Author Topic: Genetic profile results  (Read 8643 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 »
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