Rare allele data

[roxie60]

I wondered that also since I found another SNP in SNPedia that I do not have the risk alelle for and it is realted to the one I do so left me wondering if you need multiple similar bad ones to have an issue. It is all so complex.

 

[roxie60]

roxie60, from what I understand we can have the mutations, but they aren't doing any damage unless those mutated cells are turned on. Maybe I didn't understand it correctly, though? I have suffered from a lifetime of migraines, as did my own mother who died early (from cervical cancer). EEK! My brain must be mostly white by now if you have white spots from migraines only 4-5 times a year.

For the myelin sheath, I'm fairly certain I have issues with that. I have CFS and Lyme...and in the beginning when I was in excruciating pain for nearly a year a lovely scientist recommended that I take a tablespoon of ghee per day to help with the issue, and WOW! Within three days the pain I'd suffered with for an entire year disappeared. Since that time my body has been struggling with many other issues which result in pain, so the ghee doesn't work as beautifully now as it did in the past. I'm pretty sure I came across information that hemp oil will help with the myelin sheath, also.

I'm looking forward to reading more responses for your question. I practically live on this board, lurking and learning.

I wondered why he would blame white spots on something I only get 4-5 times a year (I feel so bad for those who have to deal with migraines more frequently, they are so debilitating). Still doesnt make sense to me so makes me suspect he just doesnt know why I had white spots.

 

[frenchmoxie]

Chrom 1

rs4373782 CT
rs17366686 AC
rs28384834 AG
rs12142450 AG


Chrom 2

rs45471294 CT
rs17648863 CC
rs11695913 CT

Chrom 3

rs34911341 CT
rs1800146 GT
rs34166957 AG
rs13096071 CT


Chrom 4

rs17626658 CT
rs10446841 GG


Chrom 5

rs17435258 GT
rs13161296 CT
rs245071 CT
rs3213102 CT

Chrom 6

rs34500563 AG
rs12202093 CT

Chrom 7

rs28381714 CT
rs17876184 AG


Chrom 8

rs35909721 AG
rs17736439 AG
rs13252585 AC

Chrom 9

rs10972206 AG

Chrom 10

rs11188150 AG

Chrom 11

rs326221 CT

Chrom 12

rs61688134 CT
rs17528736 CT
rs35075600 CT
rs28360457 AG


Chrom 13

rs17080230 AG
rs9516949 AG

Chrom 14

rs11499034 CC SEL1L

Chrom 15

rs2304341 CT
rs12910678 CT
rs34261044 AG
rs8042511 AC

Chrom 16

rs1800725 AG
rs8176928 GG DNASE1
rs1152084 CT

Chrom 17

rs60831116 GT
rs2727338 AG
rs2678672 AG FAM100B

Chrom 19

rs34442879 CT BCKDHA - maple syrup urine disease
rs28399656 AT BCAM
rs3218772 CT

Chrom 20

rs3176126 AG intergenic

X chrom

rs2773 AG USP9X

 

[bel canto]

Hey, frenchmoxie - thx for posting those. Those of us who have the SNPTips add-on to Firefox can see our own alleles whenever we see the rs #'s. However, if the letters are right next to the rs# (rs444444TT), it doesn't work. With a space (rs444444 TT), it does.
Can you modify your post to add the spaces? That way we can see whether we share any of these.

 

[Valentijn]

I've run my raw data through the Rare Alleles program and find it fascinating. Valentijn, Would you like to add it to the list? If so, shall I PM it to you (lmk what format-excel or text) or post here?
THanks

Yes please - could you send it via private message?

 

[GypsyA]

Hi Valentijn!

My personal 23andme results are in. I already shared my daughter's info with you and have been learning from everyone about what's going on with my daughter's genes. Now it's time to review mine! However, my brain is kind of on a bit of a vacation the past few days. So, I need a reminder, please...

I ran my 23andme data through the Genetic Genie. There was a rare allele program I used for my daughter, but now I don't know where I found that. :-/ Can you, or someone here, remind me where to go to get the rare allele data?

Thanks!

 

[Valentijn]

Hi Valentijn!

My personal 23andme results are in. I already shared my daughter's info with you and have been learning from everyone about what's going on with my daughter's genes. Now it's time to review mine! However, my brain is kind of on a bit of a vacation the past few days. So, I need a reminder, please...

I ran my 23andme data through the Genetic Genie. There was a rare allele program I used for my daughter, but now I don't know where I found that. :-/ Can you, or someone here, remind me where to go to get the rare allele data?

Thanks!

http://sourceforge.net/projects/analyzemygenes/ is a new one me and my fiance have made, which is a download - hence much much faster than the other sites. The instructions and additional information are at http://sourceforge.net/p/analyzemygenes/wiki/Home/

This is the other one if you want to use it instead, which requires a lot of cutting and pasting: http://www.ianlogan.co.uk/23andme/minor_allele_data.htm

 

[leela]

I am having trouble understanding, since SNPedia doesn't have most of them, though diseasome was a little helpful.
So....help from Valentijn please, if you're up for it?

Still and all, cool program, @Valentijn!

ETA: the pdf is not loading. oops.

 

[Valentijn]

I am having trouble understanding, since SNPedia doesn't have most of them, though diseasome was a little helpful.
So....help from Valentijn please, if you're up for it?

Still and all, cool program, @Valentijn!

ETA: the pdf is not loading. oops.

These are just a list of very rare SNPs which some ME/CFS patients have in common. There might not be info available for many of them. Though currently I'm comparing bigger lists of homozygous mutations, which are more likely to have an impact.

Which pdf are you referring to?

 

[leela]

Sorry, @Valentijn very brainfogged today, should probably refrain from posting!
I meant the pdf of my rare alleles report from your sourceforge.

 

[SickOfSickness]

Is there a new thread for this? I see it hasn't been updated.

I ran the 10% database and I looked for all red or orange SNPs in post #42. I have only 1.

rs1799931...NAT2 which @ukxmrv has

My data is not complete because I have an old 23andme chip.

They know a lot about NAT2:
http://snpedia.com/index.php/NAT2
http://snpedia.com/index.php/Rs1799931
If I am reading it correctly, I did not read a lot: this SNP explains why I am a rapid metabolizer, which is a good thing. You don't want to be a slow metabolizer.

 

[GypsyA]

@Valentijn , I received notice that your program had an update. Do you want me to resend my results?

Love,

Wendi

 

[Valentijn]

@Valentijn , I received notice that your program had an update. Do you want me to resend my results?

Nah, no need! The updates have all been for functionality (mostly on Macs), and don't impact on the results.

 

[Tunguska]

Well this has been interesting. Thank you for this program.

How many results (snps/lines) have people gotten on average? I got exactly 100. Only one homozygous (rs13229564) but no info about it.

Interesting findings for me were two heterozygous, rs9332239 (CYP2C9) and rs28365083 (CYP3A5), involved in the processing of certain medications, including NSAIDs and others. Because it just so happens I've had serious reactions involving such medications recently.

 

[Valentijn]

How many results (snps/lines) have people gotten on average? I got exactly 100. Only one homozygous (rs13229564) but no info about it.

I think 100 is pretty average. Some have more, some less. And it also depends on the chip used by 23andMe when your results were processed. It's made to work with the prior chip, and tends to pick up far fewer SNPs on the new one (60 or less).

Your homozygous result does look like a very boring one! Anything starting with "i" instead of "rs" is usually far more interesting, and will have the rs number listed in the final column for easier researching.

The rarest SNPs can also be interesting, even when heterozygous. Usually a fair few of those are missense mutations, which can have much bigger impacts.

 

[Tunguska]

I think 100 is pretty average. Some have more, some less. And it also depends on the chip used by 23andMe when your results were processed. It's made to work with the prior chip, and tends to pick up far fewer SNPs on the new one (60 or less).

Your homozygous result does look like a very boring one! Anything starting with "i" instead of "rs" is usually far more interesting, and will have the rs number listed in the final column for easier researching.

The rarest SNPs can also be interesting, even when heterozygous. Usually a fair few of those are missense mutations, which can have much bigger impacts.

It was the new chip. I read them over again and I'm not sure my rare hetero SNPs I wrote above actually have any impact on their genes or would be missense, but interesting nonetheless.

I ran my results through the 10% database too and filtered for the homozygous; got 670 homo; looked them up to find 16 documented. Much more interesting ones there, involving correlations with retinal detachment and keratoconus, yikes. Not much CFS-related except some immunity-related one.

Anyway, just realized I posted my comment in the wrong thread, sorry.

(Oh and turns out I DID have a fatigue-related one which I've made another thread for, but it was 2% not 1% so the first pass didn't catch it)

 

[MegHurley36]

Here is my report, I have no idea how it correlates, but if anyone does know, reply here???

PS I was told years ago have chronic fatigue, chronic mono, Epstein barr, and lyme.... but I was just tested and have mito dys and metabolic syndrome from a reaction to fluoquinolones. I have healed a ton, but still need more info of course Still def in lots of minerals and vitamins, still horribly fatigued, and rashing all the time.

Wonder what was 'triggered'

NP CHRM RARE PERCENT GENOTYPE ETC

rs12116440 1 T 1.00 CT
rs3918018 1 T 1.00 CT
rs16846495 1 T 0.23 CT
rs35814900 1 A 1.00 AG
rs2232363 1 A 1.00 AG
rs11120537 1 C 1.00 AC
rs72466494 2 T 0.41 CT
rs12185694 2 T 1.00 GT
rs12619170 2 C 0.00 AC
rs10496708 2 T 1.00 CT
rs13400424 2 A 1.00 AG
rs17205728 2 T 1.00 CT
rs13012441 2 G 1.00 AG
rs12993807 2 A 1.00 AG
rs4494742 2 T 1.00 CT
rs3731062 3 A 1.00 AG
rs17201603 3 A 1.00 AG
rs10935179 3 T 1.00 GT
rs13098532 3 G 1.00 GT
rs292050 4 T 1.00 GT
rs1605208 4 G 1.00 AG
rs11573780 4 T 1.00 CT
rs11249470 4 G 1.00 AG
rs283410 4 A 1.00 AG
rs6816876 4 G 1.00 AG
rs12374404 4 T 1.00 CT
rs17402629 4 A 1.00 AG
rs4505907 5 C 1.00 CT
rs35629723 5 G 0.37 CG
rs36105360 5 T 1.00 CT
rs61754582 5 A 1.00 AG
rs6884056 5 C 1.00 CT
rs3213102 5 T 1.00 CT
rs17876047 5 A 1.00 AG
rs28404158 5 C 1.00 AC
rs11575840 6 T 1.00 CT
rs2234080 6 A 1.00 AG
rs17453041 6 G 1.00 AG
rs1424935 6 G 1.00 AG
rs34130495 6 A 1.00 AG
rs35956182 6 A 0.46 AG
rs28405775 7 A 1.00 AG
rs7799716 7 G 1.00 AG
rs1990554 7 A 1.00 AC
rs13232752 7 A 1.00 AG
rs12534162 7 G 1.00 AG
rs72555745 7 C 1.00 CT
rs6970680 7 A 1.00 AG
rs17290246 7 A 1.00 AG
rs41279857 7 T 0.09 GT
rs176479 7 C 1.00 CT
rs6471672 8 G 1.00 AG
rs2513812 8 G 1.00 GT
i5007196 8 G 0.23 AG rs121908601
rs2993177 9 A 1.00 AG
rs13286453 9 T 1.00 CT
rs17211882 9 A 1.00 AG
rs11243406 9 A 1.00 AC
rs2457838 10 G 1.00 GT
rs1943 10 T 1.00 CT
rs11598891 10 T 1.00 CT
i5009017 10 A 0.05 AG rs116040871
rs17805341 10 T 1.00 GT
rs10894690 11 C 1.00 CT
rs17722134 12 G 1.00 AG
rs17220870 13 T 1.00 CT
rs10507683 13 T 1.00 CT
rs17619183 13 C 1.00 AC
rs17458021 15 T 1.00 GT
rs611704 16 A 1.00 AG
rs12918121 16 T 1.00 CT
rs2090019 17 T 1.00 CT
rs17590785 17 A 1.00 AG
rs2016648 17 T 1.00 CT
rs12962762 18 T 1.00 CT
rs4987817 18 A 1.00 AG
rs17181586 18 A 1.00 AG
rs1538012 19 A 1.00 AG
rs193234 19 G 1.00 GT
rs11671231 19 T 1.00 CT
rs17327630 20 A 1.00 AC
rs709046 20 T 1.00 CT
rs17219643 20 T 1.00 CT
rs139740 22 A 1.00 AG
rs5752023 22 T 1.00 GT
rs1046166 22 T 0.37 CT
rs139275 22 A 1.00 AG
rs4253791 22 A 1.00 AT
rs11796544 X A 1.00 AG
rs5952669 X T 1.00 CT
rs5905625 X G 1.00 AG
rs2207084 X A 1.00 AG
rs10521360 X C 1.00 CT
rs12559201 X T 1.00 CT
rs17317849 X C 1.00 CT

 

[August59]

What program is being used to "unzip" the downloaded file. The following instructions don't seem follow WinZip or Win Rar?

RUN
6) Go to the folder where you extracted the files
7) Double-click on the "Genes"
8) A grey box with three buttons appears. The top one should be green. If it isn't, click on it to navigate to whatever dodgy location you've put the "one_percent" file in.
9) Click on the orange middle box to select your 23andMe file.
10) Click the yellow "Analyze" button, and wait for it to finish. This takes 52 seconds on my newish but basic laptop.

Thanks

 

[Valentijn]

@MegHurley36 - I'll take a quick look. Mostly I use dbSNP to see if there's anything interesting. Would you prefer I post here if I see anything of interest, or that I send you a private message via the forum Conversation function?

 

[MegHurley36]

@MegHurley36 - I'll take a quick look. Mostly I use dbSNP to see if there's anything interesting. Would you prefer I post here if I see anything of interest, or that I send you a private message via the forum Conversation function?

@Valentijn Here would be fabulous I think If it is anything truly horrible you can msg me lol. No, I like to contribute where I can.
Sorry if I am slow in responding, brain fog has been higher than norm. I accidentally took 5gm of folinic acid 2 days ago. Interesting, that my rash is now clearing, yet I feel terrible. Anyhow, thank you.