Author Archives: lassesen

Unknown's avatar lassesen 8:45 am on January 9, 2015  

Amy Yasko DNA Nutrigenomics

Livewello.com provides pre-written (and contributed) panels on DNA, for example,

NUTRIGENOMICS TEMPLATE WITH SUPPLEMENT RECOMMENDATIONS BY DR. AMY YASKO

To use them, you need to install it – which is easy:
Screen Shot 2015-01-05 at 9.46.41 AM
Then click the button. The results now appear. In my case — I am clear — the sole item listed is meaning less (DNA consists of (A,C,G,T) only so getting this match will happen to everyone!)
Screen Shot 2015-01-05 at 9.48.56 AM
 Which you then need to click Screen Shot 2015-01-05 at 3.41.23 PM to see the results. Mine are below
Screen Shot 2015-01-05 at 4.02.51 PM

With only a single red (1 of 27 or 4%) and many greens (18 of 17 – 66%), the Yasko approach is unlikely to have significant impact on me. So instead of trying it, I move on to something that seems better connected to my DNA.

For the single item that is in Red, I can click the item (VDR Bsm) and read what it is associated with.

“Normal function:

The VDR gene provides instructions for making a protein called vitamin D receptor (VDR), which allows the body to respond appropriately to vitamin D. This vitamin can be acquired from foods in the diet or made in the body with help from sunlight. Vitamin D is involved in maintaining the proper balance of several minerals in the body, including calcium and phosphate, which are essential for the normal formation of bones and teeth…..Most VDR gene mutations impair hair growth, leading to alopecia; ”

Whether this accounts for my 1,25D levels going through the roof while I had CFS (a common occurrence with many autoimmune illness) and return to the normal range with remission — I do not know.

So the process is very easy to get the information — what you do with it is another question which usually mean joining specialized groups dealing with these specific issues. Most MDs are not trained in this very new and rapidly developing area.

Unknown's avatar lassesen 8:04 am on January 8, 2015  

Canned Coagulation factors – Testing the Hemex Model

The site https://livewello.com will take your DNA and give a variety of panels looking at various health issues. The cost is $19.95 for the processing and ongoing use of their site. One of their panels is clotting. My results are below. As you can see out of 14 reported items, 2 are red (14%) and  6 are yellow (42%).  I have a rule of thumb to filter results into ‘concern’ or ‘low concern’,

  • > 10% Red with 2 or more ==> Concern
  • < 45% Green ==> Concern

So for me, the Hemex model of having inherited coagulation issues appears to be true.

Screen Shot 2015-01-05 at 9.30.04 AM

 

On the far left is the SNPs column which are linked to more information. For example, my Red ones goes to

  • CETP ” The protein encoded by this gene is found in plasma, where it is involved in the transfer of cholesteryl ester from high density lipoprotein (HDL) to other lipoproteins.” -“CETP SNP rs1800775 with higher LDL-C” (the bad one) – it leads to  my taking 500mg of flushing niacin daily.
  • F11 – ” TT genotypes for rs2289252 were associated with a significantly higher venous thromboembolism (VTE)”. “two SNPs, rs2289252 and rs2036914 in F11, appear to independently contribute to the risk of deep vein thrombosis (DVT), a contribution that is explained at least in part by an association with FXI levels.” This is why I take Piracetam on a regular basis (Inhibitory effect of piracetam on platelet-rich thrombus formation in an animal model.) and Turmeric Modulation of transcription factors by curcumin.

In short, if you dig into your REDs you will often find supplements that will mitigate your DNA risks. You may also find some that you should not take because while they help others, your DNA is different. The reds are the most important — but the yellow ones should also be reviewed.

Unknown's avatar lassesen 8:16 am on January 7, 2015  

Snps for Coagulation Defects

Dave Berg of Hemex Labs back in 1990 reported that most CFS patients have a high incidence of coagulation problems — usually genetic in origin. Getting a MD to tested for these disorders is usually very hard, and made worst by most insurance (including national insurance) not willing to pay for them unless you are having a stroke.

The following is what I have been able to track down for Coagulation SNPs on PubMed. Tomorrow — we will look at a canned set of SNPs that a different site has available.

  • Magnitude: is the risk compare to normal people (0).
  • At present, some information is hidden from download by 23andMe, the value shown is “DI” Diagnostic information
    • Check download file and https://www.23andme.com/you/explorer/snp/ – often one will read DI and the other will give the value
  • Note on getting tested for most: “Factor V Leiden mutation testing should be reserved for patients with clinically suspected thrombophilia” – Mayo labs.
    • Australia Medical Insurance: “Medicare will pay only if the pathology request identifies in writing that the patient has a personal history of venous thromboembolism. A rebate for the proven defect(s) only can also be claimed for the first degree relative of a person who has a proven defect of any of the above. A family history of venous thromboembolism alone is not sufficient. The request must specifically identify the proven defect(s).” – AKA you can’t get there from here!
  • Readings Recommended:
SNP 23andMe Links – Comments (Magnitude) My values
rs1799963 i3002432 G20210A mutation of the prothrombin F2 gene G20210A, Positive: A:A(3). A:G(3) Normal G:G ( 0.293 when controlling for other SNPs) G:G
rs6025 yes Leiden mutation, R506Q, Positive: A:A 9x risk(3.5), A:G(2.3), G:G (0) (C=3.57).
A common mutation.		 C:C
rs7538157 n/a BLZF1 A->C (C=2.69) n/a
rs16861990 yes NME7   A->C (C=2.02) A:A
rs2038024 yes SLC19A2    C->A (C=1.53) (impacts absorption of B1) A:A
rs2519093 n/a ABO A->T, A->C (A=1.69) n/a
rs495828 yes T->G (T=1.65) G:T
rs8176719 yes ABO blood type O allele]  ?-> C DI
rs118203905 na FV Hong Kong R306G ( G=1.59)
rs118203906 na FV Cambridge R306T( T=1.59)
rs1801020 na C46T ( T=1.63)  A->G G:G
rs2232698 yes R67X ( T=1.59) C->G, C->A G:G
rs5985 Factor Protector yes Factor Protector (2-4)  C->A  A:A
rs121909548 n/a A3845 ( T=2.277) C->G,  C->A
rs9804128 yes SNP Interaction [G on this one] A:G
rs4784379 yes SNP Interaction [A on this one] A:G

As you can see, I have the expected genetic mutation to pre-dispose myself to coagulation. As I result, I can be more specific in searching for appropriate supplements to reduce the type of risk each one creates. I can also regularly search PubMed for new articles. For example, searching for rs495828 -found 8 articles at present. For example

  • associated with angiotensin-converting enzyme (ACE) activity and inflammation .. and with enalapril-induced cough [2014]

For Rs6025, there are 35 articles. One of which states “The goodness of fit of the genetic and combined scores improved when significant SNP-SNP interaction terms were included.”[2014], i.e. the more you have, the greater the combined effect.

Unlike the latter two vectors associated with CFS, I have significant activity here. The absence of those two other factors may be why I have been able to slip from CFS to remission three times — my recovery is not hampered by those other factors.

Unknown's avatar lassesen 7:47 pm on January 6, 2015  

DeTox Profile from 23andMe DNA

Yesterday I mentioned the methylation results you can get from https://geneticgenie.org, today, we will look at the 2nd analysis that they offer: Detox.

For the nerds reading this, 23andMe offers a sweet API for analyis:  https://api.23andme.com/

My results are below — a single red item in this long list, so it is unlikely that I have a significant issue here. Your results may be different.

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Again, if you have the resources to spare a few dollars as appreciation of their work, make a donation!

 

Unknown's avatar lassesen 3:35 pm on January 5, 2015  

Methylation Testing via 23andMe

One of the problems many CFSer have is getting testing — especially for things at the DNA level. A lab will often charge medical insurance $1000 for such tests. The current cost of getting a human genome DNA is just $25 – talk about inefficiencies!

A recent comment asked about whether I had a methylation issue. The answer is yes, I was told that I had one according to my MD, and prescribed methylated B12. It had no apparent effect.

While researching my response, I found a site that would take my DNA results from 23andMe and do an analysis (and deeper analysis that the MD got!!).

The site is https://geneticgenie.org – they do the analysis for free (and request a token donation — if you can afford it, do so). My actual results are below. As you can see, my MD’s test likely picked the single red one below and hence concluded that I have a significant issue. Given the numbers of genes involved, many people may have one of these 26 genes being significant — it does not mean there is a problem.

Screen Shot 2015-01-04 at 11.28.47 AM

Bottom line: 23AndMe.com is a sweet testing — while they are no longer able to provide health analysis by the FDA (likely caused by patients walking into MDs office with results that 95% of MDs do not know what to do with!), alternative sites are springing up that will do it for you and give better results than your MD’s Labs… unfortunately…