Introducing somatic genomic tests

So, we have looked at how genomic testing has changed over time, but what types of tests do you need to know about?

In this two-step article, we’ll consider the key molecular and genomic tests that are available to cancer patients to guide their management. A full list of genomic tests can be found in the National Genomic Test Directory. By the end, you should have an understanding of the different tests available, the situations where they are appropriate, and their advantages and limitations.

Learn with GeNotes

As you move through these steps, feel free to click on the links in the text, many of which lead to GeNotes – a website containing educational resources to support clinicians requesting and receiving results of genomic testing. These resources will provide helpful context for the more complex parts of the course, such as this one, and open up new educational avenues for you to pursue, should you wish to. We recommend opening these links in a new tab – to do this, either right click on it and select ‘Open link in new tab’ or hold the Ctrl key and left click.

An overview of the tests we’ll be covering

There are a wide range of tests included in the National Genomic Test Directory for cancer – too many to cover in detail here. While we won’t be exploring all of them, we have chosen a selection that are particularly important and well-used. The tests fall into two categories – sequencing-based and non-sequencing-based – and we’ll look at them in turn across the two steps in this article.

_{Figure 1: An overview of key somatic genomic tests from the National Genomic Test Directory for cancer}

Let’s get started.

Targeted mutation testing and single gene sequencing

Whole genome sequencing and gene panel testing

_{Figure 2: The sequencing pathway}

Comparing paired WGS and gene panels: advantages and limitations

_{Figure 3: The advantages and limitations of paired whole genome sequencing and gene panels}

• Data can be revisited. If initial analysis doesn’t yield a diagnosis, it may be possible to go back to the original data and spread the net wider to reassess it for clinically relevant variants. While gene panel data can be revisited, analysis is restricted to the regions originally sequenced.
• Structural and copy number variants can be detected. This can give us a complete picture of the variation that has occurred within the cancer cells.
• Mutational signatures can be analysed. This allows us to identify patterns within the cancer cells, which can give clues to the causes of oncogenesis.
• Tumour mutational burden can be calculated. This is the number of somatic variants present within the tumour.
• Constitutional (germline) variants can be detected. These can indicate a person’s inherited cancer risk.

• Deeper sequencing is possible compared to WGS. This means more reads covering the same region of the genome. This is beneficial as it allows more sensitive detection of mosaicism, the presence of variants in some cells but not others, if suspected.
• Faster and more cost effective than WGS, as there is less data to generate and analyse.
• Less chance of incidental and uncertain findings arising compared to WGS, as there is less data generated outside of clinically relevant genes.
• Data storage is easier than WGS as there is less data to store.
• Unlike WGS, which requires fresh-frozen tissue, gene panels can be done on formalin-fixed, paraffin-embedded (FPPE) tumour tissue. We’ll explain more about this below.

What are virtual panels?

Virtual panels restrict which data is analysed, resulting in less data to analyse. This makes analysis faster and reduces the chance of incidental and uncertain findings. However, if a virtual panel does not yield a result, it is possible to expand the analysis to other regions that have been sequenced. Virtual panels are typically applied to WGS data, but may also be applied to large panel data.

Before we move on: a note about tests and sample types

Gene panel tests, single gene testing, or targeted mutation testing can be undertaken on DNA extracted from formalin-fixed, paraffin-embedded, or FFPE, tumour tissue.

In paired WGS, for solid tumours, fresh-frozen tumour tissue provides the somatic cancer DNA sample, with a blood sample usually providing the constitutional (germline) DNA. In contrast, for haematological malignancies, a blood sample provides the somatic cancer DNA sample, with a skin biopsy usually providing the constitutional DNA.

_{Figure 4: The different sample types required for different types of tests}

With current clinical pathways, most tissue obtained routinely is FFPE. WGS tumour testing requires fresh-frozen tissue to be available, and specific pathways and protocols need to be established to support this which may not be currently in place in all clinical settings.

More detailed information about samples and the role of histopathology in the solid tumour pathway will be discussed in the second week of the course.

Now, let’s move on to the second part of this article to learn about non-sequencing-based genomic tests.