Student Awarded

Selassie Kumordjie

Selassie Majola Sawyerr Kumordjie

Country: Ghana

Project Title: Plasmodium falciparum genetic variations underlying acquisition of malaria infections among Ghanaian children

Institution: Kwame Nkrumah University of Science and Technology

During my 3 month stay in Brown University, I will be trained in the Molecular Inversion Probe (MIP) technique for studying Plasmodium falciparum (Pf) genetic diversity and bioinformatics tools for analysing sequenced data. The MIP technique is highly sensitive and specific and has the added advantage of being low cost compared to other sequencing techniques. I will use this technique on over 600 positive clinical and asymptomatic Pf samples. Sample analysis will also be carried out using MIPWrangler pipeline to analyze sequenced data. Differences between the observed sequence and the reference sequence for each probe will be obtained by pairwise alignment using LastZ software. Single nucleotide variants and indels from the LastZ output will be annotated using Annovar software and the SeekDeep software used to estimate haplotype frequencies.

It is anticipated that the training will provide data on parasite antigenic diversity and its impact on risk of malaria within endemic populations. Data on genetic diversity in vaccine candidate genes will inform better vaccine design. The prevalence of drug resistance markers will inform national control programs.

Report Back – Skills Gained

Visit to Dr Jeff Bailey’s lab, Department of Pathology and Laboratory Medicine, Brown University, Rhode Island, USA

  • Next Generation Sequencing (NGS)
  • targeted sequencing of Plasmodium falciparum drug resistance genes
  • fragment analyzer
  • digital droplet PCR
  • MIPanalyzer
  • Recombinant Primer Amplification
  • GIMP software

African Supervisor

Anita Ghansah

Anita Ghansah

African Host Country: Ghana

Institution: Noguchi Memorial Institute for Medical Research

Laboratory: Genomics Team

Dr. Anita Ghansah is Senior Research Fellow in the Department of parasitology at the Noguchi Memorial Institute for medical research, a leading biomedical research institute in Ghana. She has a background in molecular and genomic epidemiology. She has developed Single Nucleotide Polymorphism (SNP) based methods defining sickle haemoglobin haplotypes which provide insights beyond that found with conventional methods based on Restriction Fragment Length Polymorphism.

Dr Ghansah’s lab team is interested in using genomic epidemiological tools to answer questions of public health importance in malaria and other parasitic diseases. They use population genetic strategies to identify genetic loci that contribute to drug resistance in Plasmodium falciparum. They also develop genomic tools to characterize Plasmodium falciparum diversity populations.

International Supervisor

Jeff Bailey

Jeff Bailey

International Host Country: United States of America

Institution: Brown University

Laboratory: Bailey’s Lab

Bailey lab is in the Department of Pathology and Laboratory Medicine at Brown University. The laboratory is mainly focused on the genetic variation in immunity and disease from both host and pathogen interaction. The laboratory is also interested in the role of variation of the malaria parasite on Burkitt Lymphoma a major childhood cancer found in malaria endemic areas, a disease known to be caused by Plasmodium falciparum and Epstein Barr Virus.

Together with other collaborators the team work on Type 1 Diabetes looking at T-cell receptor variation; they are also involved in optimizing methods for detection of Babesiosis a distant relative of the Plasmodium parasite.

The lab is headed by Prof Jeff Bailey an Associate Professor of Translational research. His research is an integrated one, combining experimental and computational approaches. The majority of his research focuses on the malaria parasite infection, parasite genome structure and tracking the spread of drug resistance. He has made major contributions to methods analysing whole genome sequencing in particular studying segmental duplication and copy number variation. He has more recently developed a high through-put pathogen targeted sequencing to track pathogens across space and time.