Important implications for Promethease users ...

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circular
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Important implications for Promethease users ...

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Common genetic test often wrong when identifying rare disease-causing variants such as BRCA1 and BRCA2, study says

When I use Promethease I don't dwell a lot on variants that Promethease assigns a fairly high frequency in my set population, say those over 40%. I've tended to think that variants I have that are 20% might, generally speaking, be more notable.

This article calls me out on my process:
A genetic test used to detect common traits many people share is not reliable in identifying rare disease-causing variations ... a new study has found.

The SNP test, which stands for "single nucleotide polymorphism," is used by direct-to-consumer DNA and ancestry companies to identify common traits such as eye color, height and proclivity toward cheek dimples and dandruff, to name a few.

But when SNP tests are applied to identifying rare mutations that contribute to disease, the study found only 16% of nearly 5,000 rare mutations could be confirmed by more stringent DNA sequencing tools. [Emphasis added]
I've just shuttered one of my research departments as unreliable :cry:
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circular
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Re: Important implications for Promethease users ...

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circular wrote: I've just shuttered one of my research departments as unreliable :cry:
I've just shuttered Promethease again. I looked up my own and both parents' variants for six blood clotting related SNPs in Promethease using files for each of us that contained merged results from FTDNA, AncestryDNA, LivingDNA and 23andMe. I then looked up the same SNPs at 23andMe using their browser. I have the most faith in 23andMe's accuracy for this type of DNA research. Promethease had returned at least three if not four errors, providing variants that I or one of my parents did not have. I don't know whether the errors derived somehow from using the merged file, but this underscored for me that without a thorough investigation to whether there is a certain type of file that can be trusted in Promethease, it is not at all reliable for looking up one's own variants, let alone using the results to try to hack anything.
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Re: Important implications for Promethease users ...

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circular wrote:[I don't know whether the errors derived somehow from using the merged file,.
Who merged the file and do you have access to it? Also access to raw files of the non 23andme data (I've only got 23andme).
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circular
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Re: Important implications for Promethease users ...

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Tincup wrote:
circular wrote:[I don't know whether the errors derived somehow from using the merged file,.
Who merged the file and do you have access to it? Also access to raw files of the non 23andme data (I've only got 23andme).
That's a good question! There was a time that Promethease provided the merged file if you attached the ones you wanted to merge and sent them for processing. I don't know whether they still do it, maybe for a fee. I remember being so busy at the time and staying up until midnight to download all the files from the sites and get them uploaded to Promethease for all three of us. It was either not going to be offered anymore or they were going to charge for it after midnight.

You can download your raw data from the other sites, which is how I got the merged file, but offhand I don't think they offer SNP browsers they way 23andMe do. I think 23andMe would be the most reliable and also makes it so easy to look up SNPs, but there may be some results in other companies' files that aren't at 23andMe. In my amateur opinion they just wouldn't be that reliable.
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Re: Important implications for Promethease users ...

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circular wrote:You can download your raw data from the other sites, which is how I got the merged file, but offhand I don't think they offer SNP browsers they way 23andMe do. I think 23andMe would be the most reliable and also makes it so easy to look up SNPs, but there may be some results in other companies' files that aren't at 23andMe. In my amateur opinion they just wouldn't be that reliable.
Hence, if I understand correctly, if you just imported only 23andMe into Promethease, this likely isn't an issue? It would at least be easy to back check.
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circular
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Re: Important implications for Promethease users ...

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Tincup wrote:
circular wrote:You can download your raw data from the other sites, which is how I got the merged file, but offhand I don't think they offer SNP browsers they way 23andMe do. I think 23andMe would be the most reliable and also makes it so easy to look up SNPs, but there may be some results in other companies' files that aren't at 23andMe. In my amateur opinion they just wouldn't be that reliable.
Hence, if I understand correctly, if you just imported only 23andMe into Promethease, this likely isn't an issue? It would at least be easy to back check.
Ah, I didn't see where you were going with that. This isn't exactly what you mean, but I thought I would add how it looks at Promethease when they return results from the blended file. They report the result for each company that's included in the blended file. For rs6025 (Factor V), all companies, according to Promethease, report A/C. 23andMe reports C/C for the same person.

Some day I may delete the merged file since I can't rely on it and then add 23andMe and check. I'm not sure when.
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Re: Important implications for Promethease users ...

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Here's what you see at the Promethease page before uploading a file(s):
Customers of DNA testing services (such as 23andMe, Ancestry.com, FamilyTreeDNA, Genos, etc.), biomedical researchers and healthcare professionals use Promethease to retrieve information published about their DNA variations. Reports cost $12. Most reports are produced in under 10 minutes. Much larger data files (such as imputed full genomes) have increased runtime. Uploading additional data files to create a combined report costs an additional $4 and must be done at the same time. It is not possible to add a new raw data file to one uploaded previously.
So when I created the blended file previously, it was the last chance to do it for free. I'd need to pay $12 to upload 23andMe on its own to see how that goes, so I think I won't since I can check at 23andMe.

It would be good for people to watch for and report any anomolies here as well as to see if anyone can confirm that uploading 23andMe on its own (or any other company file for that matter) is reliable.
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Re: Important implications for Promethease users ...

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I see at Promethease that my files are ‘expired’, but I can re-download them with updated, current SNPedia info. I will try to get to that and see if it makes any difference in the variant reporting for any reason.
ApoE 3/4 > Thanks in advance for any responses made to my posts.
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Re: Important implications for Promethease users ...

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circular wrote:I see at Promethease that my files are ‘expired’, but I can re-download them with updated, current SNPedia info. I will try to get to that and see if it makes any difference in the variant reporting for any reason.
Updating the files didn't make a difference. I think it's just the SNPedia database info that updates.

I submitted a support ticket at Promethease.com with screenshots.
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circular
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Re: Important implications for Promethease users ...

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circular wrote:I submitted a support ticket at Promethease.com with screenshots.
No reply from Promethease so far.
ApoE 3/4 > Thanks in advance for any responses made to my posts.
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