Missing allele found in me

[Rare_case]

DanteLabs made whole genome sequencing (30x) and I am confused with my APOE. Sequencing.com says I'm e2/e4 but I think I'm e3/e1.

Can anyone help me with this messed up gene I carry?

My cholesterol levels are also weird, for example my HDL-TG-ratio is 1:4.2 and I got xanthelasmas in both my eyelids when I was 38y old. Now I'm 41y and xanthelasmas are removed with laser.

My APOE is so rare, I can't find any good literature to help me with this issue. I hope someone here maybe can help me. And I have also my friend's genome that I use to compare different genes, and it's almost scary how much more I have data in my APOE gene. My friend is e3/e4, same age, also male and his cholesterol levels are normal.

[MicheleCC]

DanteLabs made whole genome sequencing (30x) and I am confused with my APOE. Sequencing.com says I'm e2/e4 but I think I'm e3/e1. Can anyone help me with this messed up gene I carry?

My cholesterol levels are also weird, for example my HDL-TG-ratio is 1:4.2 and I got xanthelasmas in both my eyelids when I was 38y old. Now I'm 41y and xanthelasmas are removed with laser.

My APOE is so rare, I can't find any good literature to help me with this issue. I hope someone here maybe can help me. And I have also my friend's genome that I use to compare different genes, and it's almost scary how much more I have data in my APOE gene. My friend is e3/e4, same age, also male and his cholesterol levels are normal.

Welcome Rare_case! Thank you for sharing some of your story. There are many caring and incredibly knowledgeable people on this site, many with medical educations who may be able to shine some light on your situation. As an intern on this site, I am still learning about apoe4, but look forward to reviewing your results and will comment in another post if I can help make sense of them for you. However, right now, I would like to officially welcome you to the apoe4.info website and give you a few links that may help you navigate and find the content of interest to you.

Many who are new to this site will start with the PRIMER. It's an excellent resource, written by Stavia, a medical doctor, to begin learning about apoe4. Another link you may find useful is "How-to" get the most of the apoe4.info website, which will help you navigate and find what interests you. I also encourage you to share more of your story under "Our Stories" so that others can learn more about you and from you.

Warm regards,
MicheleCC

[MicheleCC]

DanteLabs made whole genome sequencing (30x) and I am confused with my APOE. Sequencing.com says I'm e2/e4 but I think I'm e3/e1.

Can anyone help me with this messed up gene I carry?

My cholesterol levels are also weird, for example my HDL-TG-ratio is 1:4.2 and I got xanthelasmas in both my eyelids when I was 38y old. Now I'm 41y and xanthelasmas are removed with laser.

My APOE is so rare, I can't find any good literature to help me with this issue. I hope someone here maybe can help me. And I have also my friend's genome that I use to compare different genes, and it's almost scary how much more I have data in my APOE gene. My friend is e3/e4, same age, also male and his cholesterol levels are normal.

Have you matched your results with this table on SNPedia.com? https://www.snpedia.com/index.php/APOE

[Tincup]

I recall member

had done work with whole genome. Perhaps they might be able to comment.

[Rare_case]

DanteLabs made whole genome sequencing (30x) and I am confused with my APOE. Sequencing.com says I'm e2/e4 but I think I'm e3/e1.

Can anyone help me with this messed up gene I carry?

My cholesterol levels are also weird, for example my HDL-TG-ratio is 1:4.2 and I got xanthelasmas in both my eyelids when I was 38y old. Now I'm 41y and xanthelasmas are removed with laser.

My APOE is so rare, I can't find any good literature to help me with this issue. I hope someone here maybe can help me. And I have also my friend's genome that I use to compare different genes, and it's almost scary how much more I have data in my APOE gene. My friend is e3/e4, same age, also male and his cholesterol levels are normal.

Have you matched your results with this table on SNPedia.com? https://www.snpedia.com/index.php/APOE

I matched my results with SNPedia and my problem is when comparing results to my friend's whole genome sequencing results.

I can show my friend's APOE so you can see my confusion.

Position are correct but differences in our APOEs looks weird.

SNPedia says ambiguous ε2/ε4 or ε1/ε3, so it's not too easy to define my APOE with my knowledge about genetics. Sequencing.com gave me e2/e4 but I can see my e3 there so I think I have to be e3/e1 rather than e2/e4 but I can't be sure.

I'm going to lab to measure my VLDL which I think can help me define my APOE.

Some background linked to APOE besides my messed up HDL-TG-ratio and xanthelasmas is my memory that is way above normal. I don't like remembering everything.


I've been reading a lot but that e1 "missing allele" is so rare that I can't find any good literature about it. I've checked my genome few months now trying to find something useful.

Comparing my APOE to my friend's APOE really made me confused but it also explained my rare conditions from memory and high TG's to xanthelasmas.

I can take good screenshots of my whole APOE gene and it looks very different compared to my friend's APOE. I'm still learning reading my genome, so I hope someone here can help me with that. And my doctor also.

Thaks for reply.

I haven't seen any other photos of whole genome sequencing here so I thin most of users use 23andme or similar ways to find out their APOEs. Is clinical grade sequencing (30 x) still very rare?

Any ideas why these APOEs looks so very different?

[Rare_case]

DanteLabs made whole genome sequencing (30x) and I am confused with my APOE. Sequencing.com says I'm e2/e4 but I think I'm e3/e1.

Can anyone help me with this messed up gene I carry?

My cholesterol levels are also weird, for example my HDL-TG-ratio is 1:4.2 and I got xanthelasmas in both my eyelids when I was 38y old. Now I'm 41y and xanthelasmas are removed with laser.

My APOE is so rare, I can't find any good literature to help me with this issue. I hope someone here maybe can help me. And I have also my friend's genome that I use to compare different genes, and it's almost scary how much more I have data in my APOE gene. My friend is e3/e4, same age, also male and his cholesterol levels are normal.

Have you matched your results with this table on SNPedia.com? https://www.snpedia.com/index.php/APOE

I matched my results with SNPedia and my problem is when comparing results to my friend's whole genome sequencing results.

I can show my friend's APOE so you can see my confusion.

Position are correct but differences in our APOEs looks weird.

SNPedia says ambiguous ε2/ε4 or ε1/ε3, so it's not too easy to define my APOE with my knowledge about genetics. Sequencing.com gave me e2/e4 but I can see my e3 there so I think I have to be e3/e1 rather than e2/e4 but I can't be sure.

I'm going to lab to measure my VLDL which I think can help me define my APOE.

Some background linked to APOE besides my messed up HDL-TG-ratio and xanthelasmas is my memory that is way above normal. I don't like remembering everything.


I've been reading a lot but that e1 "missing allele" is so rare that I can't find any good literature about it. I've checked my genome few months now trying to find something useful.

Comparing my APOE to my friend's APOE really made me confused but it also explained my rare conditions from memory and high TG's to xanthelasmas.

I can take good screenshots of my whole APOE gene and it looks very different compared to my friend's APOE. I'm still learning reading my genome, so I hope someone here can help me with that. And my doctor also.

Thaks for reply.

I haven't seen any other photos of whole genome sequencing here so I thin most of users use 23andme or similar ways to find out their APOEs. Is clinical grade sequencing (30 x) still very rare?

Any ideas why these APOEs looks so very different?

Screenshot from same position (chr19:45,410,825-45,410,901) of two different genomes (mine and my friend's).

Looks very different and I really wanna know why and what it means.

This so hard to learn on my own but I try anyway because I wan't to understand my genome better. That is the reason I had my whole genome sequenced (and it was 179$ on black friday sale).

Picture is worth thousand words, so there you can see differences in our APOEs with your own eyes.

[Rare_case]

And if any scientist needs rare data, I will share my whole genome for science if asked.

[J11]

Tincup, thank you for pinging me!

Rare_case, your friend genotyped rs7412 (CC), rs429358 (CT), which is the reasonably common APOE epsilon 34.
There is no confusion with this genotype: one of the Cs (either one) from rs7412 must match up with the C from rs429358 and the remaining C from rs7412 must match up with the T from rs429358.

Your TC TC genotype is somewhat ambiguous, though the money is on epsilon 24; epsilon 13 is almost unknown.
https://snpedia.com/index.php/Gs189

It could help if you had more close relatives genotyped to unlock the phasing.
What might be more helpful (and cheaper, though perhaps at least somewhat tedious) is to download your aggregation file from 23 and me and look for relatives on the APOE epsilon stretch. You could contact some of these relatives and ask them for their epsilon genotype. You would be looking for a relative who genotyped epsilon 44 or 22 (or conceivably 33 (11?)). Once you knew that you must then have at least one of these alleles, your genotype would be resolved immediately.

This is very exciting that we are now down to $179 full genomes.
There will soon be a scramble for everyone to have this done.
This is truly amazing!
20 years ago sequencing a full genome cost over $1 billion and took years.

The human genome is about to fully unlock and the human species will be fundamentally changed
forever through this knowledge as a result of the inevitable genetic selection that will occur.

[Rare_case]

Tincup, thank you for pinging me!

Rare_case, your friend genotyped rs7412 (CC), rs429358 (CT), which is the reasonably common APOE epsilon 34.
There is no confusion with this genotype: one of the Cs (either one) from rs7412 must match up with the C from rs429358 and the remaining C from rs7412 must match up with the T from rs429358.

Your TC TC genotype is somewhat ambiguous, though the money is on epsilon 24; epsilon 13 is almost unknown.
https://snpedia.com/index.php/Gs189

It could help if you had more close relatives genotyped to unlock the phasing.
What might be more helpful (and cheaper, though perhaps at least somewhat tedious) is to download your aggregation file from 23 and me and look for relatives on the APOE epsilon stretch. You could contact some of these relatives and ask them for their epsilon genotype. You would be looking for a relative who genotyped epsilon 44 or 22 (or conceivably 33 (11?)). Once you knew that you must then have at least one of these alleles, your genotype would be resolved immediately.

This is very exciting that we are now down to $179 full genomes.
There will soon be a scramble for everyone to have this done.
This is truly amazing!
20 years ago sequencing a full genome cost over $1 billion and took years.

The human genome is about to fully unlock and the human species will be fundamentally changed
forever through this knowledge as a result of the inevitable genetic selection that will occur.

Hello, J11 and thank you for your comment.

I'm going to make whole genome sequencing for my son when he hits adulthood and teen years are done, he is now 13 and showing delayed growth spurt like I did. He is the one I really care.

I also will take another sequencing for me after 3 to 5 years from first one so I can see differences. Also Horvath methylation based epigenetic clock (biological age) is on my to do list soon but I think that's bit too expensive ATM. I wanna take 2 or 3 of those, one every year.

I'm from Finland and we have good and free healthcare system and my doctor will help me with my messed up lipid profile and APOE. My doctor doesn't like my HDL-TG-ratio and I am too young to get xanthelasmas, so she is interested in my case.

I really hope people will get their whole genomes sequenced so we get tons of community data to help us all. It's much easier to compare when there is thousands of genomes to compare.
I just love DanteLabs's DNA explorer. That is the source of my screenshots. It's easy to use, visually nice and really gives good data. It's very different compared to 23andMe and other "cheap copies".
I can see everything there, for example my blue/grey eyes, ginger beard, freckles and tons of other details. It has been fun learning to read my genome but it's very difficult to master at the level when I could read genome like matrix.

It will have huge benefits for science and sequenced individuals when there is one million genomes sequenced and shared. Forums like this will be very useful with proper amounts of data.

And I think I have interesting hobby for tens of years searching my genome.

My friend found familiar hemochromatosis in his genome so benefits are very real for sequencing.

If I was going to make another child, I would sequence my partner before conceiving.

If I am e1/e3 I think some scientist will want to study it (me) because it's so rare.

I will post results when I'm sure which one it really is.

Happy summer to everyone, have fun and don't stress corona. =D

[circular]

I really hope people will get their whole genomes sequenced so we get tons of community data to help us all. It's much easier to compare when there is thousands of genomes to compare ...

It will have huge benefits for science and sequenced individuals when there is one million genomes sequenced and shared.

Hi Rare_case!

I also like the citizen science approach and just to learn, so I'm looking forward to exploring my own genome as well. Since I don't have time to fit it in right now, I figure I might as well wait until I do and the sequencing will be even cheaper.

In the meantime I joined the All of Us campaign in the US (NIH) for free (there are similar massive databases underway in some other countries). An advantage to participating in these databases is that researchers will have access to the data in a controlled environment for peer reviewed studies, and they will get to a million genomes much faster.