From Data to Insight – A Practical Introduction to Interpreting Malaria Genetics for Surveillance

In this optional introductory module you will briefly review the basic epidemiology of malaria, including its transmission, health outcomes, diagnosis, treatment, and prevention. By briefly reviewing the basics of malaria epidemiology, you will be ready to apply your existing knowledge to the more advanced concepts of genetic surveillance later in the course.

Traditional surveillance is the foundation of effective malaria control, but it has some limitations. In this module, you will learn how genetic surveillance can complement traditional surveillance and epidemiological studies to fill in knowledge and data gaps. The main use cases and essential metrics of malaria genetic surveillance are also summarized.

What can the DNA of malaria parasites tell you about where an infection came from, if you will be able to detect it with a standard rapid diagnostic test, and if it will respond to antimalarial drugs? In this module you will explore the relationship between genetics and the transmission and biology of malaria, and how genetics can be used to answer these and other questions. You will also learn about genetic variation and how to interpret simple phenotypes from malaria parasites and vectors.

Drug and diagnostic resistance are two of the most relevant genetic epidemiology use cases. In this module you will explore the relationship between drug resistance marker genotypes and malaria treatment outcomes. You will also learn the genetic basis of diagnostic resistance. Finally, you will discuss how you can track drug and diagnostic resistance in the field, and what is the relevance of genetic surveillance.

Different use cases require different methods. This module explores the strengths and weaknesses of different techniques for generating genetic data, from simple and traditional methods to next generation sequencing. You will learn how to choose appropriate techniques for common use cases, including identifying vector species, TES, drug resistance, diagnostic and insecticide resistance. Finally, you will gain a basic insight into next-generation sequencing, its capabilities, and how the tools we employ to analyze genetic data operate.

Now that you've generated some genetic data, you need to choose the right metrics. In this module, you will learn how to choose the appropriate metrics derived from genetic data depending on the questions you are asking. You will also learn to match measures of genetic diversity to different epidemiological scenarios and how to assess transmission intensity and connectivity in different populations.

Genetic data are only as good as the surveillance system or study that from which they were collected. But what makes a good malaria genetic surveillance study? In this module, you will start to learn how to design effective genetic surveillance studies. Topics include study design, sampling, stratification, power and sample size. You will also learn how to critically assess the pros and cons of different approaches to study design for different use cases.

The goal of malaria genetic surveillance is to design and deliver more effective control programs, which will prevent illness and death. In this final module, you will focus on turning insights gleaned from malaria genetic data into actionable public health recommendations. You will learn how to correctly interpret combinations of results, choose the best way to present your findings to different stakeholders, and avoid common pitfalls that could lead to misinterpretation of your results.