New & confused

A primer for newbies and old pros alike.
het3ver3geet4
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New & confused

Postby het3ver3geet4 » Sat Nov 02, 2019 11:48 am

Hello:

I'm relatively new, have explored the site over several months, and I feel like "where's Waldo", except he's invisible! I'm blaming no-one but myself, mind you. :roll:

I got the book, the testing, a doctor and...I still don't know what I really have. I'm 60 and was alerted by my own father's dementia and got 23andme testing which says I have one variant of the APOE4 gene. Specifically, rs429358, variant is C or T, my genotype is C/T. What does that mean? Am I APOE3/4?

How do I figure this out? Do I need additional testing? Should I run this data through another program?

Your wise words much appreciated.
Thank you,
Robyn

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emmabarton
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Re: New & confused

Postby emmabarton » Sat Nov 02, 2019 1:04 pm

het3ver3geet4 wrote:Hello:

I'm relatively new, have explored the site over several months, and I feel like "where's Waldo", except he's invisible! I'm blaming no-one but myself, mind you. :roll:

I got the book, the testing, a doctor and...I still don't know what I really have. I'm 60 and was alerted by my own father's dementia and got 23andme testing which says I have one variant of the APOE4 gene. Specifically, rs429358, variant is C or T, my genotype is C/T. What does that mean? Am I APOE3/4?

How do I figure this out? Do I need additional testing? Should I run this data through another program?

Your wise words much appreciated.
Thank you,
Robyn


Hi Robyn,

Thanks for finally reaching out-- it seems to be the trend for most people-- visiting the site, exploring a little, and then finally taking a risk and making contact. I'm really glad you did and I will do my best to answer any of your questions.

First, to encode the values for your SNPs, check out this page to convert your results into your APOE status. I actually got this information from the wiki page, which is also an invaluable tool early in your process of exploration. I personally think the primer is the best first step to explore on this site. It was written by a medical doctor from our community that is homozygous for ApoE4 (meaning she has two copies E4/E4). Hopefully, these links will be a great support to your process.

I know it can be scary and a little intimidating to watch a parent struggle with dementia and then learn that a genetic risk exists for you. My own father passed away from Alzheimer’s a little over a year and a half ago. That experience lit all sorts of alarms for me, but fortunately it does not mean this path is our destiny. Reviewing the material on this site and connecting with others in the community has revealed clarity about the old adage: "knowledge is power." Please continue to dig deeper and feel free to reach back out to ask any question that might surface during your exploration.

Light and peace,

Emma
healing happens in relationship

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Re: New & confused

Postby NF52 » Sat Nov 02, 2019 2:33 pm

het3ver3geet4 wrote:Hello:
...I got the book, the testing, a doctor and...I still don't know what I really have. I'm 60 and was alerted by my own father's dementia and got 23andme testing which says I have one variant of the APOE4 gene. Specifically, rs429358, variant is C or T, my genotype is C/T. What does that mean? Am I APOE3/4? ...
Robyn
Welcome Robyn, from a 67 year old ApoE 4/4 who has been using this site for years and has gotten comfortable with being confused! Since few of us had genetics in high school or college, we're playing catch-up--with a lot of lived wisdom on our side!

I often use Snpedia as a go-to explanation site, and have also downloaded my 23&me raw data to Promethease, although you can Google other genetic interpretation programs. I think Promethease is free until the end of this calendar year as a special offer. You can go the link above, scroll to the bottom of the page and see some sample reports for what you'd be likely to get. Here's what they say about themselves on that page:
Promethease is a literature retrieval system that builds a personal DNA report based on connecting a file of DNA genotypes to the scientific findings cited in SNPedia.
I hope your 23&m3 report included the information that your Apoe 3/4 status is a risk, not destiny--we are much more than one pair of SNPS!

The SNP rs429358 would indicate ApoE 3/4 if a companion APOE SNP rs 7412 is C/C.
You should be able to go to your "raw data" for rs7412 using the 23&me search tool. People with ApoE 3/4 have, by one 2017 meta-analsysis of four large cohorts of people followed for a long time, about a 20-25% chance of either Mild Cognitive Impairment(MCI) or dementia by the age of 85 if they are currently 60-75. The risk for either MCI or dementia in the near future (before age 70) is much smaller than that. [If rs7412 happens to be C/T you would be a lucky ApoE 2/4, since ApoE 2 is associated with a lower than average risk of Alzheimer's disease. We have a very healthy ApoE 2/4 lady on the forum who is almost 85.]

It's likely that your father had risk factors you don't, and health issues that were not understood when he was your age. You and I both inherited half of our genes from our mothers, and may have gained some protective genes that will help us continue to play "where's Waldo" here!

To help you enjoy the forum by using quotes to be sure someone sees your replies, subscribing to favorite topics, finding unread posts, and searching for those elusive answers check out our How-To Guide.

I strongly second Emma's suggestion of the Primer as a wonderful--and reassuringly empowering---resource.

You dad would want you to embrace this challenge, and enjoy the opportunities that come along in our 60's. Let us know how we can help to make it easier to do that.
4/4 and still an optimist!

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Re: New & confused

Postby Tincup » Sun Nov 03, 2019 6:52 am

Promethease is free through the end of the year.
Tincup
E3,E4

het3ver3geet4
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Re: New & confused

Postby het3ver3geet4 » Sun Nov 03, 2019 10:06 am

First, to encode the values for your SNPs, check out this page to convert your results into your APOE status.


Thank you for your feedback. Could you please send me the complete link, not the hyperlink, which goes to my gmail account for some unknown reason. So I don't know where it's supposed to lead as yet...
e3/e4

het3ver3geet4
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Re: New & confused

Postby het3ver3geet4 » Sun Nov 03, 2019 10:08 am

Promethease is free through the end of the year.


Tincup, Regarding Promethiase being free, I'm less concerned about cost than privacy. Admittedly, its probably too late having done 23andme which is now owned by big Pharma, but how does one protect one's data when trying to interpret tests? Is there any particular service that people use with this in mind?
e3/e4

het3ver3geet4
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Re: New & confused

Postby het3ver3geet4 » Sun Nov 03, 2019 10:13 am

The SNP rs429358 would indicate ApoE 3/4 if a companion APOE SNP rs 7412 is C/C.


NF52, I'm C/C on rs7412 so I guess I'm ApoE3/4. Thanks for that pointer.

I feel as though all of us who've done these online tests and test interpretations are like insects splattered on the windshield of a fast moving car: too late... for data privacy. But I'd like to TRY and protect anything that MAY still be private. So hesitating on further interpretation in the current data environment. Not sure if there are workarounds on this.
e3/e4

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Re: New & confused

Postby Tincup » Sun Nov 03, 2019 10:30 am

het3ver3geet4 wrote:
Promethease is free through the end of the year.


Tincup, Regarding Promethiase being free, I'm less concerned about cost than privacy. Admittedly, its probably too late having done 23andme which is now owned by big Pharma, but how does one protect one's data when trying to interpret tests? Is there any particular service that people use with this in mind?


I think you can register under an assumed name. You download your 23andMe raw data to your computer (I recommend doing this for posterity anyway), then upload to Promethease. The raw file does not appear to have any identifying info in it, except in the file name, which you can change. I looked at the bottom of the file and also saw nothing that is identifying.

This is the header from mine:

# This data file generated by 23andMe at: Sat Jul 14 12:33:28 2017
#
# This file contains raw genotype data, including data that is not used in 23andMe reports.
# This data has undergone a general quality review however only a subset of markers have been
# individually validated for accuracy. As such, this data is suitable only for research,
# educational, and informational use and not for medical or other use.
#
# Below is a text version of your data. Fields are TAB-separated
# Each line corresponds to a single SNP. For each SNP, we provide its identifier
# (an rsid or an internal id), its location on the reference human genome, and the
# genotype call oriented with respect to the plus strand on the human reference sequence.
# We are using reference human assembly build 37 (also known as Annotation Release 104).
# Note that it is possible that data downloaded at different times may be different due to ongoing
# improvements in our ability to call genotypes. More information about these changes can be found at:
# https://you.23andme.com/p/15c74048b7810 ... /download/
#
# More information on reference human assembly builds:
# https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/
#
# rsid chromosome position genotype

You can also do as suggested and look at the SNP's yourself. This is the page in SNPEDIA https://www.snpedia.com/index.php/APOE
Tincup
E3,E4

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Re: New & confused

Postby rjkmhk » Tue Feb 11, 2020 9:22 am

I'm new and confused also...don't have my APOE status so I looked around on the Promethiase site and noticed this (Note that Promethease reports from Ancestry data will not return accurate ApoE status due to lack of relevant data.)...Is this common knowledge? In light of this statement, is the best testing coming from 23andme? Thanks!

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Re: New & confused

Postby mike » Tue Feb 11, 2020 10:52 am

rjkmhk wrote:I'm new and confused also...don't have my APOE status so I looked around on the Promethiase site and noticed this (Note that Promethease reports from Ancestry data will not return accurate ApoE status due to lack of relevant data.)...Is this common knowledge? In light of this statement, is the best testing coming from 23andme? Thanks!

23andMe is good, but you need to get Health, not just Ancestry level.
Sonoma Mike
4/4


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