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Doing a Whole Genome Sequencing (WGS)

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

  1. jamienoble

    jamienoble

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    For several years i have suspected that i might have a disease i was born with so i have decided to do a WGS.
    I don't know what type of disease i could have so perhaps its a small chance to find anything concrete but at least i will have the data and then i will have to do several different analysis i guess.

    On monday i will order mine from here: https://www.scienceexchange.com/labs/clinical-microarray-core-ucla
    It will cost $3500 with data analysis

    I hope i can order this myself and then i will get help here in Sweden to do a bloodtest and send it to them.

    Anyone else who has done a WGS test? Anyone who recommends another lab perhaps?
    The problem for me is that i don't know what analysis i should do, the one i will get from this lab wont probably be enough.
     
    merylg likes this.
  2. imdcout

    imdcout

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  3. Sea

    Sea Senior Member

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    I tried to join up as a PGP volunteer a year or so ago but sadly they weren't accepting volunteers from Australia. I got an email that said I would be kept informed but I've never heard from them again :(
     
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  4. jamienoble

    jamienoble

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    Thanks, i tried to sign up as well but i think you have to live in America to do this. : (
     
  5. Waverunner

    Waverunner Senior Member

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    The only company I know which offers whole genome sequencing (WGS) and whole exome sequencing (WES) direct to consumers is Gene by Gene:

    https://www.genebygene.com/

    Their prices are expensive however (1,300 USD for WES and around 10,000 USD for WGS).
     
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  6. Snow Leopard

    Snow Leopard Hibernating

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    I am definitely interested in this, though so far it seems access is limited / and it is still a bit pricey (I'd pay $1000, but not $3500)
     
    Valentijn likes this.
  7. Waverunner

    Waverunner Senior Member

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    What are you interested in? As far as I know the scienceexchange offers apply to researchers and clinical practice only (at least the offers from the US).
     
  8. Snow Leopard

    Snow Leopard Hibernating

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    WGS. It is only a matter of time until it is affordable/common.
     
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  9. jamienoble

    jamienoble

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    You can do this test as long as you have a researcher on board which i don't have atm..
    Everyone i have talked don't think this will help me because i don't know what type of disease im looking for, so im not sure if i will do this (or WES). It feels kinda hopeless..

    What can i do with the data myself? What should i look for?
     
  10. Luca_Toni

    Luca_Toni

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    Haven't you heard about Helix? It's a company associated with Illumina and rumors are that it'll offer WES+ for 500$. The main idea behind Helix is to engage general public in DNA sequencing business. Also as far as I understand they are going to create kind of app store for genomics. Interesting blog post about all this.
     
  11. jamienoble

    jamienoble

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    What do you think about this genetic test? http://www.illumina....Ins_1111314.pdf

    "TruGenome Undiagnosed Disease Test is a medical test intended to aid in the diagnosis of inherited diseases of single-gene etiology."

    So if i don't have an "inherited diseases of single-gene etiology" this test would be useless to me?
     
    Last edited: Nov 26, 2015
  12. Luca_Toni

    Luca_Toni

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    I think they mean that because of poor understanding of multi-gene disorders right now they can offer only single-gene diseases diagnosis. Practically it means that there is no better test than of this kind. By the way it's expensive test. It costs 9500$.
     
  13. Valentijn

    Valentijn Senior Member

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    That would just be "genetic diseases". The research saying that multiple SNPs on different genes contribute toward the mildly elevated risk of the same disease isn't going to be useful.
     
  14. Waverunner

    Waverunner Senior Member

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    Thank you for the hint on helix.com. The problem with analysis is that it has to be done by pateints in most cases, unless you have a special doctor in place. For the latter case, costs will increase significantly. However, as we progress, analysis should become more and more easy e.g. should be done by automated software. Unfortunately, healthcare is one of the most regulated fields you can find so it takes often decades before findings get transformed into clinical practice.

    I'm thinking about ordering WES. Would anyone of you be interested to help each other analyzing the results?
     
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  15. Valentijn

    Valentijn Senior Member

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    I certainly would. And it's not too hard to automate some aspects of analysis - basically known pathogenic mutations can be automatically flagged, as could all missense/nonsense mutations not known to be benign.

    The problem is that the existing dbSNP databases contain some duplications and errors. It's a very small percentage, but over the entire exome it would really add up. Just from 23andMe V3+V4 chips data (approximately 1 million SNPs) there's 2000 such irregularities that have to be sorted out manually. With 30 million SNPs in the human exome, that might result in around 60,000 nasty bits to sort out.

    Due to how long it's taking me to get through the 2,000, I think I'm going to do a http://sourceforge.net/projects/analyzemygenes/ update omitting those, then do a new update to add them in after sorting them out. A similar approach would be extremely simple for WES or even WGS. We have the databases in place, and could probably get the program tweaked to handle the extra data in a week or two.

    ETA: Part of what we need to know is how the WES or WGS data is presented. rs numbers? Chromosome positions? A long list without clear location identities for each SNP? How are deletions and insertions handled?
     
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  16. Waverunner

    Waverunner Senior Member

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    Thank you. I'm a complete layman. I would go for Gene by Gene but I also applied for two other personal genome projects. I think the chances to be accepted are low for the latter projects, however. Gene by Gene provides BAM, VCF and Annotated VCF. I don't know if that answers your question.
     
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  17. Valentijn

    Valentijn Senior Member

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    Okay, VCF (Variant Call Format) looks like it would basically include the same info seen in 23andMe (though not as a .txt file), with RS number when available, chromosome number, chromosome position, and the patient alleles. And possibly more data. But that should be enough to match up with most missense mutations and similar.

    It does sound like there are some special cases (duplications, etc?) which are not standardized yet in VCF, so it would be nice to see how those look in the actual raw report files.

    I think the BAM files would be more like a string of text (ACGT) for each gene? http://www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/ suggests that's the case, to some extent at least. So it would include data perhaps most useful in comparing it to normal patients, controls, or the default sequence for a gene for the SNPs with no research or rs numbers yet. It would take a lot more effort and expertise to use it, but also might pick up things missed by the standard VCF data.

    Anyhow, it looks like the VCF data would be sufficient for fast and easy processing by automatically comparing it to dbSNP and/or OMIM databases.
     
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  18. Waverunner

    Waverunner Senior Member

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    Wonderful. Regarding the time table, I wait for the answer of the personal genome project and if it turns out negative I have a doctor appointment in mid January and will either order WES through him or if the price is too high, I will go for Gene by Gene. I will let you know if anything new comes up.
     
    Valentijn likes this.
  19. jamienoble

    jamienoble

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    Valentijn, could you help me to analyse WES results as well?
    Or could you help analyse WGS results if i did that through UCLA? It looks like i will be able to do that if i want to.

    What do you think i should choose? WGS (UCLA) or WES (gene by gene)?
     
  20. Valentijn

    Valentijn Senior Member

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    Yes, the program should be able to handle that.
    I don't think an automated analysis would be able to do much with the vast majority of data which is outside of the exons. Theoretically the program could also look through it, but I doubt it would add anything of value.

    But maybe there are other resources (such as from UCLA) which would be able to make use of the extra data coming from WGS.
     
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