New Member - Raw Data questions

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Bakesbrot
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New Member - Raw Data questions

Post by Bakesbrot »

Hi all!

Like a lot of you I came on here looking for advice after discovering from 23 and me that I have ApoE 4/4 . The advice on here is great, and being 32 I have hopes that I can make changes now that will prevent against getting AD. I have also read the primer and many posts, but will keep referring back as there's a lot of info to take in!

I do have a few questions on the SNPs that I've been trying to research (well I have a lot but trying to focus on one area at a time :) ):

[*]I extracted my raw data through Promethease and it shows I have gs141, and they said - "You carry one APOE-ε3 allele and one APOE-ε4 allele." And apparently that is based on these 2 SNPs- rs429358(C;T) rs7412(C;C).
However, looking up rs429358 on my 23 and me results it shows that it's C/C (but there's a section that says variants C or T). This would correspond with 23 and me saying I have 2 APOE 4 variants. Does anyone understand why promethease is showing gs141 when it seems I must have gs216?

[*]Trying to understand protective genes, I looked on promethease again and for AD I seem to have a mix of protective and non protective but was wondering what the key ones are that I should check? I did check the PSEN1 ones as well (I didn't want to but I needed to know!), and they all came back OK.

Just wondered how everyone else faired checking this data and if there's any other websites/info they'd recommend to break this down.

I'm going to try and look into all the various blood tests etc, but being in the UK it seems some of the tests are quite limited so I'm going to have to do more research in that area. Thanks everyone, looking forward to being part of this community!
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floramaria
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Re: New Member - Raw Data questions

Post by floramaria »

Bakesbrot wrote:Hi all!

I do have a few questions on the SNPs that I've been trying to research (well I have a lot but trying to focus on one area at a time :) ):

[*]I extracted my raw data through Promethease and it shows I have gs141, and they said - "You carry one APOE-ε3 allele and one APOE-ε4 allele." And apparently that is based on these 2 SNPs- rs429358(C;T) rs7412(C;C).
However, looking up rs429358 on my 23 and me results it shows that it's C/C (but there's a section that says variants C or T). This would correspond with 23 and me saying I have 2 APOE 4 variants. Does anyone understand why promethease is showing gs141 when it seems I must have gs216?
Just wondered how everyone else faired checking this data and if there's any other websites/info they'd recommend to break this down.

I'm going to try and look into all the various blood tests etc, but being in the UK it seems some of the tests are quite limited so I'm going to have to do more research in that area. Thanks everyone, looking forward to being part of this community!
Hi Bakesbrot, Welcome to the Forums. You have already discovered many of the wonderful resources available here and now you have actively joined in the conversation with your question. One of the people who regularly responds to genetics questions probably will answer. But meanwhile, if you want to look this up yourself, I can steer you to one of the resources you might not yet have used, the Search function. You access it through the magnifying glass to the left of your user name near the top right of the page. If you enter rs429358 into the search you will see all previous posts where that is mentioned. If you look at those, you will probably find the answer to your question about deciphering your ApoE status from the raw data fairly quickly.
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Bakesbrot
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Re: New Member - Raw Data questions

Post by Bakesbrot »

floramaria wrote:
Bakesbrot wrote:Hi all!

I do have a few questions on the SNPs that I've been trying to research (well I have a lot but trying to focus on one area at a time :) ):

[*]I extracted my raw data through Promethease and it shows I have gs141, and they said - "You carry one APOE-ε3 allele and one APOE-ε4 allele." And apparently that is based on these 2 SNPs- rs429358(C;T) rs7412(C;C).
However, looking up rs429358 on my 23 and me results it shows that it's C/C (but there's a section that says variants C or T). This would correspond with 23 and me saying I have 2 APOE 4 variants. Does anyone understand why promethease is showing gs141 when it seems I must have gs216?
Just wondered how everyone else faired checking this data and if there's any other websites/info they'd recommend to break this down.

I'm going to try and look into all the various blood tests etc, but being in the UK it seems some of the tests are quite limited so I'm going to have to do more research in that area. Thanks everyone, looking forward to being part of this community!
Hi Bakesbrot, Welcome to the Forums. You have already discovered many of the wonderful resources available here and now you have actively joined in the conversation with your question. One of the people who regularly responds to genetics questions probably will answer. But meanwhile, if you want to look this up yourself, I can steer you to one of the resources you might not yet have used, the Search function. You access it through the magnifying glass to the left of your user name near the top right of the page. If you enter rs429358 into the search you will see all previous posts where that is mentioned. If you look at those, you will probably find the answer to your question about deciphering your ApoE status from the raw data fairly quickly.
Thanks! I’ve had a browse of previous posts but I haven’t seen one that identifies a discrepancy between what promethease says and actual results. I’m assuming maybe they just don’t delve as deeply to the 4/4 part? (Being new to it all I was secretly hoping it was a mistake but looking at my raw data I definitely do have 4/4).

Thanks :)
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floramaria
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Re: New Member - Raw Data question

Post by floramaria »

Bakesbrot wrote: Thanks! I’ve had a browse of previous posts but I haven’t seen one that identifies a discrepancy between what promethease says and actual results. I’m assuming maybe they just don’t delve as deeply to the 4/4 part? (Being new to it all I was secretly hoping it was a mistake but looking at my raw data I definitely do have 4/4).
Thanks :)
Hi Bakesbrot, You are certainly not the first person to have posted hoping that their results were a mistake! It is strange that Promethease would use the raw 23&Me data and come to a different conclusion.
I haven’t learned any more about genetics since the last post, but it seems that you have :D and have resolved the discrepancy between the results you saw in raw data and what Promethease reported. Whether you have one or two copies you definitely are in the right place to learn how to mitigate the risks associated with it.
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Tincup
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Re: New Member - Raw Data questions

Post by Tincup »

Bakesbrot wrote: [*]I extracted my raw data through Promethease and it shows I have gs141, and they said - "You carry one APOE-ε3 allele and one APOE-ε4 allele." And apparently that is based on these 2 SNPs- rs429358(C;T) rs7412(C;C).
However, looking up rs429358 on my 23 and me results it shows that it's C/C (but there's a section that says variants C or T). This would correspond with 23 and me saying I have 2 APOE 4 variants. Does anyone understand why promethease is showing gs141 when it seems I must have gs216?
You might try reuploading the raw data and rerunning Promethease. Seems like the data are scrambled for an unknown reason. I think the Promethease algorithms are just simple matching - if this then that.
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