Reading a genomic test report: What you need to know

A huge benefit of genomic testing of solid tumours is that it allows us to choose treatments that are tailored to the individual, but this adds complexity when interpreting results. In the following steps, we’ll work through how to read and interpret a genomic test report – the report received from the laboratory. We’ll just be covering tumour-only test results here, so this will not include whole genome sequencing.

The process

Before we learn about the report itself, it is helpful to understand the process, from initial request to patient record. Firstly, the clinical team will send a request to the genomics laboratory – this is usually paper-based. Next, the staff at the laboratory will perform wet lab genomic sequencing and then analyse the data. Findings will be sent back to the clinical team electronically in the form of a genomic report and the pathologist will incorporate them into the patient record.

_{Figure 1: The reporting pathway}

Navigating a test report

Now, we’re going to work through some genomic reports so that we can understand the elements that we might expect to see.

Below is a report for a patient with a lung adenocarcinoma who had a non-small cell lung cancer (NSCLC) gene panel analysis. Most genomic reports will look similar with comparable sections and information. We’ll look at each of the elements in the report in turn.

_{Figure 2: An example genomic test report}

Clinical summary

_{Figure 3: Screenshot of clinical summary section on example genomic test report}

The clinical summary is found at the top of the test report and contains the information that the laboratory has been sent on the test request form. This includes why the clinician wants the patient to be tested and what they want them to be tested for. The information in the clinical summary will have been linked back to the National Genomic Test Directory to work out which genes needed to be tested.

National Genomic Test Directory: NSCLC

By consulting the test directory, we can see that, for this patient, the test codes from M4.1 down to M4.11 should be used. This includes testing all the genes in the table below. These tests are not performed individually and may be done across one or two gene panels.

Test and result

This section of the report contains information about which test or tests were undertaken, in this case EGFR analysis, and the result, namely which genes have been found to contain variants and more detail about them. The result detail is in a format called HGVS nomenclature, a standardised way to describe variants.

_{Figure 4: Screenshot of test and result section on example genomic test report}

• ‘EGFR’ tells us that a variant has been found in the EGFR gene;
• ‘c.2573’ tells us that the variant is at nucleotide position 2573;
• ‘T>G’ informs us that the variant is a base pair change from a T to a G; and
• ‘p.(Leu858Arg)’ tells us that this results in a leucine to arginine substitution at amino acid position 858.

This section of the report also contains a section called VAF, or variant allele frequency, and we’ll return to that in the next step.

So, we know what test has been performed and that a variant has been found, but how do we interpret these results?

Interpretation

_{Figure 5: Screenshot of clinical interpretation section on example genomic test report}

Next, we have the clinical interpretation of the genomic test result from the laboratory. It’s usually indicated in a box or in bold so that it’s easy to see. In this case, the referring clinician is advised that the patient is likely to benefit from an EGFR tyrosine kinase inhibitor or TKI. It’s important to remember that laboratories will not use drug names in this section of the report, so don’t expect to see them here.

Notes

_{Figure 6: Screenshot of notes section on example genomic test report}

Another element you will find on a genomic report is a box called ‘Notes’ at the bottom, usually in small print. It’s important to be aware that this information exists but it’s not always crucial to read it every time you look at a report. Contained within this section are notes that go from lab to lab and will provide information about the genomic sequencing that was performed, including which genes have been sequenced and the limitations of the test. In this case, we can see the sequencing was performed by the Illumina TSO500 gene panel, which sequences 523 genes.

The notes also explain that this assay is able to detect five percent mutant DNA in a background of wild-type DNA, relating to the neoplastic cell content and VAF. We’ll come to these in the next step.

Receiving a failed report

_{Figure 7: Screenshot of a failed genomic test report}

Not all genomic tests are successful. Occasionally, you might receive a failed report and the laboratory should include a comment about what you can do next. In this case, the laboratory have recommended a repeat sample or biopsy, or indicated that circulating tumour DNA analysis may be an option.

Receiving a ‘VUS’ report

_{Figure 8: Screenshot of a VUS genomic test report}

You may also receive a report which contains a variant of uncertain significance, or VUS. A variant of uncertain significance means that a variant has been detected in a particular gene, in this case in the EGFR gene in a patient with NSCLC, and there isn’t sufficient evidence to know what impact it might have. These types of variants are rarely reported because they aren’t usually helpful for the clinician but occasionally they can be. If reported, the interpretation should be clear that the VUS can not be acted on. In this example, we can see that the laboratory have recommended against targeted treatment with an EGFR TKI after having identified this particular variant of uncertain significance.

Additional genes

You might remember from the notes section, 523 different genes were sequenced on the gene panel – far more than are included in the test directory for this indication. On the report, the laboratory might choose to provide some information about those additional genes outside the scope of the test directory. An example of this is shown in figure 9.

_{Figure 9: Screenshot of additional genes section on example genomic test report}

For this particular patient, we are primarily interested in those genes which are indicated for NSCLC in the test directory, but in this case there were no variants identified in those genes. An advantage of using large gene panels is that we can analyse additional genes which may be beneficial for the patient.

As you can see here, two gene variants have been identified in this report. The laboratory might not always interpret additional variants identified in this way, because it may not be helpful, but you can always get in touch with the laboratory and ask them to explain what any variants mean for your patient. At the bottom of the report, you can see information about a weekly Genomic Tumour Advisory Board (GTAB) meeting you could attend to discuss these results.

The benefits of reporting these investigational targets are the possibility that a patient may be eligible for a clinical trial or an Early Access to Medicine Scheme. Reporting these variants has a fast turnaround time as the testing is being done at the same time as standard of care testing. It is also an efficient use of tissue and resources, allowing us to gather more data that may end up being helpful from each test.

Now we’ve got to grips with the main sections of a genomic test report, let’s move on and look at variant allele frequency and neoplastic cell content in more depth.