Trying to figure my APOE type

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wm00
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Trying to figure my APOE type

Post by wm00 »

Hello everyone,

I have found this website after reading Dr Bredesen book and I have already learned and read a lot of useful things in the few hours after signing up.

I am 47 and a few days ago I got my DNA results from Dante Labs and in several panels (I ordered the full panels list) they say I am at risk of Alzheimer and I have 2 APOE genes but they do not say which ones. I also uploaded the data on promethease but I can't find if those are APOE4 genes or not. I am not even sure if I uploaded the correct data file as Dante Labs provide several different files for raw data and no information on which one is what (the one I uploaded is called filtered.snp.vcf.gz).

I am very concerned and really depressed also because about 4 years ago I did an extensive psychological evaluation and I was told I should check myself for Alzheimer but never took it seriously.

Anyone know how I can figure out if the 2 APOE genes I have are APOE4 or not?

Thank you!
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Jenny B
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Re: Trying to figure my APOE type

Post by Jenny B »

wm00 wrote:
I have found this website after reading Dr Bredesen book and I have already learned and read a lot of useful things in the few hours after signing up.

I am 47 and a few days ago I got my DNA results from Dante Labs and in several panels (I ordered the full panels list) they say I am at risk of Alzheimer and I have 2 APOE genes but they do not say which ones. I also uploaded the data on promethease but I can't find if those are APOE4 genes or not. I am not even sure if I uploaded the correct data file as Dante Labs provide several different files for raw data and no information on which one is what (the one I uploaded is called filtered.snp.vcf.gz).

I am very concerned and really depressed also because about 4 years ago I did an extensive psychological evaluation and I was told I should check myself for Alzheimer but never took it seriously.

Anyone know how I can figure out if the 2 APOE genes I have are APOE4 or not?
You have come to the right place, wm00. Your dedication to learning more about genetic risk factors for Alzheimer's Disease is admirable, and your concern and depression is understandable by all in this community. Please know that learning about what can be done to optimize your whole health (for instance, reading and implementing some lifestyle modification recommended in Dr Bredesen's book and others) will help prevent and reverse many chronic health imbalances no matter your genetic picture. That being said, let me give you some resources to help determine your ApoE genetic status, and I believe others in this group will weigh in as well to fill in the gaps. The WIKI resource is full of information and specifically Check E4 Status Link should get you started along with this link to the APOE-SNPedia. Another great source of information and inspiration is the Primer written by a doctor who is herself, ApoE 4/4. It is an introduction to ApoE4 and possible prevention strategies. Also, the How-To Guide can help you navigate the ApoE4.info website. You are certainly taking your health seriously now, so congratulations for that, and know that it IS enough to start where you start. You are on a path to optimizing your health and wellness, and this community is here to help where ever we can. Welcome!

Warmly,

Jen
Jenny B, ND
FMCHC, NBC-HWC
ApoE4.info Sr Support Intern
Functional Medicine Certified Health Coach
National Board Certified Health and Wellness Coach
Naturopathic Doctor
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Tincup
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Re: Trying to figure my APOE type

Post by Tincup »

wm00 wrote:
Anyone know how I can figure out if the 2 APOE genes I have are APOE4 or not?
I don't know anything about the Dante data presentation. If you can unpack it to actually look at SNP's (ask Dante how to do this?), you can figure it out yourself.

The SNP's you want are
rs429358 & rs7412

See here for the interpretation.
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wm00
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Re: Trying to figure my APOE type

Post by wm00 »

Thank you for your answers. I contacted Dante as well but I still have no answer from them.
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Re: Trying to figure my APOE type

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wm00 wrote: (the one I uploaded is called filtered.snp.vcf.gz).

Anyone know how I can figure out if the 2 APOE genes I have are APOE4 or not?
.vcf files are Variant Call Format (VCF).

This tool looks like it will view VCF files.
"VCF Requirements
IGV supports VCF Version 4.

VCF data files must be indexed for viewing in IGV, either by using igvtools or by using Tabix.

igvtools can be run from the command line or IGV itself (Tools>Run igvtools...) After launching, choose the Index command and browse to your .vcf file. The index file (.idx) will be created in the same directory as the .vcf file.
igvtools also sorts .vcf files.
Tabix creates a .tbi file. Tabix, including documentation, is available from the SamTools Web site.

https://software.broadinstitute.org/sof ... v/LoadData

.gz files are compressed, so you'd need to uncompress it first. For Windows 10.

Extract .tar.gz, .tgz, or .gz tarballs using tar on Windows 10
To extract .tar.gz, .tgz, .gz as well as .zip files using tar on Windows 10, use these steps:

Open Start on Windows 10.

Search for Command Prompt, right-click the first result and select the Run as administrator option.

Type the following command to use tar to extract the files and press Enter:

tar -xvzf C:\PATH\TO\FILE\FILE-NAME.tar.gz -C C:\PATH\TO\FOLDER\EXTRACTION

C:\PATH\TO\FILE needs to be the path to where the file is

C:\PATH\TO\FOLDER needs to be the path where you want the result to go.

On a MAC, you should be able to just double click the file in Finder and it will uncompress automatically.

On Unix/Linux, if you are using these, you likely don't need help to do this.
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Re: Trying to figure my APOE type

Post by Exodus »

Tincup wrote:
wm00 wrote:
Anyone know how I can figure out if the 2 APOE genes I have are APOE4 or not?
The SNP's you want are
rs429358 & rs7412


See here for the interpretation.
Hi Tincup - I'm looking for the same info as wm00 - my original test came from 23 & me and I ran it through Promethease - I looked at what they sent and I've stared at the SNPedia page you linked till I'm goofy, but can't quite determine exactly what I have. The genomes as they are printed out look something like this:

rs429358 19 45411941 TT
rs7412 19 45412079 CC

You seem so skilled at interpretation - thanks in advance for any help you might be able to give me . . . Exodus
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Re: Trying to figure my APOE type

Post by Tincup »

Exodus wrote:You seem so skilled at interpretation - thanks in advance for any help you might be able to give me . . . Exodus
Just saw this after a busy day. Will look at it more carefully and respond tomorrow.
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Re: Trying to figure my APOE type

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Exodus wrote: Hi Tincup - I'm looking for the same info as wm00 - my original test came from 23 & me and I ran it through Promethease - I looked at what they sent and I've stared at the SNPedia page you linked till I'm goofy, but can't quite determine exactly what I have. The genomes as they are printed out look something like this:

rs429358 19 45411941 TT
rs7412 19 45412079 CC
My interpretation:
rs429358 TT
rs7412 CC

Code: Select all

Common name	Genoset	Magnitude	rs429358	rs7412	Comment
Apo-ε3/ε3	       gs246	2				(T;T)	(C;C)	the most common
From https://www.snpedia.com/index.php/APOE
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Re: Trying to figure my APOE type

Post by Exodus »

Tincup wrote:
Exodus wrote: Hi Tincup - I'm looking for the same info as wm00 - my original test came from 23 & me and I ran it through Promethease - I looked at what they sent and I've stared at the SNPedia page you linked till I'm goofy, but can't quite determine exactly what I have. The genomes as they are printed out look something like this:

rs429358 19 45411941 TT
rs7412 19 45412079 CC
My interpretation:
rs429358 TT
rs7412 CC

Code: Select all

Common name	Genoset	Magnitude	rs429358	rs7412	Comment
Apo-ε3/ε3	       gs246	2				(T;T)	(C;C)	the most common
From https://www.snpedia.com/index.php/APOE

WOW - thanks Tincup for your speedy response - now all I need to do is figure out where to go from here - guess this explains my memory issues!?! As always - I'm open to any/all input & advice and thank everyone in advance for adding to this compilation of info and support. Exodus
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Re: Trying to figure my APOE type

Post by Tincup »

Exodus wrote:
Tincup wrote: WOW - thanks Tincup for your speedy response - now all I need to do is figure out where to go from here - guess this explains my memory issues!?!
ApoE3/3 is the most common and not at high risk for memory issues.
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