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Showing posts with label Dna. Show all posts
Showing posts with label Dna. Show all posts

Saturday, May 9, 2020

MS and Research logs


Some on line know me for research or blogs I have allowed scientist to pursue, On certain questions about MS that may be helpful. Others lead to more questions.  Above is a relative known as "White Peter" Google is a great starting point.

I am part of AllOFUS.ORG. AllOFUS.ORG, a research program , I may never see results in my lifetime, but was one of the first joining.

Patientslikeme.com  Patientslikeme.com was another research program, but they sold out all my information to United Health Group. So not sure where they are going now. They have a lot of history, snapshots of DNA over time, lab charts, and more. They are good at tracking every symptom, medicines, labs, and many conditions.

 I ConqureMS.com  iconqureMS.com is yet another company for research I answer questions for. They combine a lot of information, and you can upload your labs, so science can see.

 UBiome.com, has a lot of information about my gut issues. I was a test patient for them, sending in stool samples, getting reports back to share.  Their platform sent me to selfhacked.com, to understand information.  In 2019, they were busted by FEDS for insurance fraud billing. Got greedy. No more reports.

Last year at christmas, 2019, I did a VIOME.COM. VIOME.COM test of my gut bacteria.

 I also did a TELLMGEN.COM  DNA
TELLMGEN.COM test of my entire DNA, and to see how my prescription medications interact, Diseases it may pick up, and Research for them to do for quite sometime.


The TellmeGen goes into PHARMACOLOGICAL ACTION of different medicines that you use.  They have  your individual make up of DNA.  So the results will be different for everyone.

There is a lot of good reading, about interaction, RESEARCH STATUS, PHARMACOLOGICAL ACTION of many medicines on the market.  I gave them the specific list of twenty five medicines, so they could have their scientist see how I may metabolize them, and perhaps help future generations.  This I am sure will take time to analyze.  They have been great with email updates on questions I have asked.

I had a call the other week, from
BioMedical Insights, a health care consulting firm, and they were researching hereditary hemochromatosis on behalf of a client interested in treatment development.  They received their information from
Rare Patients Voice
  https://rarepatientvoice.com/EverchangingMS/
https://rarepatientvoice.com/EverchangingMS/

A recent study provided them with my contact info.  It provided a useful hour of talking about a new treatment. Think that's great!
It was a fun filled hour on a conference call, explaining My Rare H63d Genes that caused hereditary hemochromatosis, and a new drug treatment that could help thousands and thousands of people. Not a cure, but sounds promising for all.

Rare Patient Voice, LLC provides patients and caregivers with rare diseases an opportunity to voice their opinions through surveys and interviews to improve medical products and services. they will also send you a $5.00 gift certificate for joining, and a stipend for interviews qualified for.  I have seven conditions listed with them.  More information to come.

My GP, was kind enough for my request to learn about pharmegentics, as such a new field, FDA may not look into it for years. This I will talk about in another blog.

First I will talk about my most recent GUT test done by Viome.com

The Sample for my Gut was sent in December 26, 2019.  that generated a report of My Active Microbes.
Their are a lot listed, which I will have a dietician at UC Davis look at.  They also helped me with a food map, that my GI, wanted me on. This listed foods to Avoid, Super Foods, and foods to take in moderation with my Gut Condition that a microbe was taken of.

There were
SCORES TO FOCUS ON

Inflammatory Activity
Intestinal Barrier Health
Butyrate Production Pathways
LPS Biosynthesis Pathways
Putrescine Production Pathwaya
Oxalate Metabolism Pathways

SCORES THAT ARE GOOD
SCORES WITHIN RANGE

First was No Butyrates, or Probiotics were found.  That was a area that I could address with my GI Dr.   I am on linzess, lactulose, and metoclopramide to keep things flowing of constipation and Diarrhea. Perhaps the Gut Lining is needing a Boost.

"This score assesses the levels of activity of all microbial pathways that lead to the production of a beneficial nutrient - butyrate. Butyrate is a short-chain fatty acid known to beneficially affect many wellness areas from gut lining to insulin sensitivity and satiety (feeling full). A score that needs improvement means that your microbial butyrate production could really use a good boost! Individuals with low butyrate production activity would benefit from supplements or foods that either feed or add butyrate producing microbes into your gut ecosystem. "

This led me to What is leaky gut?

Leaky gut is a popular term used for increased intestinal permeability. This phenomenon occurs when the tight junctions of the intestinal walls become loose, which can allow harmful substances to enter the bloodstream. This means bacteria and toxins are able to “leak” through the intestinal wall more than normally expected.

I bought some Iberghast,  and a bottle of Vital nutrents  that contains: pancreatic 500mg and ox bile200mg ..protease 111k usp, amylase, 122k usp, lipade 17k usp

45 days later Viome gave me more recommendations.  I went over these with my GI dr. He said to try one at a time.
These consist of Berberine, mixed Polyphenols, Glutathione, Zinc Carnosine, probiotics strain Lactobacillus KE99,  probiotics strain L. reuteri DSM 17938, L. reuteri ATCC PTA 6475,  digestive support of Peppermint leaf extract, horse chestnut extract, quebracho extract, perilla extract, another probiotics strain Lactobacillus plantarum.

With my Multiple Sclerosis paying a huge part in my Gut, or perhaps the other way around, that the Gut is responsible for some of the Multiple Sclerosis.

I have not tried everything yet, some of it is cost related.

Zinc-carnosine is a unique product that appears to enhance the stomach's mucosal defenses, providing significant improvements in gastric ulcer patients. It also supports small intestinal mucosal integrity and inhibits the inflammatory responses in H. pylori.  I have been on regular zinc to keep colds away, without over reacting my immune system. Important for people with MS


Does L-glutamine work for IBS?  https://www.medicalnewstoday.com/articles/320850
https://www.medicalnewstoday.com/articles/320850

Berberine – A Powerful Supplement With Many Benefits
Berberine link to healthline.com. This one may help combat my high triglycerides, along with Vascepa I tak

https://www.healthline.com/nutrition/berberine-powerful-supplement#section4



Bile Acid Supplements May Ease Symptoms of Progressive MS

https://multiplesclerosisnewstoday.com/news-posts/2020/03/31/bile-acid-supplements-may-ease-inflammation-symptoms-progressive-ms

https://multiplesclerosisnewstoday.com/news-posts/2020/03/31/bile-acid-supplements-may-ease-inflammation-symptoms-progressive-ms

(MS) patients have lower than usual levels of molecules called bile acids circulating in their blood, a  study found. These molecules, produced in the liver to aid fat absorption in the gut, also appear to block inflammation and nerve cell damage in the brain.

Another step was looking  to the bile salts.

Product Information Butyraid 100 Tabs - Featuring butyric acid from the salts of calcium and magnesium, Nutricology ButyrAid is in an enterically-coated tablet designed to release in the small intestine. This short chain fatty acid is produced by certain probiotic bacteria and appears to support intestinal integrity

And as my GI told me, everything may be just going thru me daily. Something I need, so not to be costipated, but to have bowel movements without major straining. I do not understand alternating constipation and Diarrhea during bowel movement, and followed by three, then good for the day.  But better than having accidents, as I was before. Part of MS. Or the H63d Gene not allowing iron back into my system a year and a half later.

Had anybody tried any of the above?
Thank you for reading
JoeY

Saturday, February 8, 2020

Multiple Sclerosis DNA





                                       Photo of gene from wikipedia.org


Multiple Sclerosis blog of DNA Technical reading.

I did a 23and me home testing.
If you did a health dna, this will show up under celiac diseases.
It may take some reading, and researching, but this will show up.
The HLA-DRB/DQA gene

There are links to folllow, but for less confusion, just Google the gene.
there are many variants I show below, having a complete DNA done of me. Everybody may be different, but hope this helps science.

https://ghr.nlm.nih.gov/gene/HLA-DQB1#conditions
https://ghr.nlm.nih.gov/gene/HLA-DQB1#conditions

Look up on Google this gene, and look under auto immune disorders

HLA-DQB1 gene

major histocompatibility complex, class II, DQ beta 1

Normal variations of the HLA-DQB1 gene have been associated with several additional disorders. Most of these disorders have an autoimmune basis, which means they occur when the immune system malfunctions and attacks the body's own tissues and organs. Autoimmune disorders that have been associated with HLA-DQB1 include multiple sclerosis, pemphigus, and type 1 diabetes (described below).
Multiple sclerosis is a chronic disorder of the brain and spinal cord (central nervous system) that causes muscle weakness, poor coordination, numbness, and a variety of other health problems. Several variations of HLA-DQB1 appear to increase the risk of developing this disorder. One of these variations, HLA-DQB1*06:02, is the same version of the gene that increases the risk of narcolepsy.
Some evidence suggests that the HLA-DQB1 gene may also play a role in several forms of pemphigus, a condition that causes severe blistering of the skin and mucous membranes (such as the moist lining of the mouth).
It is unclear how different versions of the HLA-DQB1 gene influence the risk of developing autoimmune disorders. These disorders typically result from a combination of multiple environmental and genetic factors. Changes in other HLA and non-HLA genes, some of which remain unknown, also likely contribute to the risk of developing these complex conditions.

23and me

We detected a variant linked to the HLA-DQ8 haplotype.doing


                                                    Photo from wikipidia.org

https://en.m.wikipedia.org/wiki/HLA-DQB1

Multiple sclerosisEdit

Certain HLA-DQB1 alleles are also linked to a modest increased risk of multiple sclerosis.[11][12]

See scientific details
I am not a doctor, or scientist, just researching, trying to understand the aspects of Multiple Sclerosis is having on me, and the commonalities this disease has of raging they my body.

Further investigation shows these SNP I have.

SNP : rs12487066

SNP : rs312993

SNP : rs3135388

SNP : rs6897932

SNP : rs7326018



Technical Report for these genes from DNA done 12/2019

SNP : rs12487066

Gen o Región : 3q13.11

UserSNP usedGenotypeAdjusted Odds Ratio*lrs12487066CT0.97

Multiple sclerosis has a clinically significant heritable component. It was conducted a genome-wide association study to identify alleles associated with the risk of multiple sclerosis.

It was used DNA microarray technology to identify common DNA sequence variants in 931 family trios (consisting of an affected child and both parents) and tested them for association. For replication, we genotyped another 609 family trios, 2322 case subjects, and 789 control subjects and used genotyping data from two external control data sets. A joint analysis of data from 12,360 subjects was performed to estimate the overall significance and effect size of associations between alleles and the risk of multiple sclerosis.

A transmission disequilibrium test of 334,923 SNPs in 931 family trios revealed 49 SNPs having an association with multiple sclerosis (P<1x10(-4)); of these SNPs, 38 were selected for the second-stage analysis. A comparison between the 931 case subjects from the family trios and 2431 control subjects identified an additional non-overlapping 32 SNPs (P<0.001). An additional 40 SNPs with less stringent P values (<0.01) were also selected, for a total of 110 SNPs for the second-stage analysis. Of these SNPs, two within the interleukin-2 receptor alpha gene (IL2RA) were strongly associated with multiple sclerosis (P=2.96x10(-8)), as were a non-synonymous SNP in the interleukin-7 receptor alpha gene (IL7RA) (P=2.94x10(-7)) and multiple SNPs in the HLA-DRA locus (P=8.94x10(-81)).

Bibliography

International Multiple Sclerosis Genetics Consortium. Risk alleles for multiple sclerosis identified by a genome-wide study. N Engl J Med. 2007 Aug 30;357(9):851-62.

SNP : rs3129934

Gen o Región : C6orf10

UserSNP usedGenotypeAdjusted Odds Ratio*rs3129934CT0.97

Multiple sclerosis is a chronic inflammatory demyelinating disease of the central nervous system with an important genetic component and strongest association driven by the HLA genes.

It was performed a pooling-based genome-wide association study in which Comabella et al. described eight SNPs validated in Spanish Caucasian cohort and US Caucasian cohorts. The most significant association was obtained for SNP rs3129934, which neighbors the HLA-DRB/DQA loci. Said SNP is associated with an increased risk for multiple sclerosis. The OR was 3.0 (CI: 1.8-5.0; P = 1.4×10(-5)).

Another studied polymorphism was rs7326018 which is one of the eight SNPs associated with increased risk for multiple sclerosis. Its OR was 1.8 (CI: 1.1-2.9, p = 0.0228).

Bibliography

Comabella M, Craig DW, Carmiña-Tato M, Morcillo C, Lopez C, Navarro A, et al. Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms. PLoS One. 2008;3(10):1–9.

SNP : rs3135388

Gen o Región : 6p21.32

UserSNP usedGenotypeAdjusted Odds Ratio*rs3135388GA1.81

Multiple sclerosis has a clinically significant heritable component. It was conducted a genome-wide association study to identify alleles associated with the risk of multiple sclerosis.

It was used DNA microarray technology to identify common DNA sequence variants in 931 family trios (consisting of an affected child and both parents) and tested them for association. For replication, we genotyped another 609 family trios, 2322 case subjects, and 789 control subjects and used genotyping data from two external control data sets. A joint analysis of data from 12,360 subjects was performed to estimate the overall significance and effect size of associations between alleles and the risk of multiple sclerosis.

A transmission disequilibrium test of 334,923 SNPs in 931 family trios revealed 49 SNPs having an association with multiple sclerosis (P<1x10(-4)); of these SNPs, 38 were selected for the second-stage analysis. A comparison between the 931 case subjects from the family trios and 2431 control subjects identified an additional non-overlapping 32 SNPs (P<0.001). An additional 40 SNPs with less stringent P values (<0.01) were also selected, for a total of 110 SNPs for the second-stage analysis. Of these SNPs, two within the interleukin-2 receptor alpha gene (IL2RA) were strongly associated with multiple sclerosis (P=2.96x10(-8)), as were a non-synonymous SNP in the interleukin-7 receptor alpha gene (IL7RA) (P=2.94x10(-7)) and multiple SNPs in the HLA-DRA locus (P=8.94x10(-81)).

Bibliography

International Multiple Sclerosis Genetics Consortium. Risk alleles for multiple sclerosis identified by a genome-wide study. N Engl J Med. 2007 Aug 30;357(9):851-62.

Gregory SG, Schmidt S, Seth P, Oksenberg JR, Hart J, Prokop A, et al. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet. 2007;39(9):1083–91.

SNP : rs6897932

Gen o Región : IL7R

UserSNP usedGenotypeAdjusted Odds Ratio*rs6897932CC1.06

Multiple sclerosis is a demyelinating neurodegenerative disease with a strong genetic component.

Previous genetic risk studies have failed to identify consistently linked regions or genes outside of the major histocompatibility complex on chromosome 6p. There is a study in which was described the allelic association of a polymorphism in the gene encoding the interleukin 7 receptor alpha chain (IL7R) as a significant risk factor for multiple sclerosis in four independent family-based or case-control data sets (overall P = 2.9x10(-7)). Further, the likely causal SNP, rs6897932, located within the alternatively spliced exon 6 of IL7R, has a functional effect on gene expression. The SNP influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silencer.

This gene encodes a protein called alpha-IL7R. This protein plays an important role in how two growth factors (IL-7 and TSLP) affect specialization and maintenance of various immune cells.

IL7R-alpha protein can take two different forms. One way is anchored in the membranes of immune cells, while the other form is released by the cells into the bloodstream. The relative amounts of the two forms can affect the signalling amount mediated by IL-7 and TSLP, and therefore change their action on the immune system. Rs6897932 allele (C) increases the amount of free IL7R-alpha.

Since multiple sclerosis could be seen in autoimmune diseases, it makes sense that a SNP in a protein involved in the immune system would be associated with the disease. Furthermore, it has been observed that IL-7 signaling is altered in such patients.

Changes in IL-7 signaling could lead to the development of multiple sclerosis in several ways: through spontaneous reactions in immune cells and decreasing the ability to defend them, favouring chronic infections.

Bibliography

Gregory SG, Schmidt S, Seth P, Oksenberg JR, Hart J, Prokop A, et al. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet. 2007;39(9):1083–91.

Lundmark F, Duvefelt K, Iacobaeus E, Kockum I, Wallström E, Khademi M, et al. Variation in interleukin 7 receptor alpha chain (IL7R) influences risk of multiple sclerosis. Nat Genet. 2007 Sep;39(9):1108-13.

International Multiple Sclerosis Genetics Consortium. Risk alleles for multiple sclerosis identified by a genome-wide study. N Engl J Med. 2007 Aug 30;357(9):851-62.

SNP : rs7326018

Gen o Región : 13q31.3

UserSNP usedGenotypeAdjusted Odds Ratio*rs7326018TT2.09

Multiple sclerosis is a chronic inflammatory demyelinating disease of the central nervous system with an important genetic component and strongest association driven by the HLA genes.

It was performed a pooling-based genome-wide association study in which Comabella et al. described eight SNPs validated in Spanish Caucasian cohort and US Caucasian cohorts. The most significant association was obtained for SNP rs3129934, which neighbors the HLA-DRB/DQA loci. Said SNP is associated with an increased risk for multiple sclerosis. The OR was 3.0 (CI: 1.8-5.0; P =1.4×10(-5)).

The rs7326018 polymorphism is one of the eight SNPs associated with increased risk for multiple sclerosis. Its OR was 1.8 (CI: 1.1-2.9, P = 0.0228)

I hope this Technical report will be useful, and would love feedback from scientist, Drs, or you, exploring genes related to Multiple Sclerosis, and if others are coming up, or I will add to this page when other genes from DNA are found.

Cheers
JoeY