Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects
| dc.contributor.author | Damena, Delesa | |
| dc.contributor.author | Denis, Awany | |
| dc.contributor.author | Golassa, Lemu | |
| dc.contributor.author | Chimusa, Emile R | |
| dc.date.accessioned | 2019-12-10T09:13:27Z | |
| dc.date.available | 2019-12-10T09:13:27Z | |
| dc.date.issued | 2019-08-14 | |
| dc.date.updated | 2019-08-18T03:25:43Z | |
| dc.description.abstract | Abstract Background P. falciparum malaria has been recognized as one of the prominent evolutionary selective forces of human genome that led to the emergence of multiple host protective alleles. A comprehensive understanding of the genetic bases of severe malaria susceptibility and resistance can potentially pave ways to the development of new therapeutics and vaccines. Genome-wide association studies (GWASs) have recently been implemented in malaria endemic areas and identified a number of novel association genetic variants. However, there are several open questions around heritability, epistatic interactions, genetic correlations and associated molecular pathways among others. Here, we assess the progress and pitfalls of severe malaria susceptibility GWASs and discuss the biology of the novel variants. Results We obtained all severe malaria susceptibility GWASs published thus far and accessed GWAS dataset of Gambian populations from European Phenome Genome Archive (EGA) through the MalariaGen consortium standard data access protocols. We noticed that, while some of the well-known variants including HbS and ABO blood group were replicated across endemic populations, only few novel variants were convincingly identified and their biological functions remain to be understood. We estimated SNP-heritability of severe malaria at 20.1% in Gambian populations and showed how advanced statistical genetic analytic methods can potentially be implemented in malaria susceptibility studies to provide useful functional insights. Conclusions The ultimate goal of malaria susceptibility study is to discover a novel causal biological pathway that provide protections against severe malaria; a fundamental step towards translational medicine such as development of vaccine and new therapeutics. Beyond singe locus analysis, the future direction of malaria susceptibility requires a paradigm shift from single -omics to multi-stage and multi-dimensional integrative functional studies that combines multiple data types from the human host, the parasite, the mosquitoes and the environment. The current biotechnological and statistical advances may eventually lead to the feasibility of systems biology studies and revolutionize malaria research. | |
| dc.identifier.apacitation | Damena, D., Denis, A., Golassa, L., & Chimusa, E. R. (2019). Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects. http://hdl.handle.net/11427/30693 | en_ZA |
| dc.identifier.chicagocitation | Damena, Delesa, Awany Denis, Lemu Golassa, and Emile R Chimusa "Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects." (2019) http://hdl.handle.net/11427/30693 | en_ZA |
| dc.identifier.citation | BMC Medical Genomics. 2019 Aug 14;12(1):120 | |
| dc.identifier.ris | TY - Journal Article AU - Damena, Delesa AU - Denis, Awany AU - Golassa, Lemu AU - Chimusa, Emile R AB - Abstract Background P. falciparum malaria has been recognized as one of the prominent evolutionary selective forces of human genome that led to the emergence of multiple host protective alleles. A comprehensive understanding of the genetic bases of severe malaria susceptibility and resistance can potentially pave ways to the development of new therapeutics and vaccines. Genome-wide association studies (GWASs) have recently been implemented in malaria endemic areas and identified a number of novel association genetic variants. However, there are several open questions around heritability, epistatic interactions, genetic correlations and associated molecular pathways among others. Here, we assess the progress and pitfalls of severe malaria susceptibility GWASs and discuss the biology of the novel variants. Results We obtained all severe malaria susceptibility GWASs published thus far and accessed GWAS dataset of Gambian populations from European Phenome Genome Archive (EGA) through the MalariaGen consortium standard data access protocols. We noticed that, while some of the well-known variants including HbS and ABO blood group were replicated across endemic populations, only few novel variants were convincingly identified and their biological functions remain to be understood. We estimated SNP-heritability of severe malaria at 20.1% in Gambian populations and showed how advanced statistical genetic analytic methods can potentially be implemented in malaria susceptibility studies to provide useful functional insights. Conclusions The ultimate goal of malaria susceptibility study is to discover a novel causal biological pathway that provide protections against severe malaria; a fundamental step towards translational medicine such as development of vaccine and new therapeutics. Beyond singe locus analysis, the future direction of malaria susceptibility requires a paradigm shift from single -omics to multi-stage and multi-dimensional integrative functional studies that combines multiple data types from the human host, the parasite, the mosquitoes and the environment. The current biotechnological and statistical advances may eventually lead to the feasibility of systems biology studies and revolutionize malaria research. DA - 2019-08-14 DB - OpenUCT DP - University of Cape Town KW - Genome-wide association study KW - P. falciparum malaria KW - Susceptibility KW - Resistance KW - Heritability KW - Pathways KW - Fine-mapping KW - Multi-omics KW - Systems biology LK - https://open.uct.ac.za PY - 2019 T1 - Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects TI - Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects UR - http://hdl.handle.net/11427/30693 ER - | en_ZA |
| dc.identifier.uri | https://doi.org/10.1186/s12920-019-0564-x | |
| dc.identifier.uri | http://hdl.handle.net/11427/30693 | |
| dc.identifier.vancouvercitation | Damena D, Denis A, Golassa L, Chimusa ER. Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects. 2019; http://hdl.handle.net/11427/30693. | en_ZA |
| dc.language.rfc3066 | en | |
| dc.rights.holder | The Author(s). | |
| dc.subject | Genome-wide association study | |
| dc.subject | P. falciparum malaria | |
| dc.subject | Susceptibility | |
| dc.subject | Resistance | |
| dc.subject | Heritability | |
| dc.subject | Pathways | |
| dc.subject | Fine-mapping | |
| dc.subject | Multi-omics | |
| dc.subject | Systems biology | |
| dc.title | Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects | |
| dc.type | Journal Article |