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Understand your genome

Understand your genome

06/12/2017
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Merogenomics


The day had arrived when I was going to see my doctor to receive my own genome sequence data and interpretation. I won't deny that I felt little bit nervous! I thought today could be a day in which I find out that I have an incurable disease, or a predisposition to cancer. Am I ready to face such truths? I have grappled with that question before, and it took me a very long time to decide what kind of information I wanted to receive from my genome sequence. Do I want to find out about having mutations predisposing me to diseases for which there are no cures? Like Huntington disease, or Parkinson's? In the end I decided yes. And there were good arguments for it.

First of all, I knew that I am not someone who would stress for the rest of my life if I found out such information. That is probably the most important question one has to answer for themselves prior to committing to obtaining such records from their own genome. What's the point of knowing that information if you are going to stress about whether the disease will materialize or not, and when that would happen? That stress in the end might end up doing more damage than the phantom disease.

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I obviously discuss this topic with practically everyone who asks me what I do and finds out that I help provide commercial access to genomic technologies. It is interesting to see what people's immediate decision to such a dilemma is. I recall talking to one friend of mine with a history of cancer in the family. We debated the possibility of using genomics to find out their heritable predispositions. But my friend told me, in the end, that if it was a known possibility, the stress over wondering if cancer will materialize would probably be a more likely cause of cancer than the inherited genetics. So better to leave it alone.

This is probably a good time to add that with genomics, no outcomes are ever absolutely guaranteed. Yes, some mutations involved in disease development can have quite definitive clinical evidence, but ultimately the prediction is only as good as the accumulated past history statistics of such disease development in a population. Studies do suggest that finding pathogenic genetic mutations indeed puts you at an increased risk of developing a disease, whether more predictable monogenic diseases (conditions that arise from mutations in a single genomic location), or far less predictable multigenic diseases (where many mutations throughout the genome contribute in some complex fashion to a condition development, like diabetes or a heart attack).

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This likelihood of disease formation is referred to as disease penetrance, and it can vary dramatically between different conditions. Some mutations have been observed to result in a high penetrance of the disease. An example of that could be the ill-famed BRCA1 and BRCA2 genes mutations that lead to breast and ovarian cancer syndrome. Other mutations, due to many confounding factors that might not even be known, can have only a mild penetrance. An example of that is the PCSK9 gene mutations that can result in familial hyperchoresterolemia with a possible outcome of death, but compared to other genes also involved in this serious condition development, its penetrance is low. And even for highly penetrant diseases, there can be unusual protective genetic factors that are yet to be uncovered, which has been observed in the past.

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The take-home message is that genomic information is not a guarantee of a condition or trait development. But it can be hugely informative of what might show up, and you can either try taking mitigating steps, or prepare accordingly. Preferably with no stress!

So if you are a person that can easily experience anxiety, you might want to avoid obtaining information related to untreatable conditions, or perhaps not even use genome sequencing for diagnostic purposes unless absolutely needed.

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I decided I wanted to know everything. I thought it was better to know than not to know, for a couple of reasons. Firstly, I could start preparing for an end of life. This sounds dramatic, but in such an instance, there could be some important legal preparations to be made ahead of time, such as who will be taking care of me and my estate when I am no longer competent to make decisions due to disease progression.

Another reason would be that foreknowledge of an untreatable disease would allow me to sign up for any clinical trials with novel treatment towards such a disease. Novel treatments and medications are generated all the time, and often it can take dozens of years before they become a standard therapy. I would rather know that I might end up with an incurable disease, and, if possible, do something about it, than to one day end up with the disease when it might be far too progressed to do anything about. And if you find yourself in that situation, one digital health company that can help with clinical trials I recommend is Clara.

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Not to mention that scientific studies indicate that people usually have no major psychological issues from obtaining genetic information, whether dealing with serious conditions or mood and behaviour changes due to complex genetic traits spurred by many genomic variations.

I only elected to sequence my genome once I knew very clearly if I wanted all of the information or not. But the sequencing test I chose in the end is not a typical commercial choice. Once I made my decision, I was still procrastinating, studying different available market options (which after all is part of my job). I even contacted companies that did not offer testing for commercial purposes, like BGI which recently came out with a novel sequencing platform. Although only available for research application, I asked if my genome could be sequenced using their newest (and one of the cheapest at the time), technology. I informed them that the process would be under medical supervision and that I would independently verify any pathogenic results.

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But along the way I received an invitation from Dr. Robert Green to participate in an upcoming program in which healthy participants could have their whole genomes sequenced and interpreted clinically. The program is called Understand Your Genome, and is run by the world's largest producer of genome sequencing machines, Illumina. It is typically hosted by different institutes around the world, and this particular event in which I was invited to participate in is hosted yearly by the Broad Institute in Boston.

I had obviously already heard about the Understand Your Genome events, which collectively have produced one of the world's largest databases of fully sequenced genomes of healthy individuals. It is still considered to be a pioneering event in this moment in time for a healthy person to sequence her or his genome, although likely will become quite the norm in the not too distant future.

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In the world of sequencing, it is a quite a famous event. Not only can participants obtain their full genome DNA sequence and interpretation, they also obtain secure access to the Illumina website portal where one can view their entire genome sequence, including all the uncovered mutations. This was a brainchild of a former CEO of Illumina, whose genome is available for all participants to view and become familiar with the website portal prior to obtaining access to their own genome code. Finally, the program also includes a single-day conference where the participants can listen to the best local speakers on the topic of genome sequencing in clinical use and how it is shaping the world of medicine, as well as learn how to view the website for personal genome overview and gain a personal passcode to do so at the event.

I have also known about the renowned Broad Institute, which has participated heavily even in the very first draft of the human genome ever created, the famed Human Genome Project. To this day it is a powerhouse in human genome sequencing, and as I found out later, it still is on a massive scale. But the summary of the conference associated with Understand Your Genome will be the topic of next post.

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I actually always wanted to participate in an Understand Your Genome event. If you are into genome sequencing as much as me, it is like wanting to go to a concert of your favourite artist, or a game of your favourite sports team. So although there are a lot of options available with different perks, when I got that email from Dr. Green, who is also quite famous in the world of genomics, overseeing the work of the Genomes 2 People which participates in some very big genomic studies, work that I very closely follow, in conjunction to the event taking place in Boston, one of the main genomic meccas of the US, I was very quickly swayed. The fact that Illumina heavily subsidized what otherwise is quite an expensive procedure, also sweetened the deal.

So how does the process unfold? You need to pay first, and in this case the whole genome sequencing cost was $2000 US. You can get it for a whole lot less than that, but considering who was involved in the interpretation, which is the most challenging part, and the true differentiator between good and the best DNA test access, that is not much money to spend to gain access to my personal biological blueprint that can now provide me with information for the rest of my life. In a way, it is like buying insurance for life, and it's good for your life, and your kids' lives, and your kids' kids' lives. Potentially, multiple family generations can derive medical value from a genome DNA test of a relative.

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Next I had to go to my doctor to have him sign the requisition form. Without doctor oversight, there is no sequencing. If my doctor did not agree to sign that test order, I'd be forced to search for a new primary care provider. So I came to my doctor prepared with the biggest speech of my life, and even my family pedigree (family tree), showing our medical history which is suggestive of potentially heritable problems. Yes, I was going to go that far! When my doctor heard what this was about, and what kind of information can be obtained, he just wanted to know where to sign. Pedigree not needed!

After that, a DNA test kit is sent to your home. Most of the time, such DNA kits are meant to collect saliva. This one was to collect blood. I talked to multiple companies offering genome sequencing that do either, and these days they claim the quality of the sequence is same for either sample type. But blood requirement meant I had to book an appointment with a local clinic, and since it was for a private personal use, I had to pay for the blood collection. The nurses at the clinic had never encountered such a reason before, and therefore were fascinated.

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The DNA test kit included couple of vials for blood, labels with bar codes for the vials, and the documents I was to ship back with blood (my agreement to participate, referred to as my informed consent, my doctor’s signed requisition form, my agreement to have my genome sequence uploaded to the secure web portal later in the future, and my selection choices of what information I wanted to obtain from the genome sequence). The blood clinic took care of the shipping (prepaid envelope provided), so I made sure that it was crystal clear that all of the required documents were going to be included. Maybe I was a bit paranoid, but it was already a stressful situation because I was passed the due date. My genome kit had arrived late because of hurricane delaying shipments by few days. This meant that it was not guaranteed that my genome would be sequenced in time for the one day conference.

My doctor also requested blood and urine analysis along the way and a thorough examination, including a yearly physical and echocardiogram, to coincide with obtaining my genome sequencing results. Definitely proactive thinking!

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The next step in the process is that the company informs you by email what is happening. You are informed that samples are obtained and processed. DNA has to be isolated from the blood, go through quality controls, and be prepared for sequencing on a machine (this step is nick-named "library construction" so that your DNA can be subsequently "read" by the machine). You are informed when your sequence is decoded, when interpretation begins, and finally when the results are sent to your doctor.

In this case, both the report and the sequence are sent to a doctor (others can provide secure sequence download portals for the client while the doctor gets the report, while still others can provide separate reports for the client and the doctor). I knew my doctor had my sequence and interpretation results a week before my previously scheduled appointment! I almost thought of changing the appointment for an earlier day! But I told myself to calm the seq down and wait it out.

When I was finally sitting in my doctor’s office, waiting, another physician brought in the results. I know what these reports look like. I studied them from multiple companies already, and I have seen webinars about them and read multiple scientific publications on the topic. I quickly scanned the report even before my doctor arrived!

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I was clear! I had dodged the genomic bullet! Well, almost. There were no mutations indicating untreatable conditions. I breathed a sigh of relief. But there was other stuff. Nothing major, nothing to lose sleep over, nothing that will kill me tomorrow. But something I am definitely glad will now go to into my medical record. I learned that I had a mutation that could impact how I handle certain infections, like during cancer chemotherapy. Luckily the penetrance for this condition varies widely across the entire spectrum, with many affected individuals never showing any symptoms.

There was also information related to my carrier status of diseases that do not show up in me, but if my partner had mutations in the same genes, our children could be affected. I am a carrier of four diseases, including what seemed like some nasty stuff. I could take comfort in that practically everyone is a carrier as there are so many diseases floating around in our genomes. I quipped to my friend later that my wife better sequence her genome before we have kids. She told me that I’m so unromantic, but why run that risk if it could be completely avoided? We could still have kids and not take that random chance.

The last major bonus of genome mapping is the pharmacogenomic information, on how I handle certain medication, influencing drug dosing, or if a drug might even be appropriate for me or not. Also very glad this will be going into my medical record. But I didn't even had a chance to see which medications were mentioned. The doctor came in.

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Typically this is the time where the doctor explains the findings to you, what was uncovered, which genes were affected, and what that might potentially mean for your medical care. If something serious is uncovered, the doctor should inform you that genetic counseling should be booked to further discuss the results with another professional who will explain the risk of the disease, how that might impact reproductive planning, and potentially other family members, and how to prepare for these eventualities, including important family communication. You see, there is a lot to think about when deciding to sequence your own genome.

In my case, I explained the report to my doctor. I clarified what the different sections of the report were, and basically advertised why they were significant for my doctor to know for the future. I told my doctor that at least there was nothing that would immediately require action, but that could easily be a different case with a different patient. And if so, where the information in the report would be found.

My doctor was impressed. And sold on sequencing utility. Even though there was no immediate need to impact my current medical care, there was the information related to future medication use (I am not on any meds now). And that might always change. The whole genome DNA test provided interpretation on currently clinically validated mutations or ones with obvious predicted pathogenic outcome, but the sequence also provides thousands upon thousands of variants of unknown significance, or mutations that currently are not known or understood if they are benign or pathogenic. In my case, there were over 1200 variants in almost 1700 medically significant genes. There is no knowledge of what their role is at the moment. But one day they could be informative. Progress in genomic interpretation is moving on a very rapid scale, fostered by the ever increasing number of human genomes being sequenced for medical research purposes.

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That means once you get your genome sequence, you should be interpreting it many times throughout your life. Down the road, much is expected to be deduced from genome sequence, both in terms of monogenic diseases and complex common multi or polygenic diseases.

In addition to the clinical focus, the Illumina test also provides some information on personal traits, but very little, only 10. It is most likely because of the current poor predictability of more complex traits. There is eye color in case you can’t look in the mirror; your likeliness to sneeze while staring at the sun if for some reason you really want to make sure you can never see your eye color while blindly looking in the mirror; how likely you are to taste bitterness, flavour-wise (the emotional disappointment would probably fall in the complex trait category); or if you are likely to turn beet red when drinking alcohol, in case you still haven’t tried that yet. But some are cool, like one’s muscle fiber type and whether it builds for power or endurance, along with sugar sensitivity, or propensity for baldness development (another sigh of relief)!

What this test does not inform you about at all is ancestry information or any information towards the common complex diseases. I am still a fan of that information, even if it does not have much clinical significance at the moment, so I am sure to assess my genome for this information in the future using different tools. Alternatively, you can always seek a different provider. And if you are lucky, you will dodge genomic bullets. Or if you are lucky you will discover early on a predisposition to a disease for which intervention is available and your life could be saved. It's all matter of perspective. And if you need a hand to find out where your own genome sequencing journey will take you, we can get you there.

Happy sequencing!

 

This article has been produced by Merogenomics Inc. and edited by Kerri Bryant. 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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