FMO3 gene results with GENOS

I got my Exome test results back from Genos (DNA test).
Cost was $399 (time limited special offer).
Exome is coding part of the Genome (essential part).
For FMO3 the test listed my 2 'wrong amino acid' variants, but not the 'silent' one.
I can't be sure it is FULL SEQUENCING, but rather a 'list of suspects'.
Overall I think it was worth it.
Best overall DNA tester I know (being both for consumer and none of the obstacles of clinical labs).

I got my exome DNA results back from GENOS.
I am very happy with the service, the process, support, and the info given.
My only gripe is I am not sure if it is FULL SEQUENCING (i.e. every codon of a gene).
It possibly is, I don't know yet.

Ways DNA labs test and give results :

1. Test for list of suspect variants/codons only (usually cheapest way).
This is no use really. Still too much unknown of the other bits. This is where they test suspect codons only. This means they choose the list of known suspects, but many more variants may yet to be discovered as fault-causing. You want to know every variant you have, not just suspects.

2. FULL SEQUENCING, but only give SELECTED variants/codons info to the person.
This means they tested every codon but they may only give what they think is relevant info on certain variants. So you still can't be sure you are getting the whole picture.  

3. FULL SEQUENCING and give ALL VARIANTS whether they be thought relevant or not.
This would be as good as FULL SEQUENCING in theory I guess.

4. FULL SEQUENCING (i.e. every codon of the gene)
This is best/good, though I guess in theory you only need to know the variants, so #3 may be more practical. #3 is the same as #4 but without the 'perfect' parts (which presumably won't affect function).

I am hoping Genos is #3, but I have not found out yet. It may be #2 which would not be so good.

EXOME, GENOME :
Exome  = coding for all the proteins in humans
Genome = everything (Exome + Junk + promoter regions etc)

It's thought maybe 80% of faults are in the exome part.
The main reason for EXOME testing rather than GENOME is cost (at the moment).
Exome is obviously the part you can't do without. The essential part.
But people can have faults in the junk part of a gene and it can cause deficiency even though it's junk.
   
MY GENOS DNA RESULT
I have fully sequenced the FMO3 gene before so knew my FMO3 coding part result.
It spotted my 2 carrier copies of the common variants at codon 158 and 308.
These are reasonably common (in caucasians anyway).
There is debate if they affect function (obviously I would say they do).
Some say only if they were from same parent, or if person is homozygous (carry 2 copies).

It didn't spot a silent variant I carry. This is what makes me wonder if they only test a 'suspect list'.
Silent variants are where one of the nucleotides is wrong but the amino acid ends up the same.

FMO3 gene
532 x 3 (1596) nucleotide sequence.
makes up 532 amino acid sequence (+ stop at 533).
makes up the FMO3 protein.
Which means 532 codons where variants can be.

Clinvar list of FMO3 variants

IS IT A GOOD WAY TO DNA TEST FOR FMO3?
Well this is where I don't know (yet).
The best way is to have your full 532 coding sequence, or at least all the variants in that 532 coding sequence (even if they are currently deemed to not matter).
But I don't seem to have the full sequence (not that I can see so far), or all the variants (as they missed a silent one).
The give a raw file but I don't know how to open it.
Answer : I think so but I don't know.

FMO3 DATABASE
In my opinion we should get a FMO3 database going.
But how to, I don't know.
Ideally this would be both the Exon and Intron parts of FMO3 (not just the exons)
Intron is the 'non-coding' part of the gene (which could be junk + promoter region etc).
This would be a pipe dream.

My philosophy on spending on 'systemic malodors'
My philosophy is we don't know what causes it yet, so better to spend money on testing rather than spending on supplements.

FINAL COMMENT
So I can't say for sure GENOS is a great option for DNA testing, but it may be.
And at current price $399 it's cheaper than most FMO3 DNA gene testing .
Plus it's meant for the public and easy to test (saliva).
The question is how much prices will drop quickly and how well competitors do.
In the end you will probably be able to do GENOME testing for maybe $100, but when ?
Also remember, you may find results of other genes you might not want to know (e.g. prone to parkinsons, carrier of cystic fibrosis) so you need to factor in whether you want to know such things.

Note :
I am no expert, so terminology, facts may be wrong.

Links :
Genos DNA TEST LAB FOR CONSUMER

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By sysbodyodor

fecal body odor, fmo3, FMO3 DNA saliva test, metabolic malodor, my results, my test results, systemic body odor, systemic malodor syndrome, tmau, TMAU research, tmau test

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Exome testing for systemic body odor

Exome test for $399 (beta price, summer 2016).
Direct to consumer (not NY or FL).
Genos (based San Francisco).
A 'beta phase' price offering that may increase. 
This might be a good affordable way of testing your coding genes rather than just 1 gene (e.g. FMO3).

Exome testing for systemic body/breath odor
My guess is that FMO3 enzyme flaws will be responsible for most cases of systemic/metabolic body/breath malodor. But, I may be wrong, or it may be more complex than that (e.g. compounded enzyme faults acting together to create a bigger flaw).

So for that reason I still consider the genetics of systemic body/breath malodor to be unknown, and any testing would need to be very exploratory and broad. Currently DNA testing is still at an early stage and the main limitation for most is probably cost.

Genos Exome testing ($399 'beta price' Summer 2016)

Genome : this is your full DNA code including all the junk.

Exome :  this is the 'coding part' of your DNA, so the most important. About 3% of genome / about 24,713 genes. 

Gene : the exome is made up of all the important gene's coding part.

SNP/mutation : this is the sole faults in a gene. you can have a few in a gene (compounded)

Until recently probably testing a single gene (e.g. FMO3) would be the most affordable, but obviously limited to that sole gene. Genomic testing will someday become the norm but is still too expensive. But Exome testing is now getting to a price that it probably makes sense to do Exome testing rather than single genes. A bit like getting the whole box of sweets rather than having to pick one.

Exome testing direct to consumer (DTC) :
DTC genetic testing can be difficult to access due to the traditional set-up of the health system (probably worried about money loss rather than health). 23andme tests a range of variants but it's a pretty random list. Also they have been 'crippled' by the FDA since 2012.

Genos exome testing :
Genos look like they may have found a way to offer dtc Exome testing without the FDA clamping down (for now).

I like the look of Genos Exome test because (but I could be wrong) :
Looks the cheapest exome test at the moment ($399, beta price).
Is a US Venture-backed startup (one investor is BGI) based in San Francisco.
Sequencing service is currently performed at a CLIA certified referral lab located in USA.
Similar set-up to 23andme.
Saliva sample.
Other reasons (can download raw data, delete account and data, I own data)

Why I may Exome test for systemic/metabolic malodor :
I already have my FMO3 code (which cost me about the same as this Exome test). But so little is known about systemic/metabolic (same meaning) breath/body odor that I do not want to rule any gene out.
In particular, I am interested in the broad-spectrum 'detox' enzymes. This would be the the 'oxidizer' enzymes (alongside FMO3) such as the CYP450 enzymes, and the conjugation/'phase 2' enzymes such as sulfation, glucorinidation etc. These enzymes often alter drugs (pharmakinetics).
My bias would be to look at the 'oxidizers' but I may be wrong. That's what's good about exome/genome testing.

We have 1,000s enzymes but it seems to me the enzymes above are the only real 'broad spectrum' enzymes that alter many different compounds. If someone smells of 1 thing, then I would guess it could be any enzyme, but when you can smell of many different (unpleasant) things then my guess it is one (or more) enzyme that alters many different compounds.

So for reasons of price compared to single gene testing, the scope of genes tested, and other reasons, this is why I may Exome test at some point (until genome testing becomes cheaper), and at the moment Genos would be my likely lab to test with.

Final thought
So now I don't suggest doing the single gene test for FMO3 anymore. Probably for the same price (or cheaper) and without the hassle of a standard CLIA lab's traditional procedures, you can now test FMO3 and all the other important genes in an EXOME TEST.

Keep in mind the $399 price will probably not last long, but in general DNA testing prices are continuing to fall.

Note :
I am no DNA expert, so ...
Genos exome test may not meet my expectations.
You will need to read more about them yourself.
I haven't done this test.

Update Nov 2016 : 
Genos contacted me to correct something. I said they were owned by Chinese company BGI.
They replied :
'Actually, Genos is a venture-backed startup.  BGI is one of our investors, but we are not owned by BGI.  The headquarter of Genos is located in San Francisco, CA, USA.  Our sequencing service is currently performed at a CLIA certified referral lab located in USA as well.'  

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By sysbodyodor

FMO3 DNA saliva test, systemic body odor, systemic malodor syndrome

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Exome/Genome Consumer Test list

To me, it's getting to the point where it's possibly economically and future-proofing best to Exome or Genome test rather than test for single genes (partly or fully) or groups of genes. And Direct to Consumer (no need for Dr, health professional and their fees etc)

So here is my list ...

Aims :
Exome or Genome testing
Direct to consumer
Note : For health-related testing the advice seems to be to go for 30x coverage at least

my List : Exome / Genome Consumer Test companies

COMPANY	EXOME / GENOME	COMMENT
Full Genomes link	Exome 33x $775 Genome 30x	Other links : ISOGG Facebook
Veritas Genetics link	Genome 30x  £999	Other links :

update : 19 May 16

Exome is about 1.5% of the Genome.
But Exome is the CODING PART, whereas rest of Genome is junk / promoter region etc.
But you can have faults in the junk part which can affect the gene coding.

Main reasons for choosing Exome or Genome
Exome is the coding part, and probably cheaper to do
Genome includes everything, and perhaps in future more will be known and you will already have your full data.

FMO3 :
Readers will be aware I currently suspect FMO3 enzyme as the main suspect for most cases of Systemic Body Odor. FMO3 coding part would be included in both Exome and Genome testing.

FMO3 gene code : 532 amino acid sequence (532 codons from 1596 (532x3) Nucleotides) plus stop codon at codon 533.

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By sysbodyodor

fmo3, FMO3 DNA saliva test, genetics, systemic body odor, systemic malodor syndrome, tmau test

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Worldwide FMO3 DNA saliva test service

Note :

This test supplier has been cancelled for another supplier .

See this new post for details

FMO3 DNA test

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FMO3 DNA testing (saliva)
Full coding region (532 codons)
Worldwide testing
Test lab is in Spain
Test kit will be provided
Price : £210/265 Euros/$337 if you wait for batches of 24
Individual price : £320/405 Euro/$512 if you wish to test without waiting for 24 to be reached

No money is involved until the batch number is reached. Financial transactions are between you and the lab..

FMO full coding region DNA test (532 codons)
Available worldwide
Saliva test (kit sent out)
No rush to return sample as it does not spoil for years

Prices : (including test-kit sent out but not return shipping)

Cost of being in a 24 batch sample :
£210 / 265 Euro /  $337

Cost of testing immediately :
£320 / 405 Euro / $512

Interested ?
Send an email to sysbodyodor@gmail.com

Who can test :
Anyone worldwide

What you will get :
Full list of your FMO3 coding region (532 codons)
An interpretation of the results

I have been able to arrange a FMO3 DNA testing program via a lab in Spain. This will be testing of the full FMO3 coding region (532 codons). I have been offered 2 prices for 2 options :

Batches of 24 : If you wait until a batch of 24 is reached, it will be the cheapest price. This means waiting until 24 samples have been collected. This is a typical arrangement as it is most economic to test in batches.
Cost :£210 / 265 Euro / $337

Individual testing :
If you wish to test instantly and not wait for a batch of 24, this can be done but it is more expensive.
Cost £320 / 405 Euro / $512

This is a new service.

How to test :
If you are interested, send an email to me at sysbodyodor@gmail.com
You will be put on the waiting list (for the batch list) or if wanting the individual option your email will be sent to the lab direct.

T
the test kit used is the Oragene OG-510 by DNAgenotek

What is the test :
You will be sent a saliva test kit free of charge. You spit in the kit and return it..

Returning :
You need to arrange return shipment. As it is saliva and does not need to reach the lab urgently, it should be relatively cheap to ship.    

Payment :
Payment will be arranged once the batch number is reached. Payment is by Credit card.
Those testing individually (not in batches) can arrange credit card payment with the lab

Results :
You will get a copy of your 532 codon FMO3 coding region
Also an interpretation will be given

Note about results :
Although all the 532 codons of the FMO3 coding region, it is possible to get 'false negative' results. This is mainly due to 2 reasons :
1. People can have faults in their 'intron' or 'promoter region which is not part of the coding region, and this can cause faults in FMO3 function even idf the coding region is normal
2. Although the 532 codons of the FMO3 coding region are known. it may not be known if all differences from the norm will affect function at all. Over time if new 'fault causing' differences will be discovered. However if you have your full coding list, you can then check if/when new 'faults' are discovered in the future. By this I mean, the interpretation will be to the best of the labs knowledge at this time, subject to whatever their opinion is at this time.

How to register an interest :
Send me an email at sysbodyodor@gmail.com
Let me know what country you are in and if you want to be in the 24 batch or want to test individually immediately at the higher price.

email sysbodyodor@gmail.com
Let me know what country you are in
State if you want to be in the 24 batch or test individually
Anyone for the 24 batch will be put on the 24 batch waiting list
Open to anyone worldwide and there is no rush to return the sample

 

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By sysbodyodor

announcement, FMO3 DNA saliva test

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