What are genomic technologies?

The process by which scientists can obtain genetic information from an individual (or to identify pathogens, for example) has evolved considerably over the past few decades. What follows is a general overview by a non-specialist for non-specialists. Corrections and clarifications from specialists are, however, welcome, and the intention is that this section will evolve over time to incorporate a list of useful references and starting points for those interested in better understanding the basics.

For many years, genetic information was obtained using tests which were collectively known as “Genetic tests”. Genetic tests can take a variety of forms. One example is FISH (fluorescence in situ hybridisation) testing, which can identify key chromosomal abnormalities but provides a relatively low resolution view of the whole genome. One common application of FISH testing is to measure the amount of the HER2/neu gene in cancer cells in patients with breast cancer in order to determine whether Herceptin therapy is appropriate. Another example of a genetic test is Sanger sequencing, which can be used to analyse the coding sequence of a gene in order to identify mutations relevant to disease diagnosis, prognosis or to guide treatment decisions.

The past two decades have seen considerable advances in genetic testing, such that scientists are now able to obtain far more genetic information, more quickly and more accurately. The tests that allow them to do this are collectively known as “Genomic tests”. Again, these can take a variety of forms. Whereas FISH testing can identify broad chromosomal changes, a genomic test called microarray testing can provide a view of the whole genome at a much higher resolution, increasing the rate of detection of chromosomal abnormalities and permitting the detection of combinations of genetic changes, better informing disease diagnosis and prognosis, or guiding treatment decisions.

Next generation sequencing (NGS) technologies also exist which improve on Sanger sequencing by permitting the simultaneous analysis of all coding sequences of genes. NGS technologies can take several different forms. If the whole genome is sequenced, including exons (protein-coding sequences) and introns (non protein-coding sequences), this is called whole-genome sequencing (WGS). If only exons are sequenced, this is whole-exome sequencing (WES). Some NGS approaches can result in clinically relevant mutations being missed, which has led to the development of a third variation: targeted NGS. This is a reduced form version of NGS in which a selected panel of genes (a targeted sequencing panel) known to be involved in a particular disease are sequenced in greater depth to minimise this error rate. NGS technologies are still relatively expensive (as of late 2016), but costs are falling all the time, and the different forms of NGS (in particular WGS) will eventually become the ‘workhorse’ genomic test, rendering genetic tests and less informative genomic tests such as microarray testing redundant.

So, broadly speaking, genomic technologies are tests such as microarray testing and the various applications of NGS, which, compared to commonly used genetic tests, provide a greater quantity of better quality genetic information, with the potential to enable improved disease stratification and individually tailored therapies. With these improvements to clinical practice come new challenges for health economists conducting economic evaluations of these technologies, and it is these challenges that are the focus of this blog.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s