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Variants of Unknown Significance (VUS) – doctors  beware!

Variants of Unknown Significance (VUS) – doctors beware!

27/07/2020
Posted by:

Dr.M.Raszek


The very first Canadian patient to get a DNA/RNA cancer predisposition test

We start with the story of a cancer survivor who just recently completed an advanced DNA/RNA sequencing combo test for cancer predisposition; it was not only the very first time this test was used in Canada, it was the first time it was used anywhere in the world outside of US. This test is so new that we were a little bit jealous that the patient would end up seeing the DNA testing kit even before Merogenomics had the chance to analyze one!

The patient is a female who was diagnosed with breast cancer at age 47 with three other family members diagnosed with breast or colon cancer (one in 50s and one also in 40s), so this person was a good candidate for cancer predisposition testing. It was especially important to her to determine if there were heritable DNA mutations involved in her cancer development for the sake of protecting her children. The idea was to find out if she did inherit such a cancer predisposition. If so, the company which was offering this advanced test, Ambry Genetics, would offer her complementary testing of her entire family if there were pathogenic or likely pathogenic mutations (or variants as mutations are referred to in scientific circles) uncovered. The reasoning behind this is that if a genetic predisposition was passed from mom to daughter, then the daughter could take the best informed, preventative measures. In addition , she could also commence an early and thorough screening process. Hopefully, in the unfortunate event that if the daughter develops cancer, then it would be discovered as early in the cancer development as possible, which typically increases the chances of a successful cancer treatment.

Image of Merogenomics article quote on free cascade DNA testing

Recently, the patient concluded her anti-cancer treatments and received the wonderful news that imaging exams revealed no further presence of the condition. Thus, the genomic testing was strictly for protective and preventative purposes.

 

Genetic privacy of Canadians is protected by law

Now, this patient’s action might seem counter-intuitive because if you could obtain a genetic diagnosis that could help you protect your loved ones, why would you not go for that option? But believe it or not, not that long ago, many women with cancer in Canada were too afraid to undergo such genetic testing for an even greater fear than the loss of the protective benefits of having a genetic diagnosis at hand.

This greater fear was of the possible future discrimination that their children could face due to any positive results of the genetic test. Meaning, if a parent were to be confirmed by DNA test that she (or he) had a genetic predisposition to cancer, then this would place their children at risk of not being able to insure themselves, or they might even face difficulties obtaining employment. This fear was so great that some parents took the risk of premature death rather than jeopardize the future safety of their children. And the reason why this fear even existed is because Canada had no legal protection against genetic discrimination. That is until recently, our genetic privacy was not protected by any laws.

But now it does! Our genetic privacy is fully protected in Canada, and no goods or services can be denied to any Canadian on account of their genetics. This was first sanctioned as law in 2017, as Bill S-201. This law has recently been further sanctioned by the Supreme Court of Canada when the Genetic Non-Discrimination Act was disputed as unconstitutional (on the account that it is a federal form of interference into provincial governance of such services as insurance or employment).

Image of Merogenomics article quote on genetic privacy Canada

The act was introduced by the now-retired Senator Jim Cowan along with Barbara Kagedan his Senior Policy Advisor, who had heard enough stories about the tragic consequences of fears of discrimination based on one’s own genetic make-up that they decided that they had to act and do something – anything - to protect the Canadians.

As you can imagine, this law is very dear to Merogenomics and it supports our goals to help bring Canadian patients and clinics access to DNA testing of medical value (as opposed to just entertainment or novelty value ). Merogenomics has been following this story for a very long time and had a chance to sit down with Cowan and Kagedan in Vancouver for a brief discussion even before Bill S-201 became law. We thought we would bring it out from the archives on account of the recent historic Supreme Court decision.

At the time of the interview, the future of the law was still very much up in the air as it was being heavily opposed by the insurance industry. Cowan had lots to say on that topic: “the first iteration of the argument [from insurance companies] was that people are going to go out and have a genetic test, find they have a predisposition to something, some condition and go out and buy multi-million dollar insurance policies. Then they are going to contract the condition, die and we will have to pay it out, and all the rest of you, your premiums will have to go up to pay for that. Ok, and that’s called adverse selection. It hasn’t happened anywhere else. And so why would we think it would happen here? They don’t answer that question. It’s just that people don’t do that. […] If I had a genetic testing and it showed that I had a predisposition to some cardiac condition, I don’t think my first reaction would be to go out and mortgage my house to buy insurance policy. I want to live! So I’m going to say ok, what can I do to change my chances of living? That’s where I’m going to spend my money I would think.”

We couldn’t agree more and exactly what Senator Cowen was describing is one of the top advantages of genetic testing we listed in our past posts. Cowen continued: “the privacy commissioner of Canada has done two studies and has concluded that for the foreseeable future, this legislature would have no impact on the insurance, or negligible impact on the insurance.”

Image of Merogenomics article quote on DNA testing and lifestyle choices by Senator Cowen

Knowing that “increased premiums” was a weak argument against such an important law, the tactics were changed in an attempt to sink the law, eventually attacking it on constitutional grounds.

Cowen elegantly explained what indeed turned out to be the future legal show-down at the highest level. “The real problem that we are up against now is lawyers in the department of justice are saying that this is provincial jurisdiction and […] that insurance is regulated at the provincial level. Much employment, employers are regulated provincially but the answer to that, and we got all kinds of highly qualified constitutional lawyers experts who say no, […] criminal sanctions are federal so it is perfectly legitimate for federal Parliament to legislate generally to prohibit or discourage something that they consider to be bad. So what we are saying is discrimination is bad, so we are, the bill would prohibit and penalize discrimination based upon this [personal genetics] as would with discrimination based upon other things. So as long as we don’t target a particular […industry like] insurance or employers, then the opinion that we received, it is ok, so long it is just a general prohibition. But if you start to target a particular industry then you run afoul of that jurisdiction.” If you were wondering why the jurisdictional dispute took place, Cowan summarized it years ago and provided a verdict that just recently was upheld by the Supreme Court.

When asked by Merogenomics how it all started, Cowen responded: “Barbara was there right from the beginning. When we first began to talk about it, and people like Bev Heim-Myers [CEO of Huntington Society of Canada] would come to the Hill to talk about, talk to the legislators about these kinds of issues, and then there were media stories, and then we began to reach out […] and hear the sort of real front line stories. And then you say ok, you know, we can give a speech about, or we can ask people, launch kind of an inquiry or study or something, and we concluded that the best way to do was to actually put something on the table.” Barbara Kagedan then also added: “I think the turning point for both of us was when we met Ronnie [current president and CEO of SickKids Hospital] for the first time and he told us some of the stories of what he was encountering in the SickKids hospital”, referring to the trauma that families encountered first hand with regards to genetic testing and the subsequent fear of a genetic discrimination.

It was a wonderful feeling to meet the people behind creating a law deemed so valuable by Merogenomics, plus seeing that the drive behind this legislation was so much passion to ease the suffering of ordinary Canadians touched by tough genetic conditions.

Merogenomics also supports the recent decision of the Supreme Court.

Now back to helping ordinary Canadians.

 

DNA and RNA testing is the new future of analysis

Our cancer survivor patient was excited to participate in this first-of-its kind cancer predisposition DNA and RNA test in Canada. So was Ambry Genetics which, through Merogenomics, is eager to introduce its expertise to physicians in western Canada. The uniqueness and value of this test cannot be understated. The addition of RNA into this test greatly increases the complexity of the test, so the development and validation of this test for clinical use took an immense effort by the company. Their reward is the first of its kind DNA and RNA test screening for inherited cancer predisposition. Testing both DNA and RNA significantly increases the depth of the test for its detection power. Ambry Genetics is a renowned company that is famous for many exceptional first-to-the-market genetic testing deliveries, including the first commercial gene panel testing of any kind, the first ever cancer predisposition gene panels, or first clinical testing of all genes (referred to as exome testing) including fetal screening. In addition, with over a million samples processed, the immense depth of experience is very impressive with this company.

Image of Merogenomics article quote on genetic privacy Canada

We previously mentioned this in the post dedicated to cancer DNA testing, but the take home message was that mutation events in the DNA might truly exhibit its effect only at the RNA level, (or the RNA can experience its own mutations but this then has nothing to do with hereditary predisposition because RNA exists only for short period of time). Chemical molecules making up DNA and RNA are nearly identical, and RNA is a tiny copy of DNA. If that RNA is then used as a guide map to produce proteins (these are the molecular robots within the cells that are working hard to make sure that the cell survives), that fragment of DNA is called a gene. But RNA is usually spliced together from multiple such copy fragments before it is considered mature. Sometimes mutations in the DNA can affect how the RNA is actually spliced together and thus, if correct splicing does not take place, the RNA could then act as a guide map to produce a malfunctional protein that could have a cancerous impact. For example, if that protein was a molecular robot checking when cells are supposed to divide, and it is now broken due to a wrong RNA splicing (which resulted in inaccurate guide map to produce the necessary protein), then this could possibly lead to cancer due to some cells experiencing uncontrolled growth.

Our cancer survivor was kind enough to send us photos of her kit. You can see that there are two different looking tubes present in the genetic test kit. Both are for blood collection. One tube is for isolation of DNA (the purple tube). The second one is for RNA isolation.

Image of DNA RNA test kit

The test results were overseen by Dr. Glenna Ramsay in Edmonton, AB. At the time when she agreed to order the test for the patient, she did not know that she would be the first in Canada to participate in this unique genetic “event”. We were not sure either. But Ambry agreed to extend to us access to their service that was only available before in the US. Merogenomics was invited to be present when Dr. Ramsay disclosed the results to the patient. It was impressive how well she understood everything from the report. Really, Merogenomics was there to add support in case anything in the report was not well understood, but Dr. Ramsay was well prepared. Merogenomics is very encouraged and excited by that. Look, not many doctors use medical DNA testing, yet. It is still a bit of an enigma to many medical professionals. So, for a doctor to step in and oversee a DNA test that might be totally unfamiliar is very impressive, and even more so when they show solid grasp of it. We at Merogenomics hope we can be part of this experience much more often!

The test results look potentially very easy to understand, but ironically, this is where a very serious mistake can be made if caution is not properly exercised. This is where we definitely want to raise awareness about and use this opportunity to educate doctors about Variants of Unknown Significance (VUS).

Do not mistake the unique significance of what a VUS really means to the patient’s care! You are not supposed to act clinically based on a reported VUS! Take caution. Definitely pay attention to the VUS description.

 

VUS and other variants reported to doctors

VUS might sound like a re-engineered SUV, but in essence it means a mutation that we don’t know what it does so we have no basis to act clinically. Since we do not know what it does, we should not act on it as that could potentially harm the patient. This has happened in the past. If you recall that variant is another word for mutation, then a variant of unknown significance becomes self-explanatory. But without connecting those dots, a simple VUS in a test result could be confusing.

VUS is only one of a few categories of DNA variants that are reported back to the doctor.

The most important and significant are the pathogenic variants and likely pathogenic variants. These variants always have to be taken into consideration and along with patient medical and family history context, the ordering doctor might consider altering how the patient’s condition is managed. The difference between pathogenic and likely pathogenic is the degree of accumulated evidence. Pathogenic variants have enough evidence supporting their clinical outcome such that the evidence is considered to be definitive. We feel very strongly that we understand very well how pathogenic mutation contributes to disease development. Likely pathogenic is below that evidentiary level but still requires careful attention by the treating physician.

Image of Merogenomics article quote on reported DNA variants

Next in line are those VUSes we mentioned earlier. Remember, management of the patient condition is not supposed to be altered based on variants of unknown significance because we do not know enough about what it does. Some companies report VUSes that they upgrade to a status of potentially pathogenic, but even then doctor is not to act on that unless they have some very convincing evidence that was not known to those issuing the report. For example, a hospital might see certain types of mutations in their immediate population and they might understand the clinical significance while that mutation is not known to the wider audience because it has never been formally reported. But how often do you expect that to actually take place?

VUSes are typically not even reported because so many could be identified. We all have hundreds if not thousands of mutations that might not be understood because we just do not know what they are and what they cause. Until that is discovered, they must surely remain labelled as VUS.

If a VUS is reported it is usually because it might be considered suspicious, and it is reported as a reminder to monitor such VUSes for potential, future reclassification. A VUS can be reclassified to a pathogenic or likely pathogenic variant in the future and that does happen - apparently not unfrequently.

Let us take the example of VUS reclassification in hereditary cancer genetic testing, like the one our cancer survivor had. In an analysis of 1.67 million tests, the authors of this analysis discovered that 7.7% of variants of uncertain significance were reclassified. 91.2% of these were downgraded to benign status while 8.7% upgraded to pathogenic or likely pathogenic variants. The median time to change the status of VUS to the pathogenic level was 1.86 years.

Merogenomics Blog Figure VUS Reclassification2

Adapted from Mersch J et al. 2018. JAMA 320(12):1266-1274

And as we just gave away, below the VUS grade are variants that are considered benign or likely benign (again, difference between these two is the level of evidence).

Doctors obviously are never supposed to act on benign DNA variants either and so these are never reported to a doctor anyway.

Now that we know about VUSes, let’s circle back to RNA testing. The reason why RNA analysis is so valuable is because it catches events that otherwise would not be obvious from DNA mutation. This way DNA mutations that otherwise would remain enigmatic can be linked to how the RNA is processed and that is how we can link DNA mutations to disease development. But without seeing the impact in RNA, we would not even know of the significance of these DNA mutations! They would have remained VUSes. Therefore, RNA testing can dramatically reduce the number of VUS results by helping to classify such variants as actually pathogenic or not. Ambry Genetics data suggests massive VUS reclassification on account of RNA test addition – up to nearly 90% of VUSes are switched to either benign or likely pathogenic categories in 13 genes that were assessed (now commercially offering 18 gene RNA analysis for cancer predisposition). That is staggering improvement.

So what did our cancer survivor found out?

You probably guessed it by now - she had a VUS reported! Her VUS even fell in that category of the 1/10 that are still not reconciled after RNA testing. So the most important message was that no pathogenic information was found in all of the cancer predisposition genes and their corresponding RNAs that were analysed, and that the reported VUS in one of her cancer predisposition genes, well - we don’t know what it does clinically and the doctor did not obtain information that could impact patient management or counselling.

That does not mean it can be guaranteed that she has no hereditary predisposition to cancer. It might exist elsewhere in the DNA that was not investigated by the test.

Or it might be one of those variants of unknown significance that one day might turn out pathogenic.

Luckily, these are now very small remaining odds.

But at least she could be rest assured that she could take the genetic test without fear of any discrimination to either herself or her children. And that her children did not inherit anything obvious that we know is linked to cancer predisposition.

If you are interested in using DNA/RNA testing for cancer predisposition for your personal use, or if you are interested in offering such genetic testing to patients at your clinic, please contact Merogenomics.

Let’s knock those VUSes down!

 

This article has been produced by Merogenomics Inc. and edited by Jason Chouinard, BSc. Reproduction and reuse of any portion of this content requires Merogenomics Inc. permission and source acknowledgment. It is your responsibility to obtain additional permissions from the third party owners that might be cited by Merogenomics Inc. Merogenomics Inc. disclaims any responsibility for any use you make of content owned by third parties without their permission.

 

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