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Introducing somatic genomic tests

We explore four somatic genomic tests that are important to know about in the first instalment of this two-part article.
© National Genomics Education, NHS England

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.

Sequencing-based tests: Targeted mutation testing; single gene sequencing; gene panel testing; whole genome sequencing (WGS). Non-sequencing-based tests: fluorescence in situ hybridisation (FISH); molecular tumour profiling; homologous recombination deficiency (HRD) test; immunohistochemistry (IHC); microsatellite instability (MSI) testing
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

Targeted mutation testing is used when there is a known variant that we need to test for the presence or absence of. In these cases, it is only necessary to sequence the parts of the gene containing the variant of interest, or just the specific variant itself, rather than the whole gene. An example of this would be testing for the BRAF V600E variant in colorectal cancer or melanoma.
Single gene sequencing is useful when testing for conditions with a single genetic cause. However, there are very few situations where a single gene is the only known clinically relevant target in cancer, and so this is not commonly used in tumour DNA testing.

Whole genome sequencing and gene panel testing

Whole genome sequencing (WGS) sequences all genes and the majority of non-coding regions of the genome. Gene panels sequence specific genes of interest for a particular condition or phenotype, and can vary in size from just a handful of genes to much larger panels.
Whole genome sequencing and gene panels are conducted using massively parallel sequencing, sometimes known as next-generation sequencing, a process that allows us to sequence many thousands of DNA fragments simultaneously, leading to much faster, more cost effective, high throughput sequencing. After sequencing takes place, we get a large amount of raw data, which is processed and analysed using a bioinformatics pipeline. This results in a shortlist of variants, which are then analysed to determine whether any of them have clinical significance for the patient.
Pathway showing left-right: Massively parallel sequencing technology; raw sequencing data; bioinformatics pipeline; 'shortlist of variants'; variant analysis.
Figure 2: The sequencing pathway
When we talk about ‘paired WGS’, we mean where the tumour genome is compared to the patient’s genome. This can help to identify tumour variants of importance, but it can also identify if the person has a constitutional (germline) variant affecting their chance of developing cancer.

Comparing paired WGS and gene panels: advantages and limitations

Figure 3, below, directly compares paired WGS and gene panels, followed by more information on the main advantages of each.
Table with the advantages and limitations of paired WGS when compared to gene panels
Figure 3: The advantages and limitations of paired whole genome sequencing and gene panels
The main advantages of paired WGS include:
  • 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.
The main advantages of gene panels include:
  • 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.

Solid tumours: Fresh-frozen tissue (somatic) and a blood sample (constitutional); Haematological malignancies: Fresh-frozen tissue (somatic) and a skin biopsy (constitutional)
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.

© National Genomics Education, NHS England
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Genomics in the NHS: A Clinician's Guide to Genomic Testing for Cancer (Solid Tumours)

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