Don't know enough to understand 23 &Me results

[LanneP]

Hello,
This is my first post, though I've been reading up around this site trying to understand all of this genetic info better, especially as it pertains to CFS and thyroid & adrenal dysfunction. I've been doing ongoing research over the last 3 1/2 yrs for my now 20 yo daughter in attempt to figure out the cause of her declining health. After multiple doctors and tests we recently got back 23andMe results and ran them through Gentic Genie, Nutrahacker, and Yasko's reader. I need someone to direct me to other posts/ sites/ MD's/ etc, to see if these results may be contributing to her deteriorating health issues or if I should look elsewhere, AND what to do about it.

METHYLATION
PATHWAYS
COMT V158Mrs4680AG+/-
COMT H62Hrs4633CT+/-
COMT P199Prs769224GG-/-
VDR Bsmrs1544410CC-/-
VDR Taqrs731236AA+/+
MAO A R297Rrs6323GG-/-
ACAT1-02rs3741049GG-/-
MTHFR C677Trs1801133GG-/-
MTHFR 03 P39Prs2066470GG-/-
MTHFR A1298Crs1801131GT+/-
MTHFD1 G1958A
MTHFS
MTR A2756Grs2236225
rs6495446
rs1805087AA
C
AA+/+
+/+
-/-
MTRR A66Grs1801394AA-/-
MTRR H595Ynot foundn/an/a
MTRR K350Ars162036AA-/-
MTRR R415Tnot foundn/an/a
MTRR A664Ars1802059AG+/-
BHMT-02rs567754CT+/-
BHMT-04not foundn/an/a
BHMT-08rs651852CT+/-
AHCY-01rs819147TT-/-
AHCY-02not foundn/an/a
AHCY-19rs819171TT-/-
CBS C699Trs234706GG-/-
CBS A360Ars1801181AA+/+
CBS N212Nnot found
n/an/a
SHMT1 C1420Tnot foundn/a

n/a


DETOX PATHWAYS
CYP1A1*2C A4889Grs1048943TT-/-
CYP1A1 m3 T3205Crs4986883TT-/-
CYP1A1 C2453Ars1799814GG-/-
CYP1A2 164A>Crs762551AC+/-
CYP1B1 L432Vrs1056836GG+/+
CYP1B1 N453Srs1800440TT-/-
CYP1B1 R48Grs10012CC+/+
CYP2A6*2 1799T>Ars1801272AA-/-
CYP2A6*20rs28399444 II-/-
CYP2C9*2 C430Trs1799853CC-/-
CYP2C9*3 A1075Crs1057910AA-/-
CYP2C19*17rs12248560CC-/-
CYP2D6 S486Trs1135840CC-/-
CYP2D6 100C>Trs1065852GG-/-
CYP2D6 2850C>Trs16947GG-/-
CYP2E1*1B 9896C>Grs2070676CG+/-
CYP2E1*1B 10023G>Ars55897648GG-/-
CYP2E1*4 4768G>Ars6413419GG-/-
CYP3A4*1Brs2740574TT-/-
CYP3A4*2 S222Prs55785340AA-/-
CYP3A4*3 M445Trs4986910AA-/-
CYP3A4*16 T185Srs12721627GG-/-
GSTP1 I105Vrs1695AA-/-
GSTP1 A114Vrs1138272CC-/-
SOD2 A16Vrs4880GG+/+
NAT1 R187Qrs4986782GG-/-
NAT1 R64Wrs1805158CC-/-
NAT2 I114Trs1801280CT+/-
NAT2 R197Qrs1799930GG-/-
NAT2 G286Ers1799931GG-/-
NAT2 R64Qrs1801279GG-/-
NAT2 K268Rrs1208GG+/+

I've been reading posts here and from heartfixer, Yasko, mthfrease, MTHFR.net since getting these results. I see the words and am beginning to understand the terminology associated with all of this, but I don't know what to do with it all. I've searched all the sites I can find and haven't found any health care provider that is familiar with these sorts of problems. I understand there may be a need to start in one place and move to another with diet, supplementation, etc. - but we've tried many different things with the promise that it should help, only for her to end up feeling no different at best and being put on the couch not being able to do anything at worst. So, we're hesitant to do much more without knowledgeable direction. I apologize if I've given too much info, but if anyone needs more to help make sense of all of this, I'd be glad to give it if I can.

She's presently diagnosed with being hypothyroid, hypoadrenal (on meds for these) and something's not working right w/ pituitary; Raynaud's and APS (on baby ASA); she's anemic and low ferritin (though has periods of high iron saturation); low Vit D, low Vit B12, low zinc; been told she has CFS (as she meets the criteria), but I'm not sure if it's that, under treated thyroid/ adrenal, something genetic, or some combination thereof that's taking away her health.

Also, what does the "n/a" mean? And, if it means the gene is not present, does that have any implications? I don't understand the "II" either. In addition, the MTHFD1 and MTHFS were not part of the Genic Genie results, but were identified from other gene readers as being significant. Finally, there were plenty of other genes that came up heterozygous, but I don't know of their significanceCETP, FII, F7, F9, FOLR2, DAO, FUT2, GAD1, FD1L, NOS2, NOS3, PEMT, SHMT2, TYMS; CTLA4, FOXE1, NDUFS7, NDUFS8, APOE, TNF, SULT1A1, & SULT2A1)

You all are such a wealth of information, I'd be grateful for any feedback/ input/ direction. Thanks in advance for any and all help -
Lanne P

 

[LanneP]

OK, that came out a mess. I apologize. If someone can tell me how to fix it or resubmit with a better format I'd be glad to do so.
Lanne P

 

[Sea]

N/a means 23andme no longer tests those snps. They used to test 967 000 snps and recently dropped to 602 000

II means insertion/insertion. Some snps are a change in the letter at that position on the gene, some are where one or more letters are inserted or deleted. So II means homozygous for insertion, but doesn't tell you whether that is a problem. Sometimes it is the insertion which is a problem, sometimes it is the deletion, sometimes neither is a problem. Other variations for that result would be I/D or D/D.

 

[Critterina]

@LanneP ,
With those endocrine issues, have they done any hi-res imaging of her pituitary? I have those issues (approximately) and when we did the imaging we learned that I have a small pituitary tumor. I would like to have a CRH test to determine whether the tumor is coincidental to a malfunctioning hypothalamus, but overall, I'd like it out. I've always been one out of bed and out the door first thing in the morning, and now getting out of bed is a challenge, and I do not have CFS.

 

[Valentijn]

She's presently diagnosed with being hypothyroid, hypoadrenal (on meds for these) and something's not working right w/ pituitary; Raynaud's and APS (on baby ASA); she's anemic and low ferritin (though has periods of high iron saturation); low Vit D, low Vit B12, low zinc; been told she has CFS (as she meets the criteria), but I'm not sure if it's that, under treated thyroid/ adrenal, something genetic, or some combination thereof that's taking away her health.

If she has ME/CFS, she should have post-exertional malaise - that is, she'd be very sick a day or so after "excessive" exertion, and it could last for days or weeks. In some cases, excessive exertion can be something as minor as taking a shower.

Is APS antiphospholipid syndrome? If so, it can be secondary to Lupus, which has some ME/CFS-like symptoms.

Have her vitamin D, B12, and zinc been adequately treated? Simple deficiencies can also cause fatigue, or some ME/CFS symptoms, but should resolve when the deficiency is treated.

None of her methylation SNPs which I'm familiar with (most of them) have anything which looks problematic.

I have a program at http://sourceforge.net/projects/analyzemygenes/ which you can download and run with her unzipped 23andMe file. The default database will pull out her rare results where an allele is present in 1% or less of the population. Results starting with "i" are often known to be disease causing, and homozygous results can be especially interesting as well.

 

[LanneP]

@Sea - Thank you, that all makes sense.
LanneP

 

[LanneP]

@LanneP ,
With those endocrine issues, have they done any hi-res imaging of her pituitary? I have those issues (approximately) and when we did the imaging we learned that I have a small pituitary tumor. I would like to have a CRH test to determine whether the tumor is coincidental to a malfunctioning hypothalamus, but overall, I'd like it out. I've always been one out of bed and out the door first thing in the morning, and now getting out of bed is a challenge, and I do not have CFS.

Yes, her last doc thought of that and ordered a brain MRI looking for abnormality of pituitary, but it was unremarkable. If it had been +, it might have given us a better direction to take. Hope you can get some answers for your situation.
LanneP

 

[Seven7]

@Valentijn Is there a work around to make the download of your program work on Mac? I get the is not from trusted source or appstore something like that error.

 

[LanneP]

@Valentijn - Thank you for your response.

If she has ME/CFS, she should have post-exertional malaise - that is, she'd be very sick a day or so after "excessive" exertion, and it could last for days or weeks. In some cases, excessive exertion can be something as minor as taking a shower.

Yes, she does have post exertional malaise. It is worse at times, though we haven't found any rhyme or reason - ie. sits around and unable to do more than very light duty stuff (read, walk, talk) at best; laying on couch resting/ sleeping, not able to talk sometimes and unable to do more than go to BR the following day(s) at worst.

Is APS antiphospholipid syndrome? If so, it can be secondary to Lupus, which has some ME/CFS-like symptoms.

Yes, APS refers to antiphospholipid syndrome. I asked both the rheumatologist and endocrinologist if that was a possibility (esp since she had +ANA & there is history of SLE in my mother and her side of family) and they both dismissed it.

Have her vitamin D, B12, and zinc been adequately treated? Simple deficiencies can also cause fatigue, or some ME/CFS symptoms, but should resolve when the deficiency is treated.

Vit D was 6.8 when her symptoms first started. She supplemented with 5 - 10,000 IU/D and they got as high as 70's. She's backed off and they've dropped to 30's again. She's back to supplementing w/ 5 - 10,000/ day.
Vit B 12 was low, she tried to supplement, but B's seem to make her feel foggy and actually put her to sleep after about 20 min., so she is reluctant to take them. She is in 400's now.
Zinc has been in 70 - 80 range. She was supplementing with zinc carnosine (I think) for presumed GI issue (based on +RAST test, anemia, and low Vit D & Vit B-12), but she has never had ANY GI symptoms. She was put on GF/DF diet, much to her dismay, and has felt absolutely no difference (other than feeling foggy headed after cheating on dairy). I have observed her blood counts to go down when she has not been GF/DF). So, there may be some "leakiness" going on, but I would expect she'd "feel" something associated with that.

Of her methylation SNPs which I'm familiar with (most of them) have anything which looks problematic.

That's encouraging, I think. Was wondering if something there would make her not tolerate Vit B (not sure which one it would be though).

I have a program at http://sourceforge.net/projects/analyzemygenes/ which you can download and run with her unzipped 23andMe file. The default database will pull out her rare results where an allele is present in 1% or less of the population. Results starting with "i" are often known to be disease causing, and homozygous results can be especially interesting as well.

That's incredible! I don't understand how you do it, but I'm sure many people appreciate your endeavor and will benefit from it. I did run her data through your program and only one was +/+ (rs1338457) and two were +/- (rs 6816809 and rs13133587).

You've given me food for thought. Thank you.
LanneP

 

[LanneP]

@Valentijn Is there a work around to make the download of your program work on Mac? I get the is not from trusted source or appstore something like that error.

I have a Mac and was able to use it without difficulty - and I am NO computer guru
LanneP

 

[Valentijn]

@Valentijn Is there a work around to make the download of your program work on Mac? I get the is not from trusted source or appstore something like that error.

It's something my fiance needs to look into - either how to make the program trusted by some Mac OS versions, or how Mac users can get their macs to let them use it anyhow. But he's been very busy lately, especially since I'm currently bedbound and adding to his workload

 

[Valentijn]

Yes, she does have post exertional malaise. It is worse at times, though we haven't found any rhyme or reason - ie. sits around and unable to do more than very light duty stuff (read, walk, talk) at best; laying on couch resting/ sleeping, not able to talk sometimes and unable to do more than go to BR the following day(s) at worst.

In that case pacing is probably very important. I use a finger pulse oximeter to make sure I'm keeping my heart rate low enough while "active", and I'm usually already in trouble if my oxygen saturation starts dropping or bouncing around.

Yes, APS refers to antiphospholipid syndrome. I asked both the rheumatologist and endocrinologist if that was a possibility (esp since she had +ANA & there is history of SLE in my mother and her side of family) and they both dismissed it.

Is it possible to get a 2nd opinion or push the point a bit? With APS + ANA + family history, it seems rather stupid of them to dismiss SLE.

Vit B 12 was low, she tried to supplement, but B's seem to make her feel foggy and actually put her to sleep after about 20 min., so she is reluctant to take them. She is in 400's now.

Which forms has she tried? Some people react differently to methylB12 versus hydroxoB12 versus cyanoB12. A lot can't handle the methylB12, but some need it. And cyanoB12 and hydroxoB12 have to be converted, so something could be going wrong there.

That's incredible! I don't understand how you do it, but I'm sure many people appreciate your endeavor and will benefit from it. I did run her data through your program and only one was +/+ (rs1338457) and two were +/- (rs 6816809 and rs13133587).

Usually it generates a list of about 60 SNPs. Was the program interrupted while it was running? It takes about 30 seconds to go through the entire 23andMe file.

 

[LanneP]

In that case pacing is probably very important. I use a finger pulse oximeter to make sure I'm keeping my heart rate low enough while "active", and I'm usually already in trouble if my oxygen saturation starts dropping or bouncing around.

Is it possible to get a 2nd opinion or push the point a bit? With APS + ANA + family history, it seems rather stupid of them to dismiss SLE.

Pacing is something she hasn't learned yet. When she feels good, she wants to "do" and sometimes she can do, but that seems to be getting farther and fewer between.
As far as getting a second opinion, I hadn't thought of that till now. When they each dismissed it, so did I. Will have to think about how to do that. She has been dismissed by the endo as not knowing what more to do to help her. We chose not to go back to the rheum. doc as he wanted her to trial very expensive GI steroid &/or have a muscle bx done under general (which I didn't think she was well enough to tolerate and it was an expensive procedure).

Thanks, again -
LanneP

 

[LanneP]

Which forms has she tried? Some people react differently to methylB12 versus hydroxoB12 versus cyanoB12. A lot can't handle the methylB12, but some need it. And cyanoB12 and hydroxoB12 have to be converted, so something could be going wrong there.

At the suggestion of the MD who diagnosed her with CFS, she started on Dr. Teitelbaum's Revitalizing Energy (cyano., I believe). However, she did not tolerate this. Her doc wrote Dr. T. to ask why she might respond this way, but he did not have an answer. Later, he tried Dr. T's general methylation protocol using NAC 600 mg BID, SAMe 200 mg BID, and B Supreme by (Designs for Health) 1 tab/ D - contains Naturefolate 200 mcg and methylfolate 250 mcg. Stopped d/t being “knocked out” afterwards. She continued to feel lousy, so that is when we pursued the endocrinologist to "better manage" her thyroid and adrenals. He had her taking a small dose of methylcobalamine, which she took hit & miss d/t how it made her feel. Doesn't seem like anything has been managed well.

LanneP

 

[LanneP]

Usually it generates a list of about 60 SNPs. Was the program interrupted while it was running? It takes about 30 seconds to go through the entire 23andMe file.

Sorry! Should have said that the rest were -/-. So, I guess there's not much help there either to give some direction. Thanks for offering your thoughts.

LanneP

 

[Valentijn]

Sorry! Should have said that the rest were -/-. So, I guess there's not much help there either to give some direction. Thanks for offering your thoughts.

The original 23andMe file should have over 600,000 SNPs, and about 60 of those should turn up as being very rare ... if only 3 results turned up, something didn't work right. It should never list anything as -/-. Most results won't have anything in the "ETC" column because it only adds extra data for homozygous and "i" results. But all of the results generated are very rare, and potentially relevant.

 

[Valentijn]

At the suggestion of the MD who diagnosed her with CFS, she started on Dr. Teitelbaum's Revitalizing Energy (cyano., I believe). However, she did not tolerate this. Her doc wrote Dr. T. to ask why she might respond this way, but he did not have an answer. Later, he tried Dr. T's general methylation protocol using NAC 600 mg BID, SAMe 200 mg BID, and B Supreme by (Designs for Health) 1 tab/ D - contains Naturefolate 200 mcg and methylfolate 250 mcg. Stopped d/t being “knocked out” afterwards. She continued to feel lousy, so that is when we pursued the endocrinologist to "better manage" her thyroid and adrenals. He had her taking a small dose of methylcobalamine, which she took hit & miss d/t how it made her feel. Doesn't seem like anything has been managed well.

HydroxoB12 might be worth trying instead, if you can find it. The methyl groups in methylB12 can make it difficult for some people to tolerate, and cyanoB12 has cyanide in it which might be difficult for some people to detox.

 

[LanneP]

The original 23andMe file should have over 600,000 SNPs, and about 60 of those should turn up as being very rare ... if only 3 results turned up, something didn't work right. It should never list anything as -/-. Most results won't have anything in the "ETC" column because it only adds extra data for homozygous and "i" results. But all of the results generated are very rare, and potentially relevant.

I see. I'll PM you after I re-run the program.
Thank you, again, for your assistance.
LanneP

 

[LanneP]

HydroxoB12 might be worth trying instead, if you can find it. The methyl groups in methylB12 can make it difficult for some people to tolerate, and cyanoB12 has cyanide in it which might be difficult for some people to detox.

Will see what I can do about finding the other B12 formulations.
Thank you,
LanneP

 

[Sea]

MTHFD1 is a gene in the folate pathway. The G1958A is quite a common snp (34%) but it can be significant. It is over represented in neural tube defects which suggests that it has an effect on folate sufficiency.

I know that a MTHFR defect can be overcome with supplementation of Methylfolate. I would presume that it would be helpful in the MTHFD1 defect as well but I have not found any research that says that is the case.

It is not good to take Methylfolate without taking B12 as well, especially so if one is deficient in B12.