 99%

Role of genomics literacy in reducing the burden of common genetic diseases in Africa

Mboowa

Sserwadda

2019

Molec Gen & Gen Med

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Background In Africa, health practitioners and the current knowledge of the public on genetics and genomics is still very low and yet this has potential to reduce the burden of common genetic diseases. Many initiatives have promoted genomic research, infrastructure, and capacity building in Africa. What remains to be done is to improve genomics literacy among populations and communities while utilizing an array of strategies. Genomic literacy and awareness are key in the management of genetic diseases which includes diagnosis, prevention of complications and therapy. Africa is characterized by great cultural and language diversity thereby requiring a multidisciplinary approach to improving public and community genomics literacy and engagement. However, this is further complicated by having the fact that sub‐Saharan Africa is comprised of countries with the lowest literacy rates in the world. Methods We applied the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines to review genomic literacy in Africa using PubMed database. Results We found very limited evidence of genomics literacy for genetic diseases in Africa. Conclusion We propose a number of approaches that if adopted will significantly increase the genomic literacy and reduce the burden of genetic diseases in Africa.

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“…For example, H3ABioNet members and the Sickle Cell Disease community joined forces to develop an ontology covering aspects related to SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. Experts in SCD from around the world contributed to the development of the SCD ontology at a hands-on workshop, the proceedings of which were published [Mulder N. et al 2016]. We settled on Protégé for an initial implementation of ontology structures and have used its web interface WebProtégé [Horridge et al, 2014] for the follow up developments by domain experts.…”

Section: Data Curation and Standardisationmentioning

confidence: 99%

Development of Bioinformatics Infrastructure for Genomics Research

Mulder

Adebiyi

et al. 2017

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Background and objectives Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a Pan African bioinformatics network, was established to build capacity specifically to enable H3Africa researchers to analyse their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet’s role has evolved in response to changing needs from the consortium and the African bioinformatics community. The network set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage and analysis. Methods and results Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrolment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Since H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System and eBiokits. A set of reproducible, portable and cloud scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. Conclusion For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities and training programmes. Here, we describe the infrastructure and how it has impacted genomics and bioinformatics research in Africa.

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Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

Cited by 16 publications

References 25 publications

Sickle Cell Disease—Genetics, Pathophysiology, Clinical Presentation and Treatment

Sickle Cell Disease—Genetics, Pathophysiology, Clinical Presentation and Treatment

Role of genomics literacy in reducing the burden of common genetic diseases in Africa

Development of Bioinformatics Infrastructure for Genomics Research

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