Geoscience Reference
In-Depth Information
quencing technologies can now be conducted faster and less expensively than
was possible with previous generations of technologies. Next-generation se-
quencing technologies are substantially different from those based on the origi-
nal Sanger method (Box C-1) and promise remarkable increases in sequencing
capabilities.
Next-generation sequencing instruments have made it possible to sequence
huge amounts of DNA quickly, thoroughly, and affordably and have opened
opportunities to study a wide array of biologic questions, from the metagenom-
ics of water, to characterization of the genetic basis of species differences in
response to environmental insults, to human variability in susceptibility to envi-
ronmentally related diseases. Third-generation sequencing promises to provide
full genome sequencing of individuals (humans or other organisms) for less than
$1,000 per genome by the end of 2013 (Valigra 2012), and at least one company
already offers such services at about $5,000 per genome (Knome 2012).
TRANSCRIPTOMICS
The sequencing of the human genome, and of the genomes of hundreds of
other model organisms of great importance for human and environmental health
constitutes an enormous step forward in understanding genetic origins of dis-
ease, genetic variability, evolutionary biology, and many other subjects of scien-
tific relevance to EPA. However, from a biologic perspective, it is the expres-
sion of the genes in specific cells and tissues that ultimately defines an organism
and how it responds to its environment. Thus, measuring the extent of gene ex-
pression at a given time in a particular cell or tissue is potentially even more
informative of biologic mechanisms. The universe of small RNA molecules that
are transcribed from DNA and that are present in a cell or tissue at any given
time is referred to as the transcriptome. In the last 2 decades, new tools have
been developed that allow one to analyze the entire transcriptome in a cell or
tissue and to study changes in gene expression that might be created by changes
in the environment, such as exposure to a chemical. There are now microarray
methods that allow for the analysis of virtually all mRNA molecules that are
transcribed from active genes. Typically, these arrays contain hundreds of thou-
sands of unique features that quantitatively identify the amount of a particular
mRNA transcript in the sample. Having multiple features that can use the array
to look at different parts of a single gene, such as different exons or exon-intron
boundaries (potential splice sites), provides a remarkable snapshot of what genes
are functioning in a cell at a particular time.
To study complex and common diseases that may be influenced by envi-
ronmental factors (such as cardiovascular disease and cancer), human studies
typically require high-quality DNA from thousands of patients, often from small
quantities of tissues or blood. Several common commercial microarrays for
RNA applications in studies of this sort have been available for more than a dec-
ade and measure the expression of individual genes. However, understanding the
human transcriptome is much more complex than simply measuring the com-
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