Clinical Chemistry - Podcast

Unconventional Diagnosis Based on Somatic Findings through Germ Line Whole-Exome Sequencing

Jaime Lopes

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Jaime L. Lopes, et al. Unconventional Diagnosis Based on Somatic Findings through Germ Line Whole-Exome Sequencing. Clin Chem 2020;66:48-50.


Dr. Jaime Lopes is a Fellow at the Genomics Laboratory in the Department of Laboratory Medicine and Pathology at the Mayo Clinic in Rochester, Minnesota.


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Bob Barrett:
This is a podcast from Clinical Chemistry, sponsored by the Department of Laboratory Medicine at Boston Children’s Hospital. I am Bob Barrett.

Molecular diagnostics is now firmly entrenched in laboratory medicine and the January 2020 issue of Clinical Chemistry is devoted to this topic. In that issue is a case report that presents an unconventional diagnosis based somatic findings through germline whole-exome sequencing. Joining us in this podcast is the lead author of that case report, Dr. Jaime Lopes, who is currently a fellow at the Genomics Laboratory in the Department of Laboratory Medicine and Pathology at the Mayo Clinic in Rochester, Minnesota. So, Dr. Lopes, what is whole exome sequencing?

Jaime Lopes:
Whole exome sequencing, also referred to as exome sequencing, is an advanced laboratory technique that quickly and simultaneously sequences the entire protein coding regions in a genome. So, only 1% of the human genome is actually translated into protein coding regions which are collectively referred to the exome. And it’s much cheaper to sequence the exome as compared to the entire genome because with exome sequencing, we just focus on that 1% which is the part that we understand best, at least in terms of human disease. And the goal of this more exploratory approach is to identify genetic variants that alter protein sequences and cause genetic disease at a much higher diagnostic yield than traditional technologies which typically only look at one or a few genes at a time.

Bob Barrett:
And who typically gets whole exome sequencing?

Jaime Lopes:
Well, at least in the clinical setting, exome sequencing as a diagnostic tool is relatively new. It was originally pretty costly, so it was reserved for those that would benefit most and that would be young children with severe genetic disorders that remained undiagnosed even after undergoing numerous traditional genetic testing methodologies. And the benefits of having a genetic diagnosis in these cases are many.

For example, a particular diagnosis might indicate one treatment over another. Also knowing the underlying cause is necessary to counsel family members as to their own risks, or even recurrence risks for future pregnancies. And many times, having a diagnosis can help guide expectations of the disease course. Now, as the costs of exome sequencing have significantly decreased with time, the clinical utility has expanded. So, we are now seeing older and healthier patient populations undergoing whole exome sequencing for much broader clinical indications that may not, at least with our current understanding have a large underlying genetic component. And while many times there’s a real benefit for these patients, because we are looking at all of the genes in the genome, there is a real risk of also uncovering secondary findings that the patient wasn’t really expecting. So, it’s just important that the patient understands that this is a possibility and therefore, genetic counseling prior to testing is recommended for anybody who’s considering whole exome sequencing.

Bob Barrett:
Secondary findings, that sounds like a can of worms. Could you discuss what you mean by that?

Jaime Lopes:
Sure. So, in a genomics laboratory at least, secondary findings refer to clinically meaningful genetic variants that do not directly relate to the reason of referral. So, for example, a seven-year-old undergoes whole exome sequencing to uncover a possible genetic cause for his seizures, and we find a disease-causing mutation in the BRCA1 gene. Now, mutations in BRCA1 incur a high risk of breast or other cancers but are not responsible for the original reason for referral which was seizures. So, not only is there a future risk to this child being tested, but there’s a good possibility that some of the family members are carriers of this mutation and are also at risk or may have already even been affected.

So, while this finding is of great clinical concern, we can’t really report this information back to the patient or the patient’s family without their prior consent and that’s because as you can imagine, some individuals are very curious to know about additional findings while others are just having enough stress dealing with the issue at hand. But thankfully, we do have some really good guidelines to help us with secondary findings in the clinic and nowadays, prior to testing, all patients undergoing whole-exome sequencing decide upfront if they want to know about these secondary findings, and patients who consent to receive secondary findings are evaluated for known pathogenic variance in a list of 59 genes that are considered clinically actionable in accordance with recommendations by the American College of Medical Genetics, or ACMG. And these guidelines currently place a large focus on genes that incur a high risk of cancer or heart disease that are inherited in an autosomal dominant fashion and this is because intervention could be helpful, for instance, prophylactic surgeries, earlier or more frequent screening, or even preventative therapies.

And it’s important to note that this is not a static list, it’s updated as we learn more about genetic disease.

Bob Barrett:
What was unique about the secondary findings in this case?

Jaime Lopes:
Well, currently these guidelines considered germline variants when dealing with secondary findings. Germline variants are inherited genetic variants that are present at birth and typically found in all cells.

In the case featured in our report, the secondary findings in question were somatic in origin and that means they were acquired after conception. Acquiring genetic alterations is just a normal part of the ageing process and these alterations usually don’t mean anything, but some somatic variants are indicative of an underlying tumorigenic process and that’s what we found in our patient. So, while the reason for referral was to look for germline variant underlying the patient’s neurological disorder, instead we uncovered somatic variants that were evidence of an unrelated hematological abnormality that was particularly suspicious for an occult malignancy.

However, variants associated with somatic disease are not typically addressed prior to testing because they’re not included in the secondary findings guideline. And this makes sense because traditionally as I said earlier, whole exome sequencing was indicated for more younger patients with severe genetic disorders, but as costs have decreased, we have an older and healthier population taking advantage of this technology and while you can find somatic disease in any age group, they’re just more common in adults. Additionally, the sensitivity of high throughput sequencing has improved, so we detect variants that are present in even lower levels than typically expected from that of germline variants. In the end, in our case, we disclosed the secondary findings.

Our patient was then referred for a bone marrow biopsy and additional testing which eventually led to a diagnosis of what’s called clonal cytopenia of undetermined significance, or CCUS, and this is not, luckily, a myeloid malignancy, but it does have a particularly high risk of progression to malignancy, so periodic follow-up was advised and this case is unique because it demonstrates how the detection of clinically meaningful variants associated with somatic disease is now not just possible, but could dramatically change the management and even the outcome of the patient.

Bob Barrett:
So, are you saying that labs performing whole exome sequencing should disclose these findings if they’re uncovered?

Jaime Lopes:
Actually, that’s a very complicated question for a few reasons. For one, somatic variants might not even get detected to begin with. Many of these variants are in genes that aren’t associated with inherited disease and because they are acquired later in life, they’re typically present in much lower levels than those variants that are in the germline and present from birth and high throughput sequencing generates a very large amount of data.

So, variant frequency is one really good filter that we have too weed out false calls. So, depending on the filtering strategy employed by the particular lab, lower frequency calls might actually be filtered out of the review process entirely. And even when it’s detected, it’s not always clear what these variants mean, and ordering providers and laboratory scientists that are familiar with inherited disorders might not really be familiar with genetic variants associated with somatic diseases.

Our case was fairly straightforward because for one, both parents of the patient were tested and they were negative for the uncovered variant, so this information, along with the low-variant frequencies made us feel confident that the variants of interest were acquired and not inherited and also, these variants were previously reported in the literature as being associated with certain hematologic malignancies. But even so, we weren’t entirely sure if this was something that we should report since guidelines for the reporting of these variants associated with somatic disease detected through whole exome sequencing for inherited disorders don’t currently exist. There is no consent forms typically that we give our patients prior to testing that we might uncover some sort of evidence of a hematological malignancy or disorder. As you can imagine, both the detection and the interpretation and even the reporting of these somatic variants during whole exome sequencing for inherited disorders is quite complex.

Bob Barrett:
Well, finally, Dr. Lopes, to sum up, what’s the take-home message from this report?

Jaime Lopes:
Well, first, it’s important to note that as our technology continues to become more sensitive and adult populations are undergoing whole exome sequencing for more broader testing applications, the detection of somatic variants like the ones that we found in our case will likely only increase. And specifically, since peripheral blood is the standard sample source for exome sequencing, the possibility of uncovering an undiagnosed hematological abnormality or malignancy is most apparent. Other types of malignancies outside of the hematologic system are unlikely to be detected by whole exome sequencing performed on whole blood. And finally, I just hope that this case serves to increase awareness and possibly initiate a discussion on when and how to integrate similar findings into clinical care moving forward.

Bob Barrett:
That was Dr. Jaime Lopes from the Genomics Laboratory in the Department of Laboratory Medicine and Pathology at the Mayo Clinic. She has been our guest in this podcast on her case report of an unconventional diagnosis based on whole- exome sequencing. That article is one that appears in the January 2020 issue of Clinical Chemistry focusing on molecular diagnostics. I’m Bob Barrett. Thanks for listening.