Genomics and global health

Genomics is the study of the complete DNA sequence, for example of a particular parasite, allowing us to analyse its evolution and the impact of human interventions. Alongside clinical date, we use genomics to identify mutations that are markers for drug resistance. Mapping out drug resistance then helps inform elimination programmes.

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Because of malaria, millions of African children die before their first day at school. For decades, scientists and health authorities have raised hopes of eliminating this burden on the developing world, only to have these hopes dashed, time after time, by the astonishing adaptability of Plasmodium parasites, which seem capable of becoming tolerant to most drugs we deploy. Today, genomic technologies provide a powerful new weapon against these parasites. At the Centre for Genomics and Global Health, we have developed methods for determining the genetic code of Plasmodium parasite directly from blood samples taken from infected patients. Thanks to the falling cost of sequencing, and the reliability of our approach, we are now able to sequence literally thousands of parasites from clinical cases, and map this genomic information in geographical, ecological and historical contexts. Our goal is to determine how parasite populations change as a result of human intervention and environmental change, and observe new epidemiological trends in real time, to inform and guide public health intervention. In other words, "genomic epidemiology" will monitor Plasmodium evolution, so that humanity can keep steps ahead of the parasite.

Olivo Miotto focuses on translating the massive quantities of data produced by sequencing thousands of genomes into meaningful knowledge about the epidemiology of Plasmodium falciparum. By analyzing hundreds of thousands of genomic variations in each blood sample, he studies the genetics of parasite populations in four continents, and identifies patterns of evolution associated to responses to drug pressure and other human interventions. Based in Bangkok, Olivo collaborates with many clinical research groups in malaria endemic regions, particularly in Southeast Asia, to study relationships between  response to clinical therapy and genetics of the disease-causing parasites in the patient. In the early stages, the focus is on immediate problems, such as discovering mutations causing resistance to current drugs, such as artemisinin. However, Olivo's longer-term perspective is to create tools that will identify patterns in thousands of accumulated genomic sequences, leading to a deep understanding of parasite evolution and, ultimately, to interventions that will win the struggle against the disease.

When learning about Darwin at age 12, Olivo thought evolution was the coolest thing he had heard of. It took him decades to realize that it was also the best use for his skills. In between, he studied physics and worked as a software engineer, both in the commercial and academic worlds. At various times he focussed on Web applications, graphical user  interfaces, speech synthesis, online learning, and database systems, before finally switching to bioinformatics and genomics.