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    Optimizing a Selective Whole Genome Amplification (SWGA) Strategy for Clinical Malaria Infections

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    Mariah Alawi Thesis.pdf
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    Mariah Alawi
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    Type
    Thesis
    Authors
    Alawi, Mariah cc
    Advisors
    Pain, Arnab cc
    Committee members
    Habuchi, Satoshi cc
    Blilou, Ikram cc
    Program
    Bioscience
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Date
    2019-08
    Permanent link to this record
    http://hdl.handle.net/10754/656568
    
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    Abstract
    Plasmodium is a genus well known for causing malaria, a life-threatening infection for many people where malaria is endemic. The blood-borne disease is transmitted by the female Anopheles mosquito. Till date, eight parasite species have been reported to cause malaria in humans that include P. falciparum, P. vivax, P. malariae, P. ovale curtisi, P. ovale wallikeri, P. cynomolgi, P. knowlesi and more recently P. simium. Amongst them, the most genetically understood species is P. falciparum, causing most of the deaths in children from malaria. Understanding genome variation at the population level of all malaria species is of utmost importance, including clinical cases with very low parasitemia. To achieve this purpose, we need sufficient amounts of parasite DNA material from the pool of host DNA, which always is overrepresented in clinical infections. We utilized a strategy of selective whole genome amplification (SWGA) technology on P. malariae and P. ovale curtisi (two neglected human infecting malaria parasites that often cause mild yet clinically relevant infections with low parasitemia) to efficiently enrich their genomic DNA for high-quality whole genome sequencing. Previous studies on SWGA applied on P. falciparum and P. vivax showed that SWGA could efficiently enrich the amount of starting DNA material from inadequate amounts of parasites directly from clinical samples without separating the host DNA using specifically designed primer sets. We have successfully designed multiple sets of primers and tested the efficiency of five best primer sets using polymerase chain reaction to enrich the genomes of P. malariae and P. ovale curtisi. The efficiency of primers in enriching the genome was tested on two clinical samples for each of P. malariae and P. ovale curtisi. We were able to enrich the genome of P. malariae with an average of 19-fold (19X) enrichment across both samples. For P. ovale curtisi, we could achieve an enrichment of 3 folds only. Nevertheless, we still obtained a sufficient amount of gDNA to prepare Illumina sequencing libraries and call for SNPs and Indels in a biologically reproducible manner at genome-scale.
    Citation
    Alawi, M. (2019). Optimizing a Selective Whole Genome Amplification (SWGA) Strategy for Clinical Malaria Infections. KAUST Research Repository. https://doi.org/10.25781/KAUST-ROEE3
    DOI
    10.25781/KAUST-ROEE3
    ae974a485f413a2113503eed53cd6c53
    10.25781/KAUST-ROEE3
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