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Hearing loss DNA testing

Hearing loss DNA testing

08/08/2020
Posted by:

Dr.M.Raszek


Hearing loss: a common predicament awash in genetics

In this post we wanted to recount the story of a family with children that presented with hearing loss with no prior family history. It turned out to be very unique account of unsuspected genetics - a paradigm that will continue to happen with greater frequency as more people chose to analyze their DNA. This story demonstrates the potential power of proactive screening of one’s genetic state, and even hints at when it might become a necessity with regards to planning a family.

Permanent hearing loss is one of the most commonly observed birth defects with 1-3 occurrences of childhood hearing loss per 1000 births, increasing to 2-4 per 100 cases presented at neonatal intensive care units (NICU). Just for comparison, in the US it is estimated that approximately 8% of newborns end up at NICU. While not life threatening, it can be a debilitating condition as it can affect a child’s ability to communicate, learn, and socially adjust to the surroundings. The body of evidence that has been published indicates that the earlier the identification and intervention, the better the outcomes for a child to overcome future difficulties associated with hearing loss.

Image of Merogenomics article quote on hearing loss intervention

Childhood (prelingual) permanent hearing loss can be classified as unilateral or bilateral meaning that it affects one or both ears, respectively. It is suspected that approximately 80% of childhood hearing loss is genetic in nature, with the remainder being acquired (environmental) in nature (for example, due to infections). Of the genetically caused hearing loss, approximately 20% are referred to as syndromic, meaning that hearing loss co-occurs with abnormalities in other body parts. In this category alone, there are more than 400 syndromes that include hearing loss as one of the symptoms! Syndrome is often used interchangeably with disorder or disease, but it has its specific meaning.

The remaining 80% of hereditary childhood hearing loss is referred to as non-syndromic or “stand alone” events without additional complications. Most forms of non-syndromic hearing loss are referred to as sensorineural, and indicate that loss of hearing is caused by damage to structures in the inner ear (and thus some parts no longer function properly). There is also the conductive form, which results from abnormal structural changes in the ear (parts design deviates from what would be expected for normal function). There are now many genes known to be involved in childhood hearing loss, with one of the most extreme examples of genetic complexity contributing to a specific biological outcome. As a consequence, childhood hearing loss is an example where very large gene panels are now frequently used for evaluation. We see even larger scale tests being used which would analyze either all of the genes of the patient, or even the entire inherited DNA (genes and non-gene DNA code, in other words, full genome). To read more about differences in size and scope of genetic tests, check our previous post. Those children without these genetic findings or syndromic association run the risk of missing the benefits of early diagnosis and the valuable intervention.

Here is wonderful TED talk video recounting some of the evolutionary history of hearing loss:

 

Genetic mystery: honey, where did the condition come from?

Let’s introduce our family now (as always, with permission): a little boy and little girl both affected with unilateral sensorineural hearing loss. Remember from above definitions this means only one ear affected due to one of the mechanisms in the ear not working properly, and highly likely to be genetic. Both parents have completely normal hearing. For all intentions and purposes, this came out of nowhere.

The gist was that it was the bad luck of two individuals becoming parents when each parent carried a mutation for the hearing loss condition and unfortunately, combining them together through random chance caused the condition in their children. This situation is referred to as being a genetic carrier, and essentially we all are carriers of some diseases. Every time people have kids, there is always a risk that two genetic carriers of the same condition will combine their genetic material.

Interestingly enough, the family knew of the importance of genetics and have investigated themselves extensively on their own! The mystery in all of this was that the father had sequenced his full genome already and no mutation was found in any of the genes currently associated with hearing loss! This is when Merogenomics was contacted.

Image of Merogenomics article quote on genetic carrier

Mom previously did a 23andMe DNA test which actually tests for few specific mutations associated with hearing loss. She found out that she was a carrier of one of the most common mutations (or in proper scientific term: common variants) SLC26A4 E384G. The italics denote a gene, followed by the mutation/variant description - in this case one amino acid changed to another. This was a fairly dramatic change in terms of the chemical structure of the amino acid – the amino acid (due to mutation) was twice as small as its typical non-mutated amino acid counterpart, and with different properties in terms of attracting other amino acids. Amino acids use these powers of attraction (think like the action of a magnet) for interacting with each other in an intricate manner, leading to complex three dimensional structures when they form a single long chain of amino acids glued together. Imagine if you had to design a watch with all of its internal components being linked together in a single chain, and it is up to you how you fold that chain in any way you want to make sure that the final outcome is a working watch. And certain watch pieces will have magnetic powers so they can attract one another, and help you keep it all together in your favourite preferred watch configuration. This is exactly what happens when proteins “come to life”, becoming tiny little molecular robots in our cells. In the case of the SLC26A4 gene, the resulting protein called pendrin which is essentially like a type of faucet in our cells. It allows fluids with specially selected ingredients to move from one area of the cell to the next.

Makes you really appreciate the design when you think of it that way, don’t you think? How did something so intricate get designed? Randomness apparently - in a process that we call evolution. Imagine if in your chain of watch pieces, once in a while one special piece of your watch was substituted for another. Most likely it will break everything. This is exactly what we see frequently in nature, sometimes with serious consequences like diseases. Sometimes, less frequently, it will actually improve the design and function of that watch. Or a human trait in our cases (like to be able to see further away, run faster, have six fingers, anything that improves the species survival).

Using the SLC26A4 gene, we can learn to appreciate what genetic variants are about.

One of the kids was also tested with that same 23andMe test, and confirmed to have inherited that variant in the SLC26A4 gene from mom.

But what happened with the dad then? He decoded his entire DNA to try to find an answer! He did find he had a VUS or variant of unknown significance (meaning a mutation in DNA that we do not know what it does) also in that SLC26A4 gene! This was something mysterious that had not been observed before, and thus without the ability to predict if that mutation would also destroy proper function of the protein robot. Itwas certainly suspicious, but not very helpful in solving this mystery.

This is when Merogenomics was consulted.

There are a few possibilities as to how this condition arose in the children:

1) Each kid inherited the SLC26A4 E384G mutation from mom and had a spontaneous mutation in the second copy of the SLC26A4 gene, leading to the condition. When the two identical genes involved in disease development are mutated differently, it is called a compound heterozygote. All of us are born with some spontaneous mutations not observed in parents. However, this scenario is unlikely to have occurred on the account that the same condition is observed in both kids, thus pointing to an inherited cause from both parents.

2) Each kid inherited the SLC26A4 E384G mutation from mom plus another, still not understood, mutation from dad. In essence, both parents are carriers of different mutations for the same gene. Two possibilities of dad being a carrier:

i) The variant of unknown significance that dad carries in the SLC26A4 gene somehow abrogates the function of the gene. This is very suspect especially since the uncovered VUS was an insertion, meaning extra content was inserted! That’s like inserting extra watch piece onto your chain of watch pieces. We suspected this to be the most likely scenario.

This would make the kids compound heterozygotesof SLC26A4 gene mutations, meaning that two different mutations (but in the same gene) are actually contributing to the condition, one from each parent. 23andMe would not be able to detect compound heterozygotes if the test is not selected to look for any other mutations besides the SLC26A4 E384G. And there are many such possibilities of how different mutations in the same gene can stop or abrogate the gene’s normal function. This is a serious limitation of the 23andMe medical test because often this part is not well understood by the public, sometimes giving them a false sense of reassurance from negative test results. These parents were lucky that their personal mutation was actually covered by the 23andMe test. It helped them piece their genetic evidence.

ii) Some still not understood variant affects the proper expression of the SLC26A4 gene, so while the gene itself is normal, the protein is not produced, leaving the kids with only the functional mutant pendrin protein inherited from mom. We expected this to be a small likelihood. In addition, if it is a structural DNA variant (a type of mutation affecting a large segment of DNA), it might not have been picked up by the previous genome test (because it depends on the quality and type of the genome test).

3) A completely different set of genes were being affected to cause the condition altogether, and we should not even be focusing on the SLC26A4 gene. However, this would also be unlikely that on top of that different gene that we still have to uncover, by sheer coincidence mom also happened to be a carrier in one of the primary genes responsible for the hearing loss. A little too coincidental, so we thought.

We pretty much tossed option 1 and 3 out the window as too unlikely. And in option 2, we did not give high chances for somehow gene function to be affected by some outside mutation away from the SLC26A4 gene.

Image of Merogenomics article quote on recessive condition

The family was going to attempt find the answers by applying for screening of the family with gene panels covered by healthcare. That is a great option, but doubtful anything would be uncovered that was not already captured previously with the father’s genome sequencing (and we knew this was a very high quality genome test that was done). But it was not impossible that gene panels could uncover something missed by the genome testing.

However, since dad’s genome is already sequenced and we know mom is a carrier, then perhaps no sequencing had to take place? Perhaps the focus should be on the depth of analysis of dad’s genome to determine how is he a carrier as well.

Well, we did mention the family was very genetically proactive! Believe it or not, the dad actually found a hot-off-the-press scientific paper describing the discovery of a very unusual mutation predisposing to hearing loss. Very unusual because it was not just one mutation, it was a group of mutations/variants travelling together through evolution. And they did not even affect SLC26A4 gene! They were all right next to it though.

 

Genome inheritance, like playing a deck of cards of haplotypes

When we inherit our DNA from our parents, we inherit them in chunks. Some chunks of DNA will come from mom and some chunks of DNA will come from dad, and the size of these chunks, or how we inherit them, can be preserved from generation to generation. And we can inherit a group of mutations together in such chunks of DNA. Since we do not officially call them chunks in science, they have a specific name, a haplotype. Mom discovered a paper describing a novel genetic cause of hearing loss, a haplotype called Caucasian Enlarged Vestibular Aqueduct (CEVA), which is a group of mutations travelling together through inheritance, all next to the SLC26A4 gene. That’s some amazing genetic literacy by those parents!

The analogy to describe this concept is to think of each genome you inherited from each of your parents as a deck of cards. The genome you got from mom as a pink deck of cards, and the genome you got from your dad as a blue deck of cards.

Remember, in producing gametes (sperm or eggs), that genomic information is split in half and so each gamete only gets half of those pink and blue cards(respectively) so that when a sperm and an egg unite and combine they go back to being a full genomic set to produce a new, genetically combined life: you! Basically every new cell in you becomes a shuffled combination of both of your parent's respective genomes together.

Image of Merogenomics article quote on dominant condition

In essence, your two decks of cards are shuffled, and then separated again so that each deck is still a normal deck of cards (meaning it has four 2s, four 3s... four kings, four aces, each set of four cards would be like a complete chromosome -- we inherit our DNA in bundles called chromosomes, 23 from each parent) but now each deck is composed of both blue and pink cards. Each of these multi-colored decks would now be the genome in a single gamete cell used to produce new baby.

Now think of each of these blue or pink cards in that newly produced gamete deck that represents a small segment of the genome from your parents, that is what we would call a haplotype. In other words, during the production of gamete cells, the parental genomes are shuffled in certain sized chunks called haplotypes. Since each of a parent’s original genome is split in half to give towards their child, that child always has a 50% chance of inheriting a genomic segment from either one parent or the other, along with any mutations that might be found within that segment/haplotype.

A majority of diseases require mutated haplotype copies from both parents in order to produce a health problem in their offspring. Sometimes just one will do. If both mutated haplotypes need to be inherited, that is what we refer to as a recessive condition. And if only one mutated haplotype has to be inherited from just one of the parents to produce the condition, it is referred to as a dominant condition. There is also in between option, where if only one mutated haplotype is inherited from one of the parents, it produces only a partial health problem. But typically it is either recessive or dominant. There are other complex modes of inheritance, but let's keep it simple because most of hearing loss conditions are inherited in a recessive manner.

 

Unmasking the genetic mystery now, helping the patients of tomorrow

Remember how our father in the story already sequenced his genome? Well, this happens to be one of the most ideal examples of one of the best benefits of a full genome sequencing test: capturing all of the DNA information you are born with in a single test! People usually do not recognize this. Because dad already had his genome done, he was able to look at his DNA and discover that he had every single one of that CEVA haplotype mutations in his genome (there were 12 of them)!

Full genome best benefit

This would mean a super unusual situation as mentioned above in option 2 with most likely the condition being caused in kids due to a compound heterozygote resulting from inheritance of the SLC26A4 E384G mutation from mom, and the CEVA haplotype from dad. Furthermore, the SLC26A4 gene’s proper function is likely being affected by the CEVA haplotype mutations preventing protein production. Basically, the gene activity is knocked out and the gene is all good but is not used. There was already some supporting evidence that the severity of the hearing loss condition can be a result of how much the of the pendrin protein function is affected.

And this was not the only twist in this genetic saga! But more on that in the moment...

If the kids’ condition was indeed due to the inheritance of the SLC26A4 E384G mutation from mom and the CEVA haplotype from dad then:

1) Their kids will always produce children that are carriers of either the SLC26A4 E384G mutation or the CEVA haplotype (50%:50% chance). No matter what, the children's children will inherit either the CEVA haplotype or the SLC26A4 gene mutation haplotype. That also means that the children's kids will not have the disease (just like mom does not, even though she is a carrier of the SLC26A4 E384G mutation) unless the children were to have kids with another carrier of mutations in the same gene.

This also means that it might be wise for the children in their future to screen their partners for carrier status as CEVA haplotype alone is reported to be present in about 5% of the Caucasian population in the paper that dad found. If either of the children's partners were to be a carrier, we are talking about 50% chance that children's kids would have a related disease. Not good odds. So this shows a very serious reason for those children to consider screening their partners one day for genetics prior to reproducing.

Screening their future partners will certainly help prevent the children from having their own kids with hearing loss. If the future partner is a carrier as well, the children will have a future option s of: i) not having children with that person; ii) undergoing in vitro fertilization to ensure that correct a sperm or egg was selected for fertilization from the carrier (meaning one that does not have the mutated haplotype), iii) taking a random chance that the carrier partner will provide the healthy type of the haplotype during conception (remember, these are the same odds as flipping a coin).

2) Together, these parents have a 25% chance of producing a child with the hearing loss condition, a 50% chance that the child would have only one mutated haplotype copy from one of parents (i.e. become a carrier just like either of the parents, and be healthy), and a 25% chance that the child would inherit the non-mutated haplotypes from both parents (and be healthy with no further negative reproductive consequences).

Merogenomics Blog Figure about DNA carrier options

Regrettably, from everything we have read on this condition, there is no treatment currently available.

So apart from confirming the above situation was there any additional benefit for the parents to sequence their kids?

Currently, sequencing the children will only provide some research answers, potentially very valuable to the medical community for a better understanding of this condition. Perhaps this could result in better management or perhaps some future treatment, but this might not ever be available to the children.

There are additional potential benefits from full genome sequencing that may or may not materialize:

1) To obtain additional genetic information not related to the current condition but that might be important for the overall health of children such as pharmacogenomic information, or any additional health risk factors. Unlikely benefit.

2) The expansion of the genetic understanding of hearing loss conditions affecting the children could lead to an improved prognosis allowing to finally understand from a genetic perspective as to why the hearing loss severity is different in different patients. This might help identify the expected degree of the future outcomes of the children and hence how acutely it should be managed. Unlikely benefit.

3) The parents might be able to look for clinical trials that might be happening to help to treat this condition which might require foreknowledge of genetic information. Most likely benefit.

Then the big question: how could we confirm the genetics in children?

Would the gene panels that parents were seeking to obtain through healthcare even look at the CEVA haplotype if this was just discovered? The answer was no on the account that this was the only paper at the time published about the CEVA haplotype and therefore it is still considered limited evidence. More evidence would be required before this haplotype could be used for clinical calls. The reason behind this rationale is because new scientific reports of genetic associations with traits are published all the time, and a portion of that reporting ends up being not true. Thus panels will not include such information to be analyzed, especially if it is outside the gene (which means a test has to be specifically designed to look at that area of the genome). This is the major limitation of tests that only look at fragments of DNA code - when they only look at preselected areas and if the mutation happens to be outside that area, the test cannot find it.

Merogenomics did a search of available clinical trials and there were some trials that that were attempting to build a genetic database on patients with the specific type of hearing loss that was affecting the children with hopes to better understand the condition.

Merogenomics informed the parents that participation in any of these clinical trials could provide access to a free sequencing, but likely only as a panel and not an exome (the portion of the genome that includes all of the genes which is under 2% of the genome) or full genome testing.

In the end, that is exactly what the parents did on Merogenomics’ suggestion, with the only question remaining to see if Canadian residents would be accepted in research performed by an American institute. They did get accepted and after a long time of waiting nearly 8 months, the research institute (in Maryland) confirmed that both of the kids indeed were compound heterozygotes, inheriting both the CEVA haplotype and the SLC26A4 gene variant. This likely would mark the very first such instance discovered in Canada! The DNA research this family participated in will bring increased validity towards the effect of the CEVA haplotype for future people! Who knows how many kids will subsequently be helped because of this knowledge?

Image of Merogenomics article quote on how DNA testing can help others

 

One more twist because that’s what genetics will do

But there was another big genetic surprise in store! Prior to even getting results from the US, the gene panel used by healthcare informed that one of the children was homozygous for biotinidase deficiency due to a BTD D446H variant, indicating that mutated copies had to be received from both of the parents. Which is wild because this condition can also contribute to hearing loss that can be present at birth, depending on the severity of the mutations involved! Biotinidase breaks down the dietary vitamin biotin which is then used in important metabolic processes in the body. The biotinidase deficiency can be easily treated or prevented by taking supplements of biotin. The other child was a single carrier like either of the parents. By an incredible stroke of coincidence, the parents ended up being carriers of two independent genetic conditions that both could lead to childhood hearing loss! This has to be rare incidence, with even more extreme odds that on top of that one of the kids was afflicted by both of these genetic events! This shows how valuable genetic screening prior to anyone having kids could be if access to such technology is available. As mom put it, “It shows that sometimes you are the rare case and gene testing is so important.”

But then how would we know which of the genetic conditions is actually influencing the hearing loss in one of these kids?

Merogenomics did some research on that too. We looked through what we consider the most comprehensive clinical database on biotinidase deficiency that includes this particular variant.

Parsing through the references available, the homozygous state of this variant does not seem to actually cause biotinidase deficiency or even partial biotinidase deficiency (biotinidase enzymatic activity <10% or activity 10-30%, respectively). However, this variant in conjunction with another pathogenic variant is a common cause of partial biotinidase deficiency. The only time this variant has been observed in individuals affected with profound biotinidase deficiency was when combined with two other mutations in the same gene! Yeah, complicated.

This actually explains the relatively high population frequency of this variant with around 2%. That is a lot of carriers out there! It is because the combination is rarely severely deleterious.

Individuals who are homozygous for this variant found in this family typically have a biotinidase activity that is approximately 50% of normal, which is similar to what was observed in the kid.

Furthermore, untreated individuals with partial biotinidase deficiency are often asymptomatic in the absence of confounding factors such as a significant illness. And an unusual tidbit of information was that raw eggs should be avoided because they contain avidin, an egg-white protein that binds biotin and decreases the bioavailability of this vitamin.

All this suggested that it was unlikely that it was the BTD D446H variant that was contributing to the hearing loss in that one child, but rather the CEVA haplotype and the SLC26A4 gene variant combo– but with genetics everything can be more complicated than we can ever imagine.

Image of Merogenomics article quote on genetics

The other good news that also came about was that according to the same authors that have described the CEVA haplotype, hearing loss due to the presence of CEVA haplotype in combination with another mutation in the SLC26A4 gene is correlated with a less severe hearing loss than mutations affecting only the SLC26A4 gene! This had to be very welcome news for the parents who did not know what to expect when the hearing loss was first detected in their children, and knowing that complete hearing loss in both ears could always be a possibility.

It is a strange feeling when you hope that your genetic mutations are not as severe as they could be.

In the end, mom decided to pursue DNA testing as well, a full genome sequencing with help from Merogenomics , to complete the genetic picture of the family. Indeed, it was confirmed she was a carrier of the BTD D446H and SLC26A4 E384G variants. Plus a carrier of two more conditions! As we said already, almost everyone in the world is a carrier of genetic diseases, most often multiple ones, and sometimes carriers can come together with the result of a condition showing up in a family seemingly out of nowhere. Knowing genetic diagnosis helped the parents move forward with treatment selection. As mom put it “knowing that [our kid] had a genetic, progressive form of hearing loss, we were able to decide to move forward with a cochlear implant. If I did not know the hearing loss was progressive (with potential of loss in the other ear), it may have been a harder decision to move forward with the single sided cochlear implant.”

In the future, likely everyone will be DNA sequenced completely at birth. Random partnerships between carriers of the same serious conditions will simply become rare. Right now we are often doing testing retroactively, for detective purposes. In the near future it could be common to take DNA testing proactively when people are considering children. In comparison to the impact of potential negative outcomes, such tests are cheap insurance to help screen yourself before having kids.

We hope these two affected children will also consider testing when their time comes to have kids, so their kids can avoid the risk of inheriting a hearing loss condition.

 

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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