Author Topic: Genetic profile results  (Read 10594 times)

poisfighter

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What's the best dna test, which one should I get?
« Reply #60 on: October 21, 2021, 05:12:46 AM »
I don't care about ancestry, all I wanna know is what mutations or snps are causing me trouble.
I know I suffer from undermethylation if I don't supplement, high blood histamine and food intolerances, which kind of test would be most scientific and comprehensive in my case?

Quantum

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Re: What's the best dna test, which one should I get?
« Reply #61 on: October 21, 2021, 08:32:45 AM »
I don't care about ancestry, all I wanna know is what mutations or snps are causing me trouble.
I know I suffer from undermethylation if I don't supplement, high blood histamine and food intolerances, which kind of test would be most scientific and comprehensive in my case?

Hi poisfighter,

The companies making tests for ancestry only sequence about 1% of your genome.  So if you do it for health, it is better to get 100% of your genome, a Whole Genome Sequencing ( WGS).  WGS are getting a lot cheaper now, almost the same price as the ancestry sequencing.  Of course, genomics is a new science, and we do not have the knowledge yet to interpret all the SNPs found in a WGS, but each month, new information is out in research articles

I went with Nebula Genomics, with the Whole Genome Sequencing, 30x  ( The one called Deep).  The 30x means that, on average, each position in your genome will be tested 30 times.  But in an actual sequencing, the number of valid data for each single position varies. In my data, some positions have only like 14 tests done, others can have 34 results.  Those tests are not perfect, that it why you need many results for each location. So, let's say you have 98% results giving a G (a guanine base) in a certain position, you can be sure that it is a G there, and it is homozygous (two identical bases).  If you have G and C at 57% and 43% on a position, you know that you are heterozygous G/C there.
 
This 30X sequencing is currently at $299 at Nebula.  I wouldn't choose their basic sequencing, at $99, because it is only 10X testing for each location... so let's say you get only 4 results for a specific position, and it is 3 G and 1 C... hard to say what is your real result there, and if you have an SNP or not, and if it is homozygous or heterozygous.
 The good thing about a whole-genome sequencing is that you have all your genome data, once and for all, and will not need another testing later down the road.  I also took the lifetime access to Nebula's library, so I get info about new genomic research, but it is not essential - one can do the search himself.  There are also more and more websites where you can upload your data for analysis ( just have to be careful and read their privacy policy before uploading your data)

Nebula is, I think, the cheaper 30X WGS on the market, currently, at 299$.  However, even if they say it takes 8 weeks to get your results, it takes around 6 months to get your results, so you have to be patient.

 I think the Nebula 100X is too expensive, and has no clear advantage over the 30X, in my opinion.
There are other good companies that do 30X WGS, like Dante, sequencing.com, and others - just compare price.  But some companies are still offering high prices from 2 years ago... for example, Veritas asks $599 for a 10X WGS and does not seem to offer a 30X ( it would be well over $1000, considering their 10X price).
I do not care about ancestry either, but Nebula gives you data on that anyway.  If I want to dig this one day, I will have it.

As a final note, having your genome data is one thing, and finding in it what is relevant and how to use it for improving your health is another thing.  You can use the standard reports to get basic information and run panels about well-known SNPs, but you will also have to learn about the sites, tools and databases needed to dig into your DNA, once you have done the obvious with the current reports, and want to know more.  However, if you want to know about your methylation and detox status, and your main SNPs, you will get all that, free of charge, at https://geneticgenie.org/.  They have one general report, and a methylation panel, and a detox panel.   And, in the future, they will add more free reports.  You also have many apps you can run on your data, at sequencing.com.  Some are free, others you must pay to run them.  I particularly liked the Silverberry Vitamins report, at only $9.99, giving you info on what vitamins you may need supplements for.

I hope all this information will help you in your decision.

« Last Edit: October 21, 2021, 08:55:34 AM by Quantum »
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poisfighter

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Re: What's the best dna test, which one should I get?
« Reply #62 on: October 22, 2021, 01:37:58 AM »
I don't care about ancestry, all I wanna know is what mutations or snps are causing me trouble.
I know I suffer from undermethylation if I don't supplement, high blood histamine and food intolerances, which kind of test would be most scientific and comprehensive in my case?

Hi poisfighter,

The companies making tests for ancestry only sequence about 1% of your genome.  So if you do it for health, it is better to get 100% of your genome, a Whole Genome Sequencing ( WGS).  WGS are getting a lot cheaper now, almost the same price as the ancestry sequencing.  Of course, genomics is a new science, and we do not have the knowledge yet to interpret all the SNPs found in a WGS, but each month, new information is out in research articles

I went with Nebula Genomics, with the Whole Genome Sequencing, 30x  ( The one called Deep).  The 30x means that, on average, each position in your genome will be tested 30 times.  But in an actual sequencing, the number of valid data for each single position varies. In my data, some positions have only like 14 tests done, others can have 34 results.  Those tests are not perfect, that it why you need many results for each location. So, let's say you have 98% results giving a G (a guanine base) in a certain position, you can be sure that it is a G there, and it is homozygous (two identical bases).  If you have G and C at 57% and 43% on a position, you know that you are heterozygous G/C there.
 
This 30X sequencing is currently at $299 at Nebula.  I wouldn't choose their basic sequencing, at $99, because it is only 10X testing for each location... so let's say you get only 4 results for a specific position, and it is 3 G and 1 C... hard to say what is your real result there, and if you have an SNP or not, and if it is homozygous or heterozygous.
 The good thing about a whole-genome sequencing is that you have all your genome data, once and for all, and will not need another testing later down the road.  I also took the lifetime access to Nebula's library, so I get info about new genomic research, but it is not essential - one can do the search himself.  There are also more and more websites where you can upload your data for analysis ( just have to be careful and read their privacy policy before uploading your data)

Nebula is, I think, the cheaper 30X WGS on the market, currently, at 299$.  However, even if they say it takes 8 weeks to get your results, it takes around 6 months to get your results, so you have to be patient.

 I think the Nebula 100X is too expensive, and has no clear advantage over the 30X, in my opinion.
There are other good companies that do 30X WGS, like Dante, sequencing.com, and others - just compare price.  But some companies are still offering high prices from 2 years ago... for example, Veritas asks $599 for a 10X WGS and does not seem to offer a 30X ( it would be well over $1000, considering their 10X price).
I do not care about ancestry either, but Nebula gives you data on that anyway.  If I want to dig this one day, I will have it.

As a final note, having your genome data is one thing, and finding in it what is relevant and how to use it for improving your health is another thing.  You can use the standard reports to get basic information and run panels about well-known SNPs, but you will also have to learn about the sites, tools and databases needed to dig into your DNA, once you have done the obvious with the current reports, and want to know more.  However, if you want to know about your methylation and detox status, and your main SNPs, you will get all that, free of charge, at https://geneticgenie.org/.  They have one general report, and a methylation panel, and a detox panel.   And, in the future, they will add more free reports.  You also have many apps you can run on your data, at sequencing.com.  Some are free, others you must pay to run them.  I particularly liked the Silverberry Vitamins report, at only $9.99, giving you info on what vitamins you may need supplements for.

I hope all this information will help you in your decision.

Thanks so much Quantum,

that really narrowed down the decision for me. I'm considering going with sequencing.com, while it's a little more expensive than nebula at $399, the results are supposedly there in 4 weeks, or is that an empty promise yet again? Because waiting 6 months is quite a long time.

poisfighter

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Re: Genetic profile results
« Reply #63 on: October 22, 2021, 01:48:25 AM »
Nevermind just read that the whole genome sequencing results from sequencing.com take around 10-12 weeks to arrive, gonna go with sequencing.com then

Quantum

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Re: Genetic profile results
« Reply #64 on: October 22, 2021, 11:24:46 AM »
Nevermind just read that the whole genome sequencing results from sequencing.com take around 10-12 weeks to arrive, gonna go with sequencing.com then
Sounds good.  Just make sure that you can download your results from sequencing.com, and in a format that is accepted by other dna websites.  Useful formats are CRAM, and VCF, among others.   
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Quantum

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Re: Genetic profile results
« Reply #65 on: November 22, 2021, 12:58:17 PM »
Here is some information for those who have received their genome sequencing results, have run some basic panels, like the free ones at geneticgenie.org, and do not know how to interpret all those results.  These results could look a little bit scary if you don't know how to read the reports and are not familiar with genomics.

What those results give is only a predisposition to developing a problem.  So, the nature vs nurture question, or if you prefer, your genetics vs your environments and life habits, still remains, whatever your genomics results are, for almost any condition.  There are a few conditions, like pernicious anemia or cystic fibrosis, that are called Mendelian diseases, because they are linked to one single gene.  So if you have this one single gene defect, which is often in males and on the Y chromosome, so that you have only one copy of this gene, then you have the disease.   But for diseases and health issues in general, there are complex interactions between the 25 000 genes we have.  You may have a gene that is frequently found in people who have a specific health issue, but you may also have another gene elsewhere that prevents this disease from manifesting.  You may also have life habits preventing a disease to occur, despite you having a genetic predisposition for it.

So, you will find in your genes hundreds of mutations, but those SNPs are only probabilities.  The science of genomics is not advanced enough to interpret the overall probabilities, considering all of your other genes.  You have to check the clinical manifestations and exam results, to see if you really have the disease.  For example, if you see you have a predisposition for a type of cancer, remember that we all have a certain chance of developing cancer, considering all the pollution, stress, and bad food there are in today's world.  But no reason to worry if you have no sign of any cancer, and your annual blood tests are ok.  Cancer is only a probability, not a certainty, even if you have some homozygous SNPs that is often found in people having a particular type of cancer or rare genetic disease or else. 

I have tons of bad mutations in my genes, giving me some probability of developing various diseases.  I surely do not have all those diseases!  I have so many SNPs linked to syndromes that cause many severe birth defects and mental retardation in those having the syndrome... but, I never had any intellectual problems, and I am otherwise quite "normal" if this means anything at all... those SNPs did not translate into a real, manifested syndrome, for me.  I have other genes that prevailed.  Genomics is complex, and we are just beginning to dig this fascinating aspect of biology and health.

So, here is how to better interpret sequencing results:

- First, work with the diagnosis you already have, from doctors ( known diseases).  You can go backward and find in your genome what SNPs predisposed you to these. For example, in my case, I do not see colors very well, in particular, red, so no surprise that my OPN1LW gene has many, many SNPs in it, and a few are known for being pathological. This gene is in very bad shape, compared to my average genes. ( to do such a search, you can search by "phenotypes", hence by disease, in https://gene.iobio.io/ , so you can usually find the genes causing your known diseases... the more specific you are, the narrower results you get... If I had written "color blindness", it is too large and would have received too many results...by writing "protanomaly", my specific type of color blindness, then I get more accurate results, and fewer genes to check.   Maybe, one day, in many years, there will be "POIS" listed in this app, and look for what SNPs are predisposing you to POIS.... ! )

- If you have symptoms and bad exam results not accounted for by your known diagnostics, go backward and seek what SNPs could be responsible for those symptoms, associating these to your symptoms ( but that is a lot of work, and no guarantee you will find anything significant, and you will still have to get confirmation with clinical exams)

- For all the other results showing probabilities of a particular disease, that you see in your reports (like the free reports available at geneticgenie.org), but that you have no symptoms for, just put them aside, mostly.  Just take a look at the most pathological ones, and that has a low frequency in the general population.  Then, if you someday develop a weird and unexplained symptom, you may come back to your genome results and possibly get an edge in identifying your disease ( with the help of your doctor, for sure.... genomics is not the same as a medical diagnosis)

- In addition to that, a simple search for how you absorb and manage the main vitamins could help you personalize your daily supplements.  If you know you have a problem with absorbing or using a specific vitamin, then you can optimize your health by supplementing with this vitamin.  You can do all the search by yourself, or run a test panel like https://sequencing.com/vitamin-balance-dna-report ( quite cheap, and then you dig the results and see what is really of interest, by checking all the SNPs mentioned in your report).  You can also run other reports as well, at least, the free ones, and some not so expensive. You can learn about what exercises are best for you, what food, and so on.  After some reports, you will get an idea of what kind of information it can bring you. Personally, I did not invest a lot in those reports, I prefer to dig myself - there are a lot of free websites providing free resources - SNPedia, ClinVar, geneticgenie.org, Malacards, sequencing.com, and so many others, and of course the site of the lab from which you had your genome sequenced.  But if this sounds overwhelming, paid reports are an alternative.

At any rate, if browsing your genomic results causes you too much anxiety, you should pay for the help of a professional, to help you look at them with more perspective, and in a more appropriate way.  You will then get a sound interpretation, according to what is known so far.








« Last Edit: November 22, 2021, 01:03:32 PM by Quantum »
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swell

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Re: Genetic profile results
« Reply #66 on: February 18, 2022, 03:42:32 PM »
Hi Quantum,  I find your posts insightful, though I really very skeptic about all the genetics information that exists around us, starting from Nebula itself as well other tools.  I have had my genome sequenced a full year ago, as well the microbiome.  I do believe the underlying data is a GOLDMINE, and "IF" used correctly it is infinitely precious.  And maybe I am the odd person out, and admittingly I am a noob in these tool usage, but I see SO MANY basic errors around the "application" of this precious science, heaps of wrong conclusions formed based on wrong assumptions to the extend that it: a) it impedes my own knowledge expansion effort, and b) it just disillusions me that so much lack of understanding prevails around us. 

Just a random fundamental example
Nebula quotes in one of their free reports (Alzheimers), I have snip: Gene: TREM2, rs187370608(GG).  fyi: this snip is not important 99% people have, I am only illustrating it as an example.  Now, when I go to: gene.iobio (Nebula provided tool), it shows that for gene TREM2 I have no SNPs at all.  I find Sequencing.com is even a bigger joke, they actually have a free tool that "supposedly" (as they claim) parses through your raw files and displays your genome data in excel format.  But they are total nuisance, picking up data god knows from where and displaying it to you :).  I find big gaping discrepencies from tool to tool.  I mean, when so basic data mismatches exists between various tools, it actually dissuades masses from putting trust in the science itself (which itself is immensely powerful).

Provided we look at this data correctly, genetics can inform us enormously.  These genes are like the software code 'modules', while they may or may not be activated, however if we have the right tools, and looking at our genome correctly, we can actually ascertain a lot of our epigenetics as well, which genes are up-regulated or down-regulated, which snip is protective vs which is damaging, etc.

Sorry for all this rant, the other day I was using gene.iobio (I like using that tool) but then I get a pop up message something like 'sample demo data is not available'.  Seeing that message bothered me :) god knows if Nebula is giving us this cloud based tool to browse our genome, while one stup$d mistake somewhere in the value chain has that tool tied to some demo data (instead of our personal genome), and here I am spending countless hours thinking this has been my personal data.  I do admit, maybe I am using these tools incorrectly, but what if I am using them correctly :)
 
Here is some information for those who have received their genome sequencing results
« Last Edit: February 18, 2022, 04:10:24 PM by swell »
POIS Free, 1+ yrs (daily O's with occasional lapses)
Pois symptoms: Peripheral (Skin: Urticaria, dryness, pale blotchy skin), Exasperation of: [Nerve weakness, Muscle weakness + Mental (CNS: Brain Fog, Irritation, Isolation, Speech lethargy, Anxiety)].
Other conditions: ASD, ADD, GA

Quantum

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Re: Genetic profile results
« Reply #67 on: February 18, 2022, 06:17:27 PM »
Hi swell, 

Genomics is a fairly new science, it will take many years and decades before information will come in a clear and readily usable form.
Until then, we have to dig the data and spend hours to find clues and interesting leads.  It is like searching for a needle in a haystack.
Some general and basic information, like vitamins absorption specifics, can help in the short term, though, by helping to adjust and customize nutrition and supplements for ourself.

You are 100% responsible for what you do with anything I post on this forum and of any consequence it could have for you.  Forum rule: ""Do not use POISCenter as a substitute for, or to give, medical advice" Read the remaining part at http://poiscenter.com/forums/index.php?topic=1.msg10259#msg10259

swell

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Re: Genetic profile results
« Reply #68 on: February 19, 2022, 12:37:51 PM »
Quantum that is my concern that even the very basic information like nutrients and vitamins may be ALL incorrect.  Incorrect inputs fed into a superb process otherwise has totally incorrect outputs.  I actually view 'finding needle in a haystack' concept an asset, that is where I as an atypical intrinsically shine, but I do not believe that is what we are doing with these broken tools.  I feel so mad, since this raw data we have could be so powerful (at least in my case) however I feel let down by these glaring idiotic   mistakes that pervade around the application of this otherwise powerful science. 

I am really mad, being a passionate person in things I set out to learn, sitting on top of this fascinating data I have, and yet not able to do much because of these idiotic tools.  And its not our WGS only, my microbiome (through Psomagen) has the same story.  I have a very peculiar microbiome (could inform me so much), and yet the tools are awry.  One says: I have  one keystone specie 'bifidobacterium longum', and then another while listing  the complete species list does not even list it. 

What really I think is happening is that Geneticists/Engineers that work in Labs or corporations, that have access to professional high-end tools, they are quietly reaping all the benefits of this precious science and through "our" data :), while we the consumers using these cheap or free services, are getting it totally wrong.  What I am saying is, I don't think what you are "viewing" through gene.iobio is your own data :) Nebula may have hooked everyone up to a "sample data", otherwise these basic mismatches of even these basic indexing fields, SNP Id etc should not exist.  I have written countless emails to all these providers, but they just do not respond.  And then sometimes I feel that maybe I am the crazy here?  how could there be so glaring errors everywhere around us.
POIS Free, 1+ yrs (daily O's with occasional lapses)
Pois symptoms: Peripheral (Skin: Urticaria, dryness, pale blotchy skin), Exasperation of: [Nerve weakness, Muscle weakness + Mental (CNS: Brain Fog, Irritation, Isolation, Speech lethargy, Anxiety)].
Other conditions: ASD, ADD, GA

swell

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Re: Genetic profile results
« Reply #69 on: March 12, 2022, 05:06:10 PM »
I am wondering, if there is a little simple tool, that lets one export the raw data into excel format.  I think the issue is that one excel file would not be able to handle the raw data, so perhaps if it can export it to multiple excel files? 

Our key goal is to create 'simplicity'.  Sequencing.com does have fantastic tool (if it worked) that presumably allows you to filter a single gene and simply showing all the snips (i.e. all records/rows of data).  Our raw files are actually pretty powerful, they tell a lot, even risk scoring I think.  This drives me insane, it is all so terribly simple!!!, and yet vested interests prevent us from reaping these benefits, leaving us at mercy of these fake tools that tell us what we want to hear (or they want us to hear), or maybe they are just incompetent, and all the while stealing our data.
POIS Free, 1+ yrs (daily O's with occasional lapses)
Pois symptoms: Peripheral (Skin: Urticaria, dryness, pale blotchy skin), Exasperation of: [Nerve weakness, Muscle weakness + Mental (CNS: Brain Fog, Irritation, Isolation, Speech lethargy, Anxiety)].
Other conditions: ASD, ADD, GA

Muon

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Re: Genetic profile results
« Reply #70 on: April 26, 2022, 12:47:44 PM »
« Last Edit: April 26, 2022, 01:16:05 PM by Muon »