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MEBO - UBIOME study 2018



MEBO Gut Microbiome Study
"Microbial Basis of Systemic Malodor and PATM Conditions (PATM)"
Funded by uBiome Research Grant

"Microbial Basis of Systemic Malodor and PATM Conditions (PATM)"

Dynamics of the Gut Microbiota in
Idiopathic Malodor Production

Started May 2018 - Ongoing

Current people sent kits : 100/100
3 kits per person


Participation info : LINK English

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BO Sufferers Podcasts



TMAU Petition world
TMAU UK end total:262
TMAU UK ends 23/01/20
TMAU Petition USA end total 204
USA : Moveon open
TMAU (Dominican)
Metabolomic Profiling Study

Start : Aug 2016
Stage 1 : 27 Canadian volunteers to test
Latest click here (26 oct) :
17 samples returned

Note : Stage 1 is Canada only.
Return cut-off date : passed
Analysis can take 6/8 weeks
Analysis start in/before Nov
MEBO Research is a
NORD Member Organization
See RareConnect

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Blog Archive

MEBO Research Clinical Trials

Click here to read details of the MEBO Clinical Trials
NCT03582826 - Ongoing not recruiting
Microbial Basis of Systemic Malodor and PATM Conditions (PATM)
United States 2018 - ongoing

NCT02683876 - Completed
Exploratory Study of Relationships Between Malodor and Urine Metabolomics
Canada and United States 2016 - ongoing

NCT03451994 - Completed
Exploratory Study of Volatile Organic Compounds in Alveolar Breath
United Kingdom and United States 2013 - ongoing

NCT02692495 - Completed
Evaluation of Potential Screening Tools for Metabolic Body Odor and Halitosis
United Kingdom 2009 - 2012

Thursday, November 7, 2019

FMO3 Gene Test 'liberation day' is here

want to FMO3 gene test ?
Do a Consumer Full Genome Test.
It's cheaper than a single gene test 

About :
FMO3 gene test. Easily doing this test without need for Dr.

It looks like FMO3 Gene Test 'liberation day' has finally arrived, in the form of INEXPENSIVE FULL GENOME tests for CONSUMERS. (labs such as Dante labs or Nebula Genomics).

MEBO tried to source a FMO3 gene test supplier for over 10 years without success.
The hurdles were :

1. Laws (meant to 'protect' the tester, but actually work against them ... e.g. Dr must order)
2. Cost (clinical labs still charge around $600 for the FMO3 gene test)
3. public-unfriendly service : (e.g. used blood rather than spit, public were a nuisance)
4. Didn't give raw data to tester (gives their 'interpretation only)

CONSUMER DNA tests were on the horizon over the last decade, but none fully fitted the criteria to get the FMO3 test criteria :
Reasons :
1. Full Genome test was too expensive, maybe $1000+
2. 23andme showed the way in consumer service, but don't test all the 'points' (not full genome)

Thankfully CONSUMER GENOME testing has now reached a point where it can be suggested as the FMO3 GENE TEST

1. It's now inexpensive , maybe from $150 (low pass ... x0.4 to x4 ?, but probably acceptable ?) to $400 (clinical standard ... x30)
2. Logistics are designed for the tester, (e.g. spit test, consumer test, easy, no Dr Obstacle).
3. Get the full genome and not just a SINGLE GENE. Single gene testing now seems obsolete, as you can do a full genome test instead, which will probably be cheaper.
3. Can check results online, download raw data etc.

Examples of labs offering Consumer Full Genome testing : 
Dante labs (x4 coverage for $149 ?)
Nebula Genomics (x0.4 coverage for $149 ?)
There are others.

Lab Test Comparison Site
(not verified by MEBO)
(may not include all consumer supplier options)

Coverage is how many times the lab read your code.
It seems they can make small errors in reading, which might be a lot in such a lot of data.
x4 is around 99% confidence ?
x30 is 99.9% confidence ?

Nebula cheapest is 0.4% coverage, which may mean its not FGT, but still a lot more 'points' than 23andme.
Dante cheapest is x4 coverage.
x30 coverage is traditionally regarded as 'clinical standard'.

MEBO can't recommend a test lab supplier (yet)
As we have no feedback on the tests and possible 'annoyances', we can't recommend a FGT yet.
As time goes by and community give feedback, it should become clearer.
Anyone buying the tests are community 'guinea pigs'.

When you get the results, how to find FMO3 ?
With 23andme (not a full code test), you type FMO3 in a search.
Hopefully the full code test labs are the same.
If not, you may have to look around the raw data.

WARNING : you might find out you are prone to terrible disorders
All you really want is the RAW DATA.
But to make themselves distinct and look more necessary, the lab results tend to have window-dressing in the form of telling you what serious disorders you carry or will die of etc.

So the results might take the format (not literally) :
'Hi, you will get alzheimers and parkinsons ... you carry cystic fibrosis'
'where is my FMO3 result ?'
'it's in the back, you will need to rummage around.'

1.You can work out the raw data code for FMO3 yourself, but its a case of fitting a reference site to understand the data code (the AGCTs ... e.g. ACTAAGCTTAA ... for 532x3 letters ?)
2.TRANSLATORS like Promethease can 'translate' it for you, but they might ignore variants regarded 'minor' or 'benign' (currently). But should do an ok job.
Possibly the test lab sites will translate it (unlikely ?).   

Introns are regarded as 'junk' (the gene code is on exons), or of unknown purpose ... but sadly you can have faults here that can affect FMO3 function.
At least full genome tests give intron data too, which may be useful when more is known about them.

if you want to know your FMO3 gene 532 full code (plus introns), the best way is to do an inexpensive Consumer Full Genome Test such as Dante labs.
and search FMO3 (if its possible) ... or check the raw data and work it out yourself ... or upload to a DNA data translator.

We no longer need Drs or 'official' Health System DNA labs,.
We can test from home and read the results online.
Once we hear feedback from testers we will find out the obstacles, what lab is best, or whether it is good enough to be regarded as the best FMO3 Gene Test.

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A EURORDIS and NORD Member Organization

Tuesday, November 5, 2019

1st Gene Therapy patient for Sickle Cell : FMO3 someday ?

CRISPR gene therapy will likely revolutionize treatment for 'single-gene' disorders, by being able to correct errors in the gene.
CRISPR was first documented in 2012.
It may become a clinical norm in under 15 years.
FMO3 would seem an ideal straightforward gene to edit.

1st patient has received CRISPR gene therapy for sickle cell anemia.
It seems Victoria Gray in the USA is the first patient to be treated with CRISPR gene therapy last month.
Now it's  a case of seeing how she gets on.
NPR radio overview (12 mins audio)
'This is a big moment for Victoria and for this pivotal trial. Because if we can show that this therapy is safe and effective, it can potentially change the lives of many patients,'
Daily Mail article
If you feel your 'met-bo' is caused by error in a single gene, such as FMO3 gene, then CRISPR should be a definite potential therapy in the coming years.
FMO3 : single gene (easiest for CRISPR ?)
most 'TMAU1' cases are MISSENSE variants (wrong amino in either side of 532 amino code)
CRISPR should be ideal for MISSENSE.

Anyone trying out FMO3 on CRISPR research ?
Probably not.
You'd think some government would make a lab try out each genetic disorder for CRISPR, but it seems currently left to labs doing their own thing.
We will need to get an idea of the CRISPR research lab network.
A Chinese lab did try out the CRISPR basic principle on mice for FMO3 in 2015. This is where they see if they can 'knock-out' or 'knock-in' FMO3 'on demand'. It seemed to work. 
Pubmed : China 2015 : FMO3 CRISPR

CRISPR in context for FMO3
It might be a FMO3 'cure' within 15 years.
Maybe even an outpatient treatment someday.
However helpless you feel, you can keep this in mind in the background.

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Thursday, October 31, 2019

Gene Editing and FMO3 : cure in 5-10-15 years ?

Ultimately, the cure for FMO3 Genetic Malodor (e.g. TMAU1) will be Gene Therapy.
The question is, when ?
Probably sooner than expected.

Gene therapy is where they can correct errors in the code.
A bit like word-processor correcting, or correcting with copy and paste.

There are various gene-editors, but the 'big game-changer one' seems to be CRISPR ... first published about in 2012.
Last week a new paper was published that spoke of an improvement which makes 'single letter' correcting of DNA safer and easier.
Most people with FMO3 flaws will have 'single letter' (base) flaws.

Prof Jennifer Doudna, the co-founder of CRISPR said in 2015 :
She expects clinical therapies within 10 years (so 2025 ?)
Current obstacles with gene-editing to overcome :
Probably safety, precision, worry about side effects ?, delivery to the body, cost, no human trials yet etc

CRISPR is cheap to do in a test tube, but delivery to the body, licencing cost etc will be dear to start with probably. 

FMO3 most common types of gene flaws.
Most with 'sub-par' FMO3 (either always, or transiently), will be due to NUCLEOTIDE MISSENSE  errors.
This is to do with A,G,T,C.
FMO3 protein is a 532 amino acid sequence.
The DNA will be 3 nucleotides on each side to make up the amino acid (532x3x2 letter code).
Like AA AG TC etc.
Most FMO3 people will have one of those letters wrong, making the amino acid incorrect at that codon (532 rung ladder of codons).
Examples : E308G E158K  V257M
These 3 mistakes are common, but most FMO3 people seem to carry 2 of the mistakes (either at same codon, or as a mix)

So these flaws should technically be easy to fix when the technology is ready (?)
They say the easiest type to fix are :
single gene : tick ... FMO3
single base flaws  : ... most FMO3 people have these

Has FMO3 ever been tried in CRISPR ?
It seems a Chinese lab experimented with mice in 2015 re FMO3.
Probably proving the principle for FMO3.
Chinese paper 2015 FMO3 knock-in/knock-out in mice. 
No follow up seemed to happen.
Probably as FMO3 is regarded as not an important gene, and 'sufferers' are rare (an incorrect assumption).

Where would FMO3 treated cells be delivered to the body ?
Probably the liver.
FMO3 is in a lot of places in the body, but mainly in the liver.
Sickle-cell anemia is being looked at now for CRISPR treatment, as they can take blood out and treat it. But they have to put it back in the bone marrow.
No human clinical trials have been completed yet.

Dr David Lui paper from Oct 2019 
Dr Lui of Harvard seems to have improved the CRISPR targeting for base mistakes (? base editing)
It has been tweeted by peers, so seems a breakthrough.
new gene-editing technique may be capable of fixing almost all disease-causing genetic defects 

So, whatever happens re FMO3 smells and/or TMAU, keep in mind the genetic type may be close to being genetically cured in 5-10-15 years (or sooner ... as many gene disorders will be).

Notable People to search in Gene-Editing and CRISPR world (from skim-reading about CRISPR)
Prof Jennifer Doudna (oct19 article)
Prof Emmanuelle Charpentier
Prof Feng Zhang
Prof George Church
Dr David Lui
... many more.

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A EURORDIS and NORD Member Organization