Big Data App to Explore Genomes for Clinical Relevance, Rare Variants, Drug Response, etc (Free)

nandixon

nandixon

Senior Member
Messages
1,092
@Brandit, I'm guessing that's a miscall by 23andMe. dbSNP gives the frequency for the variant (A --> G) at only 1 in 77,108 alleles, and also gives a study showing it to be pathogenic for Charcot-Marie-Tooth disease, albeit with a mild course. OpenSNP (with data mostly from 23andMe users) on the other hand gives a frequency of 20%, so that seems off.
 
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Brandit

Messages
30
This particular one caught my eye because it is mitochondrial in nature. I think my paternal grandmother had Charcot so it may be possible. I suppose that's a dead end if one database says extremely rare and one say 1 in 5
 
K

kday

Senior Member
Messages
369
Brandit said:
This one appears to be autosomal dominant negative where the one bad copy supersedes the good copy. There's no information on frequency
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That appears to be a common miscall in 23andMe. I should probably filter that variant. Has almost no frequencies about around 20% on 23andMe are AG. This is not a real variant.

1567841216605.png

https://www.opensnp.org/snps/i5008699
 
K

kday

Senior Member
Messages
369
Fixed a lot of bugs and made some important fixes so 23andMe and Ancestry data a lot more accurate the past week or so. I haven't fixed some of the bugs mentioned above or lower priority bugs yet. But those are next!

I also noticed some people have Genos data, and realized my app was not compatible because Genos data is not gzip compressed.

Genos .vcf files are compatible now, and it really surprised me how fast these exome files process. Literally within some seconds! Much faster than 23andMe/Ancestry data.
 
PracticingAcceptance

PracticingAcceptance

Senior Member
Messages
1,863
kday said:
While I'd like to think I'm solving the "how do you make tools accessible to everyone" dilemma, it's harder to solve how do you make it easy to understand for those that are less technically minded or have limited knowledge about genomics.
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I think it's amazing that you built this tool. The fact that you're sharing it openly says a lot about you :)
Designing interfaces that make it simpler for people to understand - that's an art form.
Would you be open to someone else helping you to do that?
I don't think it's necessary for you to have all the skills needed to make this work. Collaborate if you can, it's great to collaborate.
 
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BeautifulMorning

Messages
8
kday said:
Genos .vcf files are compatible now, and it really surprised me how fast these exome files process. Literally within some seconds! Much faster than 23andMe/Ancestry data.
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I've uploaded my genos file unzipped on my computer to .vcf file. The upload seems to work ok, however it runs a couple seconds, creates the screen, but all options have the following message " No variants were found in the section. Consider this a good thing! "

Is there something else I should do? My 23 and Me file processed ok a few weeks ago.
Thanks,
Pat
 
K

kday

Senior Member
Messages
369
BeautifulMorning said:
I've uploaded my genos file unzipped on my computer to .vcf file. The upload seems to work ok, however it runs a couple seconds, creates the screen, but all options have the following message " No variants were found in the section. Consider this a good thing! "

Is there something else I should do? My 23 and Me file processed ok a few weeks ago.
Thanks,
Pat
Click to expand...
Strange. If you PM me I can take a look at this and fix the issue if you are ok with sharing your data. It should work with Genos files though. How long ago were you sequenced?
 
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BeautifulMorning

Messages
8
kday said:
Strange. If you PM me I can take a look at this and fix the issue if you are ok with sharing your data. It should work with Genos files though. How long ago were you sequenced?
Click to expand...

My apologies for the delay, stumbling back from a crash... The Genos download file is named kit#_annotated.vcf.zip

Other formats that can be downloaded are PROMETHEASE, BAM/FASTQ. Sequenced in November 2017.
 
Moof

Moof

Senior Member
Messages
778
Location
UK
tornerose said:
Could you please share how you solved this? Thanks!
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There was nothing very technical about it – I just duplicated the file and then deleted the additional '.vcf' extension on the copy! I wasn't really expecting it to work, to be honest, but it did. The Mac will probably ask if you really want to change the extension, at which point you just click Yes.

This is how they now look in the file list, with the one ending '.gz' being the edited version that I uploaded.


Screenshot 2019-10-24 at 19.28.44.png


Edited to add: If your Mac doesn't show file extensions, go to Finder Preferences and click the Advanced tab. Check the Show all File Extensions box.
 
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tornerose

Messages
30
@Moof Thanks! That’s what I did too. Managed to upload the file in the app, but there was no results, except for one variant...🤔

Edit: It’s working now—got the full report!👍
Edit 2: The problem was that I uploaded the indel file and not the snp...😬
 
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pattismith

pattismith

Senior Member
Messages
3,988
kday said:
@wigglethemouse


I was wrong, sorry, it's more than double.

https://www.ncbi.nlm.nih.gov/pubmed/26429318
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CFS/ME is not mentioned in this MBL deficiency study, but an increased risk for Fibromyalgia

Numerous complications were reported, with the most common including: sinusitis (91%), bronchitis (82%), skin infections (MRSA, cellulitis, folliculitis) (55%), multiple drug hypersensitivity (36%), histoplasmosis (27%) and fibromyalgia (27%).
Click to expand...


Association Of Mannose Binding Lectin (MBL) Gene Mutations With Other Pathway Defects Spanning Innate And Adaptive Immune Responses (jacionline.org)
 
Akasha

Akasha

Messages
67
Hi!

I see this thread is not very active right now but I think I found a 23andMe miscall with this App and wanted to post it here. @kday you probably already know this (since the background of the variant is yellow, maybe you are flagging it).

It's rs267608099 in the MSH6 gene and it causes Lynch Syndrome (I read somewhere in this thread that you were aware of some database errors for Lynch). This variant interested me since my father had CRC at the age of 50, but the tumor tissue has been analyzed twice, the last one just a couple of years ago. It seemed odd they didn't look at this variant...

I checked everywhere looking for an error: SNPedia, dbSNP, GeneCards, my 23andMe raw data (chip v4), at the original published papers for this variant... But everything matched (gene, variant, location, HGVS...)
After an intense day of searching I checked my husband's 23andMe raw data and the same variant appeared (no cancer cases in his family). So this looks like a miscall fortunately.

I hope this info is not redundant and useful to someone.
By the way, thanks for the amazing work @kday . The tool is great and works perfectly. I have found more about my genes with your app than using Promethease and Livewello together. Thanks!! :)

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B

Brandit

Messages
30
Where did you have that particular SNP reported, I see it is a no call on ancestry.com, gene DX , 23andme chip 4 and 5. I see some articles where the Cancer society listed it as a target with a magnitude of 6 for statistical risk of crc.
 
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