Struggling to find my variants

[maxwe789]

I have completed a whole genome sequencing with Dante Labs in the UK and I'm trying to see which variant of APOE I have but I'm struggling a bit. I'm sure it's just a lack of knowledge in knowing how to read the results.

Dante provided a "report" which is really dumbed down and doesn't mention genes or alleles or SNPs or anything. I uploaded the data to Promethease and couldn't find rs429358, rs7412 in there as mentioned by https://www.snpedia.com/index.php/APOE.

I then uploaded the data to sequencing.com to try and use their gene explorer. Using snpedia again I was looking for position 44908684 but on sequencing.com the position come in ranges? See attached pic.

If anyone could help me figure out how to do this I would really appreciate it!

[Tincup]

J11 You've got whole genome experience. Can you help?

[maxwe789]

Screenshot didn't upload, trying again. This shows the positions in ranges, and I don't know what that is vs the specific positions mentioned on snpedia.

Screenshot 2020-09-07 at 14.53.31.png

[NF52]

I have completed a whole genome sequencing with Dante Labs in the UK and I'm trying to see which variant of APOE I have but I'm struggling a bit. I'm sure it's just a lack of knowledge in knowing how to read the results.

Dante provided a "report" which is really dumbed down and doesn't mention genes or alleles or SNPs or anything. I uploaded the data to Promethease and couldn't find rs429358, rs7412 in there as mentioned by https://www.snpedia.com/index.php/APOE.

I then uploaded the data to sequencing.com to try and use their gene explorer. Using snpedia again I was looking for position 44908684 but on sequencing.com the position come in ranges? See attached pic.

If anyone could help me figure out how to do this I would really appreciate it!

Welcome, maxwe789!

I wish I had an easy answer for you, but will at least suggest a few options. Your screen shot looks like it came from Dante Labs, since it appears to shows ranges of SNPS. I suspect that you will need Promethease to interpret this for ApoE status. You probably uploaded your raw data to Promethease, but in case you didn't, here's their advice which covers Dante Labs, which they say has "usable" data:

Do not attempt to uncompress or convert between formats. Many of the conversion tools do not work well and can do harm. Just upload your original untouched data. If you cooked up your own file you may end up with a warning about it being unrecognized. Since all of the formats from the various companies are just tab or CSV (.cvs) delimited, Promethease relies on these headers to know which format to expect.

https://faq.promethease.com/en/article/ ... romethease.

I have a Promethease report using my 23&me data. The report has a column on the right which defaults to showing "Medical Conditions" under the horizontal bar labeled "Topics". But I can scroll down from Medical Conditions alphabetically to "Alzheimer's" and the reports immediately switch to only those with Alzheimer's associations. In my case that includes 2 copies of ApoE4, but also some variants in other genes that slightly lessen my risk. If you do have a readable report, and haven't yet searched by Alzheimer's as the topic, it's possible that the reason you didn't see reports in the first pages is that you have no big risks!

Given the price for Dante Labs' report, I would hope you could reach out to their support desk and get some actual support also. Please keep us posted;

[maxwe789]

The picture is from sequencing.com's gene explorer. I have uploaded to Promethease but the important parts for calculating APOE variant is not present in the report. I'm suspecting that's because I'm using the VCF data which doesn't include genes that that are the same as a reference dataset. The BAM file is hundreds of gigs and I'm not sure that this would upload.

Do you know of another similar service to Promethease I could try or why on sequencing.com the positions are shown in ranges?

[NF52]

The picture is from sequencing.com's gene explorer. I have uploaded to Promethease but the important parts for calculating APOE variant is not present in the report. I'm suspecting that's because I'm using the VCF data which doesn't include genes that that are the same as a reference dataset. The BAM file is hundreds of gigs and I'm not sure that this would upload.

Do you know of another similar service to Promethease I could try or why on sequencing.com the positions are shown in ranges?

Sorry, I'm a neophyte when it comes to using or interpreting the raw data. But the BAM format
appears to be the problem, according to this Promethease report, which includes a link to a possible DIY fix: Can I upload a BAM file?

Unfortunately, BAM files are no longer supported by Promethease, since our current upload tool is limited to 4 GB per file. There are ways and different tools to convert BAM files into VCF format; you can learn about some of them on https://snpedia.com/index.php/VCF

[carrie]

I have completed a whole genome sequencing with Dante Labs in the UK and I'm trying to see which variant of APOE I have but I'm struggling a bit. I'm sure it's just a lack of knowledge in knowing how to read the results.

Dante provided a "report" which is really dumbed down and doesn't mention genes or alleles or SNPs or anything. I uploaded the data to Promethease and couldn't find rs429358, rs7412 in there as mentioned by https://www.snpedia.com/index.php/APOE.

I then uploaded the data to sequencing.com to try and use their gene explorer. Using snpedia again I was looking for position 44908684 but on sequencing.com the position come in ranges? See attached pic.

If anyone could help me figure out how to do this I would really appreciate it!

Hello maxwe789!

It is my pleasure to welcome you to the ApoE4.info community. In case you haven't had an opportunity to look around, I wanted to provide a few links to help you navigate the wealth of information on the site. Within these links you may find some helpful information in your search for answers to the sequencing.

How-to-Guide was created to help members navigate the site. It explains how to use the quotes button so the other member will receive an email notification of your reply. There are other handy tips explaining how to search and subscribe to your topics of interest and more.

Primer is an incredibly helpful post written by a physician member of the site. I believe this might be helpful in your questions regarding sequencing.

Our Stories is an area new members use to introduce themselves to the community. If you are inclined, please feel free to make a post about what brought you to the ApoE4.info site.

Again, a very big warm welcome. If you have any questions about the site, please don't hesitate to ask. (Be sure to use the little quotes button at the top and I will be alerted).

Best wishes to you,
Carrie

[maxwe789]

Thanks for the warm welcome. Sequencing.com has an "app" that will tell you APOE for $59 based on my WGS data. Bit frustrating that I think the data is there for the taking if only I can figure out how to read it!

[NF52]

Thanks for the warm welcome. Sequencing.com has an "app" that will tell you APOE for $59 based on my WGS data. Bit frustrating that I think the data is there for the taking if only I can figure out how to read it!

As someone who is unable to figure out how almost anything works, I am used to having to pay for someone who thinks it's easy. (I am great in a spelling bee, but that's not a skill that is routinely in demand.) Hope you find that it's well worth the British pounds!

[Matisse]

Have you tried contacting Dante Labs?