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which genetic test(s) do you recommend/find most helpful? +/-s?

Discussion in 'Genetic Testing and SNPs' started by xena, Sep 2, 2015.

  1. xena

    xena Senior Member

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    please link me if there are other threads on this already- i couldn't find them

    hi everyone, i'm thinking of getting some genetic testing done but am unsure of what to look for.
    i think my doctor is willing to order what i prefer or i can order 23andme

    main concerns for me are detox (mold), brain fog, mood stuff, and of course, methylation/fatigue

    it seems that most folks are using 23andme and the interpretation software people have built is mostly for 23andme. and i read somewhere on this forum that the blood tests are more accurate than saliva (23andme) so those things seem like considerations- anything else i should think of? what have you found more useful?
     
  2. joe12

    joe12 Senior Member

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    Valentijn and xena like this.
  3. Valentijn

    Valentijn Senior Member

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    Whole Exome Sequencing is another option. It's cheaper than WGS (whole genome sequencing), and is only looking at the exons of genes. Since a large majority of the known pathogenic mutations are on exons, and the rest can often be predicted to some extent, it might be a good alternative. Currently the cheapest I know about is $1,295: https://www.genebygene.com/pages/research?goto=exome-sequencing#
     
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  4. joe12

    joe12 Senior Member

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    What are the disadvantages of whole exome compared with whole genome? There has to be a few including a bunch of diseases not covered, I am worried that by getting this test something important will be missed or that maybe WGS will not make a diagnosis now but in the future it will so it might be a better investment for the future, maybe whole exome will be more limited in the future.
     
  5. joe12

    joe12 Senior Member

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    That info I gave is wrong, I just called them and told me it was $6,500 for exon sequencing and they are not doing genome. Its weird, I don't know why that website is wrong but it is. Its a big downer for me, I thought I might be able to afford the genome but no.
     
  6. Valentijn

    Valentijn Senior Member

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    There's not much advantage to WGS over WES at this point. While there might be a lot going on outside of the exons which we don't know about, that lack of knowledge means that it would be pretty much impossible to spot something in an intron or between genes and say "oooh, this causes that problem". And we'd need a pretty large sample of genomes from ME patients to find something brand new in that manner.

    Currently 85% of genetic disease triggering is thought to be done in the exome. Most (all?) research I've seen into SNPs in introns and between genes has shown little or no significant effect. The one major exception would be UTR regions. These can be quite relevant and have large impacts sometimes, but I don't think they are technically in exons and I don't know if they would be included in WES by any of the labs.
     
  7. joe12

    joe12 Senior Member

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    Learned today that Macrogen does clinical sequencing for just $1,600 at 30x, but without diagnostic analysis, which should be found elsewhere for a good price. So far its the best deal I have found. http://macrogenlab.com/genome-service/whole-genome/
     
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  8. student

    student Senior Member

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    A lot of CFS people have promoted and used this test. How far can you go with c.4 version 23andme testing? What is shown with shomakers testing. I am looking for suceptability of mold. Is 23a.me giving this HLA information in parts?
     
  9. Valentijn

    Valentijn Senior Member

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    It can depend on how much time you're willing or able to invest in looking into your results. There a few automated programs which list results which might be relevant to certain problems. I also have a small downloadable program at https://sourceforge.net/projects/analyzemygenes/ which pulls out very rare results. That one's in the process of being updated to show more data, such as the gene name, missense mutations, and pathogenic status, when applicable.
    Shoemaker's research into HLA types is of very poor quality, to the point where nothing useful can be determined from it. There are other threads specifically addressing the issue, which you can find with a site search.

    HLA status is primarily dependent on SNPs which have 3 or 4 known allele variants, whereas 23andMe only tests SNPs with 2 known allele variants. So they test for very little on the HLA genes, and HLA types cannot be determined for most genes. HLA-DRA types can often be determined (or could with the older V3 chip), but it's not a particularly useful one to know, especially in isolation.
     
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  10. jamienoble

    jamienoble

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    What genetic tests could discover most rare diseases? It doesn't really matter what it costs i just want to do tests that has a high chance detecting whatever possible genetics or enzyme related disease i have.
     
  11. Valentijn

    Valentijn Senior Member

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    Whole exome sequencing. But you also probably need to get the results interpreted by a geneticist.
     
  12. jamienoble

    jamienoble

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    So if i did a Whole Exome Sequencing (made sure to have someone who could interpret the results) and nothing of significance was found, then i can pretty much rule out that i have a genetic / enzyme related disease?
    There is also Whole Genome Sequencing (WGS) which costs abit more but perhaps its not necessary to do that one?
     
  13. Valentijn

    Valentijn Senior Member

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    Well, with any sequencing the state of knowledge regarding pathogenic SNPs is always going to be a factor. But if they're doing a good job of interpreting it, they should be very rare mutations which are capable of causing problems by running them through software which predicts the impact of the particular changes.

    WGS is still a lot more expensive, and I don't think there's much that can typically be done with the extra intron and intragenic data. All of the bits being translated into enzymes will be in the exons, though it is possible there is some regulating happening elsewhere.
     
  14. jamienoble

    jamienoble

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    Thanks for the info. When i look at the prices for WGS the price difference is huge between different labs. https://www.scienceexchange.com/services/whole-genome-seq

    Everything is listed as "per sample". How man samples do you think i would need to detect a possible disease i was born with?
    At this stage i want to do testings and analysis that will tell me with a very high probability if i have a genetic disease or not (that is causing my problems).
    If nothing is found i want to close the "genetics door" and look at other possible types of diseases i could have.
    If nothing is found then i also assume i can rule out that i have a disease i was born with?
     
  15. Valentijn

    Valentijn Senior Member

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    One sample would be sufficient. Genes can mutate a bit during your life, but they'll typically be in only a very small amount of cells. "Per Sample" prices are probably listed for the benefit of researchers or clinical geneticists who are buying in bulk.
    Probably. The one thing to keep in mind is that not all pathogenic mutations have been discovered by researchers. So there's always the possibility that someone has one which isn't known about yet. But if they check for extremely rare missense mutations and use a program to calculate the probability of pathogenic status, they should be able to locate those as well.
     
  16. jamienoble

    jamienoble

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    I really appreciate your answer, someone mentioned the $3500 WGS with analysis @ UCLA earlier which looks good to me.
    https://www.scienceexchange.com/labs/clinical-microarray-core-ucla
    "30X coverage: $2500 without data analysis; $3500 with data analysis"

    I don't know however if i can send this test to them from Sweden or if its even possible for me as a regular person to order such test, i really hope so..

    Edit: Joe12 wrote: That info I gave is wrong, I just called them and told me it was $6,500 for exon sequencing and they are not doing genome.
    Was this about the UCLA WGS test?
     
  17. MaulikShah

    MaulikShah

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    Hey Xena, before I tell you whether blood tests are more accurate or saliva I would like to share with you some pros and cons of both these tests as it will help you understand more about them and you will be able to take a better decision.

    Pros and Cons of Blood Samples

    Taking blood samples for DNA testing do have a few pros, including:

    · Clean blood in proper tubes minimizes chances of contamination

    · Fast and quick procedure

    · Blood samples are visible

    Cons:

    · Needles puncture the epidermis – patients will feel some extent of pain

    · Multiple attempts may have to insert the needle into small, thinner blood veins

    Pros and Cons of Swab Samples

    Swab collections have quite a few advantages:

    · No needle is used, no puncture of the skin is important

    · It’s a quick, non-invasive procedure, with no pain involved

    · The DNA gathered is good indefinitely after series if stored properly

    · Patients usually are more relaxed and less stressed regarding the DNA collection process

    Cons:

    · Bacteria can attack the cells containing DNA if not dried and stored

    · Since the cells will not be visible, there is no approach to visually verify DNA is existing.

    Both of these tests have their pros and cons. The bottom line is you will get highly reliable results from equally. From a practical perspective, it is not important which procedure you opt for. After learning a little additional about both processes, you might have a clear idea of what type makes the most sense for you personally.

    You can get additional knowledge about these tests from different sites. I have listed here some sites for your further reference. Hope they are helpful for you:

    · http://www.ncbi.nlm.nih.gov/gtr/

    · http://www.genome.gov/

    · http://geneticmedicineclinic.com/

    · http://www.cdc.gov/genomics/gtesting/
     

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