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Direct to consumer whole exome and whole genome sequencing available

Discussion in 'Genetic Testing and SNPs' started by Waverunner, Nov 1, 2014.

  1. Waverunner

    Waverunner Senior Member

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    I've been complaining, that there is no direct to consumer whole exome sequencing (WES) or whole genome sequencing (WGS). Guess I was wrong. However, Gene by Gene is the only company, which currently offers WES and WGS. They don't analyse the results to avoid getting problems with the FDA.

    https://www.genebygene.com/

    Whole exome sequencing (coverage around 70) costs 1,300 USD, whole genome sequencing costs 7,400 USD.

    https://www.genebygene.com/pages/research

    This price is not very cheap because other companies go with 600 USD to 700 USD for WES and 100x coverage but these companies only sell to clinics or clinicians who will then add their mark-up.

    I'm thinking about ordering WES but I'm not sure at the moment.
     
    Last edited: Nov 1, 2014
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  2. Valentijn

    Valentijn WE ARE KINA

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    I've been thinking about it too. There's simply so many missense mutations, HLA data, etc, missing from 23andMe. Maybe if a bag of money falls out of an airplane and lands on my head :D
     
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  3. Sidereal

    Sidereal Senior Member

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    I'm sure the price will come down eventually. It's very annoying when you come across a SNP in the literature and then you check your 23andme and it's not tested. :aghhh:
     
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  4. Waverunner

    Waverunner Senior Member

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    Was a little disappointed by the price, too. When 23andMe had its WES pilot program in 2011, with 80x coverage and for $ 999, it was cheaper, had more coverage and they wanted to add analysis as time went by. So we actually moved a little backwards and the only reason for this is, that Gene by Gene is a monopolist in the direct to consumer market now. If there was just one other company, the prices would take a huge drop.

    https://www.23andme.com/exome/
     
    merylg likes this.
  5. Sea

    Sea Senior Member

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    @Waverunner can you explain the coverage please?

    Like you I've found much cheaper prices, but only available to researchers, and with a minimum required number of samples too. I keep hoping some researcher will take up the opportunity and want to sequence us.

    Any idea of the value of exome sequencing versus whole genome? I really want whole genome but I don't know if that's reasonable. If enough answers could be found with whole exome I'd find $1300 somehow.
     
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  6. Valentijn

    Valentijn WE ARE KINA

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    The exome is estimated to contain 85% of disease-causing mutations. So it's $1,300 for that 85% and another $6,100 for the extra 15% :p
     
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  7. Waverunner

    Waverunner Senior Member

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    Coverage is the number of times a base pair has been read independently. The more, the better and the more expensive.

    Valentijn made a good point. Your exome is only around 1% of your genome. If money does not play a role I would go for WGS, otherwise I would start with WES. WGS nearly always has worse coverage (around 30).

    The problem is, that the current sequencing market is not aimed at the consumer. It is aimed at researchers and doctors. Illumina said, that coverage will get better this and next year but prices will likely stay the same. I would only go for WGS if the price drops to 1k and coverage increases to 60 but everyone has to make his/her own decision.
     
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  8. Snow Leopard

    Snow Leopard Hibernating

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    Down from hundreds of millions to $1000? Looks like WGS will soon become common.
     
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  9. biancarose

    biancarose

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    Hello.

    Which one is the best for the diagnosis of an undiagnosed rare disease ?
    Thank you for your answer.
     
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  10. Sea

    Sea Senior Member

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    Maybe if enough of us let 23andme know that we want it they would listen. I remember reading that they have concentrated their efforts on the $99 test because they believe their consumer base to not be prepared to pay more
     
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  11. mille100piedi

    mille100piedi Guest

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    Dr Kendall suggested me to do this test, but it is so expensive :(
     
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  12. mille100piedi

    mille100piedi Guest

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    I finally did the WES test and a mutation has been found in my gene muscle. The gene is MYOM1 and it stabilizes the muscles during contraction. My mother has been unwell all her life and she has been found with the same mutation. Is there anyone else that had the WES test done and what was the result?
     
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  13. Valentijn

    Valentijn WE ARE KINA

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    @mille100piedi - Do you have the rs# or name (such as "MYOM1 S32L")?
     
  14. mille100piedi

    mille100piedi Guest

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    sorry I don't understand anything about genetic, it is too complicated. The variant is Il383N. Only three other families have been found with a variant in this gene and people with myotonic dystrophy type one. Since no healthy people have been found with mutation in the same gene it is likely causing muscle disorder. Geneticists still don't know much about the gene MYOM1. After seven years looking for a diagnosis this is not a definitive answer and it doesn't tell me more then what I already knew or guess, but at least I will spare my energy and not looking for a diagnosis anymore. It is awful being sick and don't know if you could get some sort of test that might help you to recover from you illness! Doctors don't really care and I had to do all by myself
     
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  15. Valentijn

    Valentijn WE ARE KINA

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    Pretty cool. It looks like the rs# is rs374491316. dbSNP doesn't list your particular mutation there, but it's the only position where an allele change can result in isoleucine (I) being replaced by asparagine (N) for that location in the protein being created.

    Your mutation might be a lot nastier than the more "common" mutation to threonine there (which has a 0.008% prevalence rate), since your new amino acid has extremely different behavior compared to the normal isoleucine that should be there. The more "common" threonine mutation, on the other hand, isn't nearly as dissimilar.
    Yeah, very little data. Though at least they know it's there, and know where some of the more important parts of it are on the gene.
    It's also nice for removing any doubt, and shutting down any quacky suggestions from people for curing your "fatigue". And could also be useful in proving biological disability if there's ever any problems in getting social welfare benefits.

    I'm guessing you're heterozygous for it? It sounds like problems on the gene are usually autosomal dominant, meaning only one naughty allele is needed. Which would explain why your mother has similar problems, as there's a 50% chance of passing it on to offspring.
     
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  16. Valentijn

    Valentijn WE ARE KINA

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    @mille100piedi - One other quick question. Is there any chance of getting tested to measure your actual levels of myomesin-1 and whatever it connects with other proteins to create?
     
  17. mille100piedi

    mille100piedi Guest

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    thanks for you reply, you sound an expert! What do you mean with my mutation being nasty?I know I will not get better and I always knew since I have symptoms since childhood, but I really really hope I don't get worse and if my disorder progress I hope it will progress very slowly like it is happening now.
    I didn't have any type of diagnosis before, they knew that there was something wrong with me, but they didn't know what could be.
    I am on invalidity pension since many years and was no problem to obtain it. I just hope with this genetic result I can get disability parking permit, it would be nice to be able to get out more!
    They don't know how I got the mutation, I was so surprise that they don't even know this!! my father died so they couldn't get sample from him but they analyze my sister'DNA sample. She is healthy and she didn't show any mutation. I have another sister, she is not healthy as well, but she doesn't want to do the test.
    Did you have genetic test?
     
  18. mille100piedi

    mille100piedi Guest

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    no idea, my geneticist didn't mention this, but I am going to hear from her soon because I am waiting for mtDNA test result as well. To be honest I don't want to spend any more money in testing. I really want to concentrate now in how to manage better my condition
     
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  19. Valentijn

    Valentijn WE ARE KINA

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    I'm not an expert at all, just interested in genetics. So I've done a lot of reading and took a couple classes on Coursera.

    Basically some amino acids (coded for by the exons on the gene) are very similar, and behave in very similar ways. When a missense mutation results in the new amino acid being very similar to the usual one, there typically isn't much impact. But if the usual amino acid is replaced by a very different one, the protein it's on might be weaker as a result, and break down too quickly to do its job effectively.

    BLOSUM62 charts rate those differences. Scores range from +3 to -4, with -4 being the most drastic possible change. The more common mutation to threonine at the location of your mutation scores a 0, so the new mutation isn't very similar, but it's also not a huge change. Your mutation to asparagine scores a -3, which represents a much bigger difference.

    But if the mutation at that location is a problem due to other proteins connecting there, it might not make a difference to have an asparagine mutation instead of the threonine mutation. In either case, the problems arising might be due to things not fitting together quite right, and the asparagine mutation might not have any more impact than threonine mutation.

    So it depends on what is happening at that particular part of the protein created by the gene. Your geneticist might know more about it, or it might be possible to figure out a bit more from uniprot.org or similar resources. The only thing I can see about it is that it's in a "domain" (section) of the protein from position 1358-1444 which is described as "Ig-like C2-type 4". But I have absolutely no idea what that mean :D
    Yeah, I let mine lapse, since I've mostly been too sick to get out much. Which makes it harder when I do need to go to the doctor.
    Just 23andMe so far. But I'm very interested in Whole Exome Sequencing, especially since prices are getting a lot cheaper.
     
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