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Doing a Whole Genome Sequencing (WGS)

Discussion in 'Genetic Testing and SNPs' started by jamienoble, Nov 12, 2015.

  1. parpar

    parpar

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    hi , im doing genome analysis and comparing data of different people with CFS if you would like to share your results let me know
     
  2. Snoozy

    Snoozy

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    Sure, that won't be a problem at all. I expect my results in a couple of months or so (the wait time is 10 weeks for a WGS). I will say that I will (eventually) be referred for an evaluation of my sleep though - so I'm still not entirely sure whether I have CFS or not. It will be interesting to see whether my data correlates with others.
     
    pattismith likes this.
  3. aquariusgirl

    aquariusgirl Senior Member

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    @parpar any update on this? any guidance on the best service so far?
     
  4. parpar

    parpar

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    until now no one has sent me anything . i used BGI to do my exome sequencing since they give 100X coverage
     
  5. shoponl

    shoponl

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    Dante Labs now has WGS at 30x coverage for $499. Exome is $399. https://us.dantelabs.com/collections/our-tests

    Great price! But... if I'm reading this (https://us.dantelabs.com/pages/privacy-policy) correctly, pharmaceutical companies can buy "non-identifying" genetic information from Dante without my consent. My concern is that "non-identifying" information today may become "identifying" tomorrow, with technological improvements. Does this matter? And is the sale of data normal in the industry? I'm not sure.

    Thoughts? I'm tempted but hesitant.

    *edited to add:

    Here's a quote from their privacy policy. I'm okay with aggregated data being shared, but "anonymous information" has me wondering. Also the privacy policy is poorly organized; there is no section labeled 4.d.

    "What happens if you do NOT consent to Dante Labs Research?
    1. If you do not complete a Consent Document or any additional consent agreement with Dante Labs, your information will not be used for Dante Labs Research. However, your Genetic Information and Self-Reported Information may still be used by us and shared with our third-party service providers to provide and improve our Services (as described in Section 4.a), and shared as Aggregate or Anonymous Information that does not reasonably identify you as an individual (as described in Section 4.d)."
     
    Last edited: Mar 29, 2018
  6. nanonug

    nanonug Senior Member

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    That is indeed a very tempting price. However, the potential "leak" of personal information is off-putting...
     
  7. shoponl

    shoponl

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    http://www.prnewswire.co.uk/news-re...ta-driven-rare-disease-program-676636293.html
    "Meanwhile, Dante Labs has strengthened its security and privacy capabilities in advance of the European GDPR in May. In addition to its US-EU Privacy Shield Certification, Dante Labs has received the Cyber Essentials Certification, which is necessary to become a service provider to the British National Health System. "Privacy and security are paramount to us," stated Riposati. "All our samples are anonymous. Data, DNA, reports and samples have no personal identification information, not even the country of origin. Our first patent application was about a proprietary cyber security system."

    So-- maybe privacy won't be an issue after all.

    Has anyone here tested with them, and received their results?
     
  8. alicec

    alicec Senior Member

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    Genos, which I have used and received results from, gives 125 X coverage for $499. Results are provided in VCF format or a Promethease compatible version can be obtained.
     
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  9. nanonug

    nanonug Senior Member

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    It's not whole genome sequencing, though, is it?
     
    shoponl likes this.
  10. Ravn

    Ravn Senior Member

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    Have you received your results?
    And do you know if you can get the data in a format that you can use in Promethease or Enlis or similar?
     
  11. robinhood12345

    robinhood12345 Senior Member

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    So did you end up having a genetic disease? I just ordered a kit from dante labs, and look forward to getting the results from that as I assume I have a genetic disease also.
     
  12. Paralee

    Paralee Senior Member

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    Any news? I'm trying to figure out if I could even understand one of these reports after putting out that money.
    Maybe I should just get blood work instead.
     
  13. Snoozy

    Snoozy

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    Sorry for such a late response, guys - the results took a few months to come back and then I had other stuff going on.

    Yes, you can use the raw data with Promethease (gVCF or VCF files). Not sure about Enlis as I haven't tried my results with that yet, but I'm sure you could. :)

    I don't have a genetic disease or anything that leaps out, so to speak. I did find something interesting, though: I have hypothyroidism (autoimmune, like most cases) and take levothyroxine for it. Levothyroxine is T4, a storage hormone that the body needs to convert to the active T3 in order to be usable.

    I have a polymorphism of the DIO2 gene, which is an enzyme which converts T4 to T3, very much so in the brain. Based on the (small amount of) research done, it is possible to have a hypothyroid brain with normal blood lab results. Therefore, what I've done (and I don't recommend anyone else do this), is to buy natural dessicated thyroid and to dose myself at my current T4 equivalent. And I have been doing much better - as in getting up early and spending the whole day being active. I actually haven't felt this good in years.

    I've also got a polymorphism relating to folate metabolism so have upped my dosage of that a bit. Mine was a bit on the low side last time I got tested.

    At some point, when I have the money, I'll get the natural thyroid prescribed by one of the handful of doctors in the UK who even know about and/or are willing to officially switch my medication. Ultimately, I do think I've hit upon something here for myself.

    For anyone else doing this, I hope you find some clues. x
     
    Lalia, happy, Paralee and 2 others like this.
  14. Paralee

    Paralee Senior Member

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    @Snoozy , I read your post and pulled up my DIO2 gene and I think I have the same one you do, mine is hetero, but that could still make a difference. I've always suspected my thyroid, it's completely atrophied now, so I've got to figure out what's going on up there, you know? I'm wondering if this could be a dementia thing for some people.
     
  15. shoponl

    shoponl

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    DIO1 and DIO2 variations are common, so while they could be a factor, they're also not an immediate cause for alarm.

    I also have DIO2 variations, developed Graves disease, had a thyroidectomy, and now take natural dessicated thyroid. For anyone who needs thyroid supplementation, I agree, NDT is the way to go.

    Taking NDT when one is already euthyroid (usually TSH < 3, mid-range free T4 and T3) will improve mood and energy, but can lead to other problems such as insomnia, anxiety, cardiac arrhythmias, and osteoporosis.

    Selenium, iodine, and zinc can boost thyroid levels, so mineral supplements might be something to try.
     
    Last edited: Jul 3, 2018
  16. Snoozy

    Snoozy

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    Mine is also only hetero. :) But NDT has made a genuine difference to me. As shoponl says above, they're not rare mutations, but I suspect poor central (brain) conversion perhaps leads to a central kind of fatigue in my case. There could be more research into the topic. My mother is also hypothyroid and feels better on NDT, although she doesn't have the fatigue problems I do, and I likely got my bad copy from her, so there's more to it than DIO2 in my case. I do know I don't need to take Concerta (timed release Ritalin) for Inattentive ADHD on NDT because I don't need the extra stimulation, and that's big for me - I feel constantly hypoactive and sluggish without any medication.

    I'm hoping that precision medicine will eventually lead to the use of combination therapy in hypothyroid patients with genetic conversion issues. But that'll probably be some time coming, as from what I can tell, the NHS doesn't test for DIO2 and patients already on T3 are struggling to stay on it. The UK manufacturer of T3 has a monopoly on it, and charges extortionate prices. I only rate my chances of getting T3/NDT privately.

    I'm really curious as to how many CFSers have thyroid issues
     
    Last edited: Jul 3, 2018
  17. Paralee

    Paralee Senior Member

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    @Snoozy , ,I was on NDT, but developed a neurofibroma in my neck and read some articles on how hormones can make it worse, so I switched to the synthetic T4 and T3. Watching my levels, still working on it. I think I'll do some more "shopping" in the DIO2 gene. Thanks for your post.
    I'm fatigued a lot, but my cortisol is low....but I was fatigued off and on before that, so I can understand your conundrum....living it, actually.
     
  18. happy

    happy

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    Just letting you know that Dante Labs has a sale (until end of July 17 2018) on both WGS and WES. I just ordered WGS at 30X for 299 EUR :)

    Link: https://www.dantelabs.com/
     
  19. Moof

    Moof Senior Member

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    A relative in the US did a WGS at the beginning of the year, but she was also concerned about her data getting into the wrong hands. She paid using a prepaid credit card in a made-up name, and gave the address as her workplace. You apparently don't need a credit check or a bank account to set one of these cards up, so it might be an option if you're trying to create some distance between your genetic data and your real identity?
     
  20. Lalia

    Lalia

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    Hi there, thanks for this thread, some very useful information and I'm looking into Dante and Genos. I'm new to genetic testing so apologies in advance if these are silly questions.

    Could someone clarify the value in doing a WGS through one of these companies versus getting the raw data from Ancestry.com? Do you just get more data through a WGS?

    I'm working with a geneticist in Australia who will interpret the data for me (Denise Furness). She has recommended Ancestry as the most cost-effective option, but there are some specific genes I'm interested in (listed below) that I'm not sure they'll cover. Is there a way to find out which genes are covered by Ancestry? I've tried their customer service and they were zero help.

    The genes I'm interested in relate to immunodeficiency: FOX P3, TTC37, MYO5B, CRBA, STAT-1GOF, STAT-3GOF, HCTLA4, TTC7A, RAG ½, CD25, DOCK8, STAT5B. Mitochondria: DHTICD1, OGDHL and MCAS: TPSAB1.

    Any insights much appreciated, just tagging @alicec and @Valentijn as I know you both have a lot of knowledge on genetics.

    Thank you
     
    Mel9 likes this.

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