Resources- WGS
Whole genome sequencing (also known as WGS, full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.
Introduction to Whole
Genome Sequencing (WGS)
Whole genome
sequencing (WGS) reveals the complete DNA make-up of an organism, enabling laboratory
scientists and epidemiologists to better understand variations both within and
between species. Understanding these variations allows differentiation between
organisms with a precision that other technologies do not allow. Government agencies at all levels are in the
process of integrating WGS to take advantage of the improved precision. Examples include:
-
Food and Drug Administration
(FDA) has been using WGS since 2008. The
FDA is using WGS to perform basic foodborne pathogen identification during
foodborne illness outbreaks, and applying it in novel ways that have the
potential to help reduce foodborne illnesses and deaths over the long term both
in the U.S and abroad.
- Compare pathogens
isolated from food or environmental samples with clinical isolates from
patients. If the pathogens found in the food or food production environment
match the pathogens from the sick patients, a reliable link between the two can
be made, which helps define the scope of a foodborne illness outbreak. WGS
performs the same function as Pulse Field Gel Electrophoresis (PFGE) but has
the power to differentiate virtually all strains of foodborne pathogens, no
matter what the species. Its ability to differentiate between even closely
related organisms allows outbreaks to be detected with fewer clinical cases and
provides the opportunity to stop outbreaks sooner and avoid additional illnesses.
- Pair genomic
information of foodborne pathogens with their geographic location and apply the
principles of evolutionary biology to determine the relatedness of the
pathogens. Knowing the geographic areas that pathogens are typically associated
with can be a powerful tool in tracking down the root source of contamination
for a food product, especially multi-ingredient food products whose ingredients
come from different states or countries. The faster public health officials can
identify the source of contamination, the faster the harmful ingredient can be
removed from the food supply and the more illnesses and deaths that can be
averted.
FDA is spearheading an international effort to
build a network of laboratories that can sequence the genomes of foodborne
pathogens and then upload the genomic sequence of the pathogen and the
geographic location from which the pathogen was gathered into a publicly
accessible database. As the size of the database grows, so will its strength as
a tool to help focus and speed investigations into the root cause of illnesses. GenomeTrakr is a growing distributed network
of labs with the capability to utilize WGS for pathogen identification.