Extract SNPs from 23andme data to yasko/nutrigenomics notation

[hixxy]

What's the easiest way to extract SNPs in yasko/nutrigenomics notation from 23andme raw data?

hixxy

 

[nanonug]

The necessary associations are in this (not mine) spreadsheet.

 

[hixxy]

# rsid chromosome position genotype
rs4477212 1 72017 AA

So do I just search the raw data for each rsid and then cross reference the genotype with the spreadsheet for that rsid?

In the spreadsheet the genotypes are listed with +- (+A/-G) and this is not the case in the raw data. Do I just ignore the +-'s?

Is AG equivalent to GA? There are multiple GA in the spreadsheet, I can't see any GA genotypes in the raw data at all. Or do I just not have any GA genotypes?

This is a pain in the ass. Wish I had just got the nutrigenomics done... sigh.

Also, if you have 2 copies of a gene, will it be listed in the raw data twice?

hixxy

 

[LaurieL]

Hixxy,

See this thread, post #71. http://forums.phoenixrising.me/showthread.php?10973-23andme-genetic-testing/page8&highlight=23andme

Laurie

 

[nanonug]

# rsid chromosome position genotype
rs4477212 1 72017 AA

So do I just search the raw data for each rsid and then cross reference the genotype with the spreadsheet for that rsid?

I personally use the "Browse Raw Data" feature but I guess you could it your way as well.

In the spreadsheet the genotypes are listed with +- (+A/-G) and this is not the case in the raw data. Do I just ignore the +-'s?

No, the pluses and minuses are important. For example, "+A/-G" means that A is the risk allele while G is the good allele.

Is AG equivalent to GA?

Yes, it just means you are heterozygous for whatever SNP you are looking at.

This is a pain in the ass. Wish I had just got the nutrigenomics done... sigh.

I personally find Yasko's panel overpriced, opaque and very limited. 23andme provides way more info - almost 1 million SNP's if I am not mistaken - for a much better price.

Also, if you have 2 copies of a gene, will it be listed in the raw data twice?

Huh, what do you mean?

 

[richvank]

Hi, hixxy.

We all have two copies of each gene (except in genetic diseases like Down syndrome). The two letters that you have for each polymorphism listed in the raw data represent your two genes. If you are homozygous for a polymorphism, that means that you have two copies of it, and the two letters will be the same and will be the letter that represents having the polymorphism rather than having the "norm" version of it.

Rich

 

[treefrog]

I just thougt I'd post this since there is some mention of DNA testing here on this section of the forum -

GENEWATCH

DTC GENETIC TESTING: CONSUMER PRIVACY CONCERNS
By Jeremy Gruber

http://www.councilforresponsiblegenetics.org/genewatch/GeneWatchPage.aspx?pageId=285&archive=yes

-----

Might be a good idea to be cautious about getting genes tested. I read some not very good stuff about 23andme... Some people have been a bit concerned.

 

[hixxy]

If I have done this correctly, I suspect my results a very unfortunate to say the least.

ACE DEL16 No Data
CBS A360A -/- (GG)
CBS C699T +/- (AG)
COMT H62H +/+ (TT)
COMT V158M +/+ (AA)
COMT L136L No Data
COMT P199P -/- (GG)
MAO-A R297R + (T)
MTHFR C677T +/+ (TT)
MTHFR A1298C +/+ (TT)
MTHFR P39P -/- (GG)
MTR A2756G +/- (AG)
MTRR H595Y -/- (CC)
MTRR K350A +/+ (AA)
MTRR R415T -/- (CC)
MTRR S257T No Data
MTRR A66G -/- (GG)
MTRR-11 A664A +/- (AG)
NOS-3 G894T No Data
SUOX S370S No Data
SUOX A628G No Data
VDR TAQ -/- (CC)
VDR FOK No Data
ACAT1-02 -/- (GG)
AHCY-01 -/- (CC)
AHCY-02 +/- (AG)
AHCY-19 -/+ (CT)
BHMT-01 No Data
BHMT-02 -/- (CC)
BHMT-04 +/+ (AA)
BHMT-08 -/- (CC)
SHMT C1420T -/- (GG)

Does this look correct?

 

[hixxy]

nanonug, what other interesting genes are there to look at in the 23andme profile in relation to CFS/MCS? Are there any non methylation detoxification genes? I'm sure I could go through every line in the data, but that would be painful!

 

[snowathlete]

This topic is good; its prompted me to do this for my 23andme results as well.

As I understand it, A and T are synonymous, as are C and G. Correct?
These are my results if I have got them correct too. Would someone be kind enough to check mine as well as hixxy's? My results look quite different to the Genetable that was linked above, so i wonder if i got something wrong...

ACE DEL16 No Data
CBS A360A +/- (AG)
CBS C699T +/- (AG)
COMT H62H +/- (CT)
COMT V158M +/- (AG)
COMT L136L No Data
COMT P199P -/- (GG)
MAO-A R297R +/+ (T)
MTHFR C677T +/- (AG)
MTHFR A1298C -/- (TT)
MTHFR P39P -/- (GG)
MTR A2756G -/- (AA)
MTRR H595Y -/- (CC)
MTRR K350A -/- (AA)
MTRR R415T -/- (CC)
MTRR S257T No Data
MTRR A66G +/+ (GG)
MTRR-11 A664A +/+ (AA)
NOS-3 G894T No Data
SUOX S370S No Data
SUOX A628G No Data
VDR TAQ -/- (CC)
VDR FOK No Data
ACAT1-02 -/- (GG)
AHCY-01 +/- (CT)
AHCY-02 -/+ (AG)
AHCY-19 +/- (CT)
BHMT-01 No Data
BHMT-02 -/- (CC)
BHMT-04 -/- (AA)
BHMT-08 -/+ (CT)
SHMT C1420T +/- (AG)

Thanks

 

[hixxy]

Your MTRR A66G +/+ (GG) is wrong, should be -/- ?

 

[snowathlete]

Your MTRR A66G +/+ (GG) is wrong, should be -/- ?

You sure? The table says that a G is a +. Doesnt that mean i have ++?

 

[hixxy]

I think from my reading today that you just take your 23andme results and pretty much:

A and T is +
G and C is -

as per the thread Lauriel posted earlier in this thread.

I only used the spreadsheet to cross-reference the different identifiers. (ie CBS rs234706 = C699T)

That's how I have done mine anyway, so hopefully someone will confirm this for us!

 

[snowathlete]

post 70 on the previous page is what makes sense to me and is what i have followed. Here is the extract of that post to save you having to jump between threads:

Line 3 is telling you how to translate your results into Yasko's notation, but isn't saying anything about what's normal. So for COMT 4680, line 3 says +A/-G. This means that you should put down a + for each A or T you have at that SNP, and put down a - for each G or C.

So if your SNP is AA, then you mark it down as +/+. If you are AG, then you are +/-. If you are GG, then you are -/-. And, as you mentioned earlier, A=T and G=C.

 

[SickOfSickness]

Knowing which are +/+ and which are +/-, now what? I know one of my +/+ is methylation related and I was going to try Freddd's anyway. The other +/+ is one of the SUOX. I also looked up some Cytochrome P450 SNPs and I found mutations.

 

[SickOfSickness]

That's how I have done mine anyway, so hopefully someone will confirm this for us!

See the response to you in the other thread. You're doing it wrong.

 

[nanonug]

nanonug, what other interesting genes are there to look at in the 23andme profile in relation to CFS/MCS? Are there any non methylation detoxification genes? I'm sure I could go through every line in the data, but that would be painful!

In theory there is more stuff such us genes that code for phase 1 and phase 2 detox. However, I haven't had the chance to look into those. As an example, see this test from Genova: DetoxiGenomic Profile. I have been too lazy to translate those genes from Genova to 23andme speak, though.

 

[nanonug]

If I have done this correctly, I suspect my results a very unfortunate to say the least. Does this look correct?

I don't think you are doing it right. Please see my post on the other thread.

 

[greenshots]

I really doubt you have both copies of MTHFR 1298 & 677, that would be possible and its been seen in the sickest autistic kids, but not very likely in an adult unless you have several neurological or autoimmune disease (I'm talking bedridden at age 18 or something). My bet is that you are negative for both MTHFR's since the others can be serious enough to make you sick (CBS, BHMT, etc).

I find the 23& me too overwhelming when we know that methylation turns off and on so many genes. Why do I care if I have a gene for curly hair or blue eyes (mine are neither) or even liver cancer when good methylation function can turn off the switch of most bad genes. It might be interesting to look through but hasn't given me anything really useful. The methylation panel gave me a targeted treatment plan that I can live with and doesn't make me horrifically ill everytime I start something else. I think the people who haven't seen how it can be used are missing out.

Angela

If I have done this correctly, I suspect my results a very unfortunate to say the least.

ACE DEL16 No Data
CBS A360A -/- (GG)
CBS C699T +/- (AG)
COMT H62H +/+ (TT)
COMT V158M +/+ (AA)
COMT L136L No Data
COMT P199P -/- (GG)
MAO-A R297R + (T)
MTHFR C677T +/+ (TT)
MTHFR A1298C +/+ (TT)
MTHFR P39P -/- (GG)
MTR A2756G +/- (AG)
MTRR H595Y -/- (CC)
MTRR K350A +/+ (AA)
MTRR R415T -/- (CC)
MTRR S257T No Data
MTRR A66G -/- (GG)
MTRR-11 A664A +/- (AG)
NOS-3 G894T No Data
SUOX S370S No Data
SUOX A628G No Data
VDR TAQ -/- (CC)
VDR FOK No Data
ACAT1-02 -/- (GG)
AHCY-01 -/- (CC)
AHCY-02 +/- (AG)
AHCY-19 -/+ (CT)
BHMT-01 No Data
BHMT-02 -/- (CC)
BHMT-04 +/+ (AA)
BHMT-08 -/- (CC)
SHMT C1420T -/- (GG)

Does this look correct?

 

[nanonug]

As I understand it, A and T are synonymous, as are C and G. Correct?

Yes, that is my interpretation too.

These are my results if I have got them correct too. Would someone be kind enough to check mine? My results look quite different to the Genetable that was linked above, so i wonder if i got something wrong...

Based on the spreadsheet, your results appear to be right. What genetable are you referring too?

So, now it's time to go to the heartfixer website to see what all this means! :victory: