Whole genome done - now what?

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I purchased a 130X+30X whole genome test from Dante Labs (130X for the exome, 30X for the rest of the genome) and downloaded the raw files. I've heard that there are softwares you can use to scan them for genes associated with rare illnesses and so on. I assume that, unlike ME/CFS, this kind of thing is being well funded and studied heavily so there must be a lot of good info out there. Can someone point me in the right direction?

Thanks
 
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Be prepared for this to be a long journey, requiring lots of learning and reading papers on your part if you really want to dig. Check and cross-check. Learn about MAF, CADD, ClinVar, dbSNP, alleles, chromosomes, gnomAD browser............

ME patient @kday developed free tool GenVue (formally genetic genie). Donations accepted
https://genvue.geneticgenie.org/

Other paid tools folks on PR have used
https://www.enlis.com/
https://livewello.com/genetics
https://promethease.com/
https://sequencing.com/tests/health

This paper compares third party tools
Third-Party Genetic Interpretation Tools: A Mixed-Methods Study of Consumer Motivation and Behavior
 

merylg

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I purchased a 130X+30X whole genome test from Dante Labs (130X for the exome, 30X for the rest of the genome) and downloaded the raw files. I've heard that there are softwares you can use to scan them for genes associated with rare illnesses and so on. I assume that, unlike ME/CFS, this kind of thing is being well funded and studied heavily so there must be a lot of good info out there. Can someone point me in the right direction?

Thanks
https://www.enlis.com/ and https://sequencing.com/tests/health

I also purchased most of the panels Dante offered at reasonable cost. At times they had special offers.
 

mitoMAN

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Trust me.. I tried this ellie84. You wont find anyone offering this kind of service for externally made WGS or WES.

I did the WGS by Dantelabs and they now offer genetic counseling which i can fully recommend. I just had my skype consulting last week. You will need to purchase the Dante Reports however.

I have a medical WES from the hospital that my insurance covers. But usually this costs about 10k+. Because the real hard task is to evaluate the data especially for mutations and variants that are not yet listed on clinvar. Dante reports will ofc only list reports already made on ClinVar.
 

BeADocToGoTo1

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Is it really worth the time, effort and money? Are these genetics tests or epigenetics tests? It can be theoretically interesting, but are there any actionable steps that can come from knowing whether a flag is set a certain way, i.e. would it be any different?
 
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Trust me.. I tried this ellie84. You wont find anyone offering this kind of service for externally made WGS or WES.

I did the WGS by Dantelabs and they now offer genetic counseling which i can fully recommend. I just had my skype consulting last week. You will need to purchase the Dante Reports however.

I have a medical WES from the hospital that my insurance covers. But usually this costs about 10k+. Because the real hard task is to evaluate the data especially for mutations and variants that are not yet listed on clinvar. Dante reports will ofc only list reports already made on ClinVar.
Do they also offer non-skype consultation ? Can you explain a bit more what they did etc?
Are these real geneticists? And what about tests that you already did years ago, are they okay too?
 

mitoMAN

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@BeADocToGoTo1 it was very worth it to me, as I have questionalbe mitochondrial Variants that are now under new investigation in the local hospital with their own WES.

@hopeforaday22
They offer different platforms, maybe even phone. My appointment was with a researcher from an university in rome that has also publicated his own studies already. A very smart guy that was very helpful.
They outsource their consulting to real geneticists with research background. I guess, "in collaboration", they also share genetic information needed for their research ; ))))

They will only look at your DANTE data. No other data! And also only at Dante REPORTS based on clinVAR finds.
 

BeADocToGoTo1

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@BeADocToGoTo1 it was very worth it to me, as I have questionalbe mitochondrial Variants that are now under new investigation in the local hospital with their own WES..
Hopefully they will be able to provide you with some concrete help!

I am very curious what you find out in terms of epigenetic (as I am assuming that is what they are testing) settings and recommended actions (medicines, supplements, dietary changes, etc.).

Do they dive into the metabolic pathways that can be impacted by your personal epigenic settings and provide actions based on those?
 
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@BeADocToGoTo1 it was very worth it to me, as I have questionalbe mitochondrial Variants that are now under new investigation in the local hospital with their own WES.

@hopeforaday22
They offer different platforms, maybe even phone. My appointment was with a researcher from an university in rome that has also publicated his own studies already. A very smart guy that was very helpful.
They outsource their consulting to real geneticists with research background. I guess, "in collaboration", they also share genetic information needed for their research ; ))))

They will only look at your DANTE data. No other data! And also only at Dante REPORTS based on clinVAR finds.

They share genetic information? Not sure if that is good but... I mean, the patients have to be okay with it obviously and I hope they are informed of this...

And what were these questionable mitochondrial variants? They showed up in your Dante Labs Exome results?

Thank you.
 

wigglethemouse

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I've emailed the creator of Enlis via the website and elsewhere and received no response. The program is 5 years old and from reading the website if you have vcf data from WES or WGS it only recognizes hg19 (GRCh37) format and not the newer hg38 (GRCh38) format.
 
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I've emailed the creator of Enlis via the website and elsewhere and received no response. The program is 5 years old and from reading the website if you have vcf data from WES or WGS it only recognizes hg19 (GRCh37) format and not the newer hg38 (GRCh38) format.
Is it bad that the program is 5 years old?

So it's basically useless if it doesn't recognize the newer hg38? I really need to figure out this stuff
 

gbells

Improved ME from 2 to 6
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I purchased a 130X+30X whole genome test from Dante Labs (130X for the exome, 30X for the rest of the genome) and downloaded the raw files. I've heard that there are softwares you can use to scan them for genes associated with rare illnesses and so on. I assume that, unlike ME/CFS, this kind of thing is being well funded and studied heavily so there must be a lot of good info out there. Can someone point me in the right direction?

Thanks
Dant's website says you have to request the Rare Disease Report for them to generate it.

I have no idea how this could be helpful for ME except to modify nutrition to help digestion and metabolism a bit.

https://us.dantelabs.com/collection...products/whole-genomez?variant=31578560397378
 

Arius

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I'm confused - you went to a HOSPITAL, and they are HELPING YOU? What country do you live in? What hospital is this?

I live on land stolen and occupied by the government of Canada, and I can't even find one doctor who knows what CFS/ME is. And when I went to the hospital they told me they only treat acute illnesses and to go to a doctor.
 

Alvin2

The good news is patients don't die the bad news..
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I'm confused - you went to a HOSPITAL, and they are HELPING YOU? What country do you live in? What hospital is this?

I live on land stolen and occupied by the government of Canada, and I can't even find one doctor who knows what CFS/ME is. And when I went to the hospital they told me they only treat acute illnesses and to go to a doctor.
Several forum members are Canadian and i have seen several doctors who know what ME is, one even diagnosed me.
They lack effective treatments of course, but that is not exclusive to Canada.

My GP is a relatively recent medical school graduate and knows ME (perhaps not as well as i do but has never tried to sell me junk CBT/GET). I did have an immunologist tell me i have fibromyalgia and claim GET is the only treatment with any effectiveness...
 

Learner1

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Is it really worth the time, effort and money? Are these genetics tests or epigenetics tests? It can be theoretically interesting, but are there any actionable steps that can come from knowing whether a flag is set a certain way, i.e. would it be any different?
Yes, there absolutely is. My testing showed SNPs for celiac disease, confirming the need for a gluten free diet, Prothrombin for hypercoagulation for which anticoagulation drugs can be prescribed, and hemochromatosis for which phlebotomies or iron chelators can be prescribed. And a number of others, including those increasing need for vitamins D, B12, and folate.
Dant's website says you have to request the Rare Disease Report for them to generate it.

I have no idea how this could be helpful for ME except to modify nutrition to help digestion and metabolism a bit.

https://us.dantelabs.com/collection...products/whole-genomez?variant=31578560397378
Some people may find they don't have any/cfs at all, but may have some rare genetic disease creating symptoms. For others, as you mention, they might show an increased need for a particular nutrient or celiac disease.
I'm confused - you went to a HOSPITAL, and they are HELPING YOU? What country do you live in? What hospital is this?

I live on land stolen and occupied by the government of Canada, and I can't even find one doctor who knows what CFS/ME is. And when I went to the hospital they told me they only treat acute illnesses and to go to a doctor.
Sometimes the best strategy is to not lead with an ME/CFS diagnosis, which leads to no treatment, as there's no standard of care for ME/CFS. Amazingly, many of us have very treatable other problems, like chronic Epstein-Barr, celiac disease, thyroid disease, adrenal insufficiency, immunodeficiency, and autoimmunity. Going in with symptoms, and asking for help might be a better strategy, and typically hospitals are not where one finds help. However, hospitals are typically where one finds geneticists, who can determine if one has a mitochondrial disease, or a great number of other bridge genetic diseases.