Pharmacogenomics

The use of genomics to guide pharmacological treatment is now routine in many areas of medicine from infectious disease to cancer treatment and general medicine.

In infectious disease, treatment resistance generally arises due to the acquisition by the pathogen of genetic elements encoding mechanisms to escape antibiotic or antiviral control. These genetic elements can be identified by sequencing of pathogen isolates using specific probes to answer a specific question. NGS techniques allow these questions to be answered rapidly and inexpensively so that treatment can be guided by the results.

An example: the management of Tuberculosis

The potential benefit of sequencing the whole genome of a single organism is usefully illustrated by considering Mycobacterium tuberculosis. Tuberculosis is an important burden on healthcare requiring not only a prolonged course of medication for the patient but also public health intervention to manage and minimise potential spread of infection.

Timely diagnosis and identification of drug resistance is the key to successfully managing this infection. M.tuberculosis is slow growing, sometimes requiring weeks to grow. Even once a pure culture of the organism is obtained it then can take many weeks before treatment sensitivities are available.

Having access to the full genomic information from an individual patient not only enables the search for mutations associated with resistance to multiple drugs but also has the potential to significantly reduce the time taken to identify drug resistance allowing earlier treatment modification.