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

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Brandit

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30
Oh ok, what tool are you using to covert the "I" numbers in 23andme to rs? Some of the tools I have used don't catch all of them including the one you mentioned but I do see it in older 23andme chip versions but it is not in the 23andme newer versions or ancestry so it is either hidden or no longer of interest.
 
Akasha

Akasha

Messages
67
Brandit said:
Oh ok, what tool are you using to covert the "I" numbers in 23andme to rs? Some of the tools I have used don't catch all of them including the one you mentioned but I do see it in older 23andme chip versions but it is not in the 23andme newer versions or ancestry so it is either hidden or no longer of interest.
Click to expand...

I was just lucky it appeared in the SNPedia article for that SNP. :)

I'm actually finding more miscalls with SNPs converted from "I" numbers from my v4 chip, using genvenue. I won't take any variant translated from an "I" 23andMe marker too seriously, just in case.

SWAlexander said:
Great, thank you. I also have promethease report.
I don´t have “Neural tube defects”, but I have stenosis, spondylitis and I am folate-sensitive.
Is there a possibility to see "drug response"?
Click to expand...

GenVenue has a Drug Response tab :)
 
SWAlexander

SWAlexander

Senior Member
Messages
2,054
Akasha said:
I was just lucky it appeared in the SNPedia article for that SNP. :)

I'm actually finding more miscalls with SNPs converted from "I" numbers from my v4 chip, using genvenue. I won't take any variant translated from an "I" 23andMe marker too seriously, just in case.



GenVenue has a Drug Response tab :)
Click to expand...
Drug Response tab is not working.
 
B

Brandit

Messages
30
I've spoken to a representative for 23andMe on the phone about the I numbers and initially they told me that in most cases it was a location of interest that may not already have an existing position marked. But I also pressed them on the fact that most I numbers represent pathogenic disease causing gene locations that are predicted to be highly conserved areas. I also pressed them on the fact that they have a contractual agreement with Glasgow smithline and one of their biggest stockholders is Johnson & Johnson so I suspect those were positions that clinical research was interested in and probably paying for the raw data. I got a short answer that that was also part of it.
I think because of that FDA ruling years ago they've also masked a lot of disease genes afraid of liability litigation and people treating themselves.
What's interesting that most people have discovered is that the new 23andMe chip has about 1/3 of the number of snips of the older chips. I asked customer service if I raw data included all data available they said yes so what I suspect is they're probably running two tests on your sample one for you is the consumer and the second result list is the raw metadata that they sell to pharmaceutical research because there's just too many important genes that have been removed off the new chip. Long story short I'm of the opinion that the new 23andMe ship is useless for looking at serious illness but it may be perfectly fine for minor traits and of course genealogy.
 
Akasha

Akasha

Messages
67
What I found works if I'm interested in some particular gene is searching it in the "Browse Raw Data" option in the 23andMe web, then I know every "I" listed there is from that gene. The position in the genome is given and also the assembly (GRCh37 for my v4 chip). With this information I can make a search in the National Library of Medicine or any searching web that allows to search by position.

For instance:​
​
If I'm looking in the sucrase-isomaltase gene "SI", in the chromosome 3, the first "I" found is "i6054899" in the position "164712061". ​
Then i go here I select my assembly (GRCh37) and search for "Chr3: 164712061" (chromosome: position).​

Now I can see the SNP in that position and check if I have some variant and the pathogenity of the SNP (sometimes there's no SNP in that position).

Don't know if I'm doing something wrong, with this method I don't find the previous Lynch SNP. Maybe there's an easier way around this, but this is what I'm doing. Probably GenVue is doing something like that to parse the "I" numbers.
 
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B

Brandit

Messages
30
Yeah I agree my entire family did it so we have versions 3 through 5 and 3 and 4 had close to a million snips and now version 5 has about 1/3 that amount.
Akasha, that is a good way to look up the existing data for a particular gene location that's exactly what I do using the raw data on the 23andMe website to find the position, unfortunately what I'm talking about is a lot of the I numbers have simply been removed off the version 5 chip.
For instance my next door neighbor is 4th generation severe bipolar that does not manifest until age 35 it's very specific and they have a very specific gene pattern that causes it one of the brothers has the version 4 chip from several years ago that identifies the pathogenic mutation but his brother has the newer chip where it has been removed. I've also seen this one example with some of the mitochondrial diseases that cause late onset hearing and vision loss so it was pretty clear to me there was some censorship going on for serious diseases.
So I think at this point we don't have a lot of poor man options I think if we really want to know something we're going to have to get a full genome does anyone know what the cost is now?
 
B

Brandit

Messages
30
Akasha said:
What I found works if I'm interested in some particular gene is searching it in the "Browse Raw Data" option in the 23andMe web, then I know every "I" listed there is from that gene. The position in the genome is given and also the assembly (GRCh37 for my v4 chip). With this information I can make a search in the National Library of Medicine or any searching web that allows to search by position.

For instance:​
​
If I'm looking in the sucrase-isomaltase gene "SI", in the chromosome 3, the first "I" found is "i6054899" in the position "164712061". ​
Then i go here I select my assembly (GRCh37) and search for "Chr3: 164712061" (chromosome: position).​

Now I can see the SNP in that position and check if I have some variant and the pathogenity of the SNP (sometimes there's no SNP in that position).

Don't know if I'm doing something wrong, with this method I don't find the previous Lynch SNP. Maybe there's an easier way around this, but this is what I'm doing. Probably GenVue is doing something like that to parse the "I" numbers.
Click to expand...

I use the Opus application and the enlis gene application and that's what they both do to convert the I numbers to RS numbers but neither of them picked up the one you had isolated for lynch syndrome.
 
SWAlexander

SWAlexander

Senior Member
Messages
2,054
"I think if we really want to know something we're going to have to get a full genome does anyone know what the cost is now?"
Even if you get a full genome, markers with "I" have no publication. Meaning - research has not complete answers yet, not (peer reviewed).
 
B

Brandit

Messages
30
From all the ones that I've looked at some do and some don't I'd say it's about half. From what I've seen a lot of the I numbers that don't have associated RS numbers are points of interest that have yet to be researched however the ones that I'm more interested in is the other half that are quite well extensively researched but have been lightly veiled I'm assuming so people don't freak out and do what Angelina Jolie did by having a elective surgery based on a gene but not a symptom whereby which you have no idea how it's expressing.
Basically the closer you get to things that are cancer related lipid storage related muscular dystrophy neurological related or mitochondrial related requires etc . Seem to be requiring more and more extra digging in the past few years.
 
B

Brandit

Messages
30
I think Dante labs does it and now there might be more options. Someone told me once that there were a lot of labs not offering it for a full genome because geneticists and specialty labs wanted the ability to be able to charge a lot of money to run individual genes for families with hereditary diseases. I spoken to a few people here on phoenix rising and they told me that in some cases they charge $700 to have one particular gene fully sequenced. It's such a racket.
A lot of diseases are due to the number of repeats which is not covered by 23andMe so if they have familial Huntington's disease they have to go get it specifically sequenced.

Here is an example of a confusing one for me where it is listed as a pathogenic SNP and it is on the older 23andMe chip but not the newer chip, is it a miss call?

Rs119103264 mfn2 gene charcot-marie-tooth 23andme I number i5008699
 
Akasha

Akasha

Messages
67
Brandit said:
Rs119103264 mfn2 gene charcot-marie-tooth 23andme I number i5008699
Click to expand...

Can't really say if it's a miscall or not.
I have it sequenced, in my case without the pathogenic variant, I'm rs119103264(A,A) but I've also checked my husband's and he is rs119103264(A,G). GenVue is not showing him this variant as relevant, so maybe @kday filtered it as a miscall.

For the Lynch one, I'm still missing something.
It says is in the position "48032126" but in this position I've found a different SNP the rs1553332262 (also cancer related but from unknown significance). This SNP doesn't have the variants 23andMe says "—/AGTG", instead it has "A/T". So either it's not that position or the variants have no sense.
I don't know from where SNPedia and GenVue are relating "i5037859" with rs267608099.

Also If I search in 23anMe "i5037859" it returns its info (gene, position, variants and genotype), but if I search from gene MSH6, it is not included in the returned list. Clearly the web app is deciding what to show me.

This one is obviously a miscall (there's no way we both have it), but I'm just curious about how 23andMe catalogs data.
 
B

Brandit

Messages
30
i5037859 does not show up for my msh6 if I search for it by gene
If I search specifically for the I number it does show that it matches to the msh6 gene for me also but when I click on the gene that I number is no longer listed so it could be a glitch or it could be a mistake in censorship attempt.

When I look at that I number I come up with a different position number than what 23andme has, I come up with 47885633 and it is listed at 1% from a user sample size of 664.

No info on
rs1553332262

rs267608099 is showing a no call for all of my samples in Opus application and enlis so neither of them are making the correlation between that I number and that RS number.
 
Akasha

Akasha

Messages
67
Brandit said:
When I look at that I number I come up with a different position number than what 23andme has, I come up with 47885633 and it is listed at 1% from a user sample size of 664.
Click to expand...
Did you export your .txt long ago? My position was different from my husband's (in a file from 2017). I downloaded his raw data again and it matches with mine.
 
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