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Download for Rare SNP Analysis

Discussion in 'Genetic Testing and SNPs' started by Valentijn, Aug 29, 2013.

  1. Valentijn

    Valentijn Activity Level: 3

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    It'd be great if you could send me the homozygous results from your 10% list. If you don't have an easy time getting those sorted from the rest of the 10% results, then cutting and pasting your entire results to me would be great. Private Messaging (Conversation) works well for just the homozygous list, but if it's too big for a normal PM, let me know and I can give you my email address.
     
  2. Valentijn

    Valentijn Activity Level: 3

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    Currently I'm running all of the heterozygous results through a column in excel, and setting it to flag any repeats. Me and Roxie60 have 25 in common, and I can easily add additional results into the mix. It'd be hard to produce full results that everyone can look at on here, but I can cut and past the repeated results in the rare allele thread or some such.
     
  3. Valentijn

    Valentijn Activity Level: 3

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    I have no idea how extracting zip files works on a Mac ... is there anyone who can help with that? Though even without unzipping first, the Genes file should be able to run and produce most of the relevant results.
     
  4. bel canto

    bel canto Senior Member

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    I didn't have to unzip anything - it happened automatically after downloading. Sea - I saved the downloaded folder to my Applications folder, then double-clicked the Genes.jar. That brought up the screen with buttons. When you select the file for your genome, it takes a bit to load, so don't give up for awhile.

    There was an apple alert re: JAVA recently: http://derflounder.wordpress.com/20...-in-versions-prior-to-june-2013-java-updates/. However, if you are current on updates, I wouldn't think that this would be a problem. Apparently, the 13.9.7 version I see is a part of JAVA 6.
     
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  5. Sea

    Sea Senior Member

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    Yes it is the 13.9.7 version of Java 6 that I have. When I double-click the Genes.jar I get this message:

    The Java JAR file "Genes.jar" could not be launched. Check the console for possible error messages.
     
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  6. Bluebell

    Bluebell Senior Member

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    Valentijn likes this.
  7. snowathlete

    snowathlete

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    Great program. Thanks Val and fiance for providing it!

    Here are my 1% results. If I understand this right, these rare ones are interesting because they are rare and I can run some searches online to see what is known about them. Best sites to search on?
    But homogenous results are particularly bad because you have two copies of it? If so that's bad because if it is a dodgy gene then it can have double the effect? Or have I got it wrong?

    Does 0 litterally mean that no one in the database (how big is that database btw?) has been recorded with that result before?

    SNP CHRM RARE PERCENT GENOTYPE ETC
    rs11584467 1 A 1.00 AG
    rs212987 1 G 1.00 AG
    rs12125529 1 A 1.00 AG
    rs3917020 1 G 1.00 GT
    rs17598321 1 T 1.00 CT
    rs12084554 1 A 1.00 AC
    rs12132342 1 T 1.00 GT
    rs17402243 2 G 1.00 AG
    i5002444 2 T 0.27 CT rs121908515
    rs10490395 2 C 1.00 AC
    rs7587534 2 G 1.00 AG
    rs887987 2 T 1.00 CT
    rs3188996 2 G 1.00 AG
    rs838087 2 T 1.00 CT
    rs10166998 2 A 1.00 AG
    rs41265961 2 A 1.00 AG
    rs13032621 2 A 1.00 AG
    rs13071214 3 C 1.00 CT
    rs17193729 3 G 1.00 AG
    rs358977 3 A 1.00 AC
    rs4135292 3 A 1.00 AG
    rs4361233 3 G 1.00 AG
    rs9832105 3 A 1.00 AG
    rs17398428 3 C 1.00 CT
    rs10935179 3 T 1.00 GT
    rs13063210 3 G 1.00 AG
    rs72550820 4 A 1.00 AG
    rs223469 4 T 1.00 CT
    rs4833304 4 T 1.00 GT
    rs2322180 4 A 1.00 AC
    rs7670986 4 T 1.00 CT
    rs13133439 4 T 1.00 CT
    rs17302526 5 T 1.00 CT
    rs34203073 5 A 1.00 AG
    rs12188139 5 G 1.00 AG
    rs17336381 5 T 1.00 CT
    rs1051309 5 A 1.00 AG
    rs4151681 5 A 1.00 AG
    rs10482714 5 T 1.00 CT
    rs10042724 5 A 1.00 AG
    rs62638207 5 C 0.05 CT
    rs17183864 6 A 1.00 AG
    rs2071302 6 C 1.00 CT
    rs1829212 6 T 1.00 CT
    rs542023 6 T 1.00 CT
    rs17070199 6 C 1.00 CT
    rs17648408 6 T 1.00 CT
    rs311354 6 C 1.00 CT
    rs11755474 6 C 1.00 CT
    rs12534162 7 G 1.00 AG
    rs28746501 7 A 1.00 AG
    rs6968076 7 C 1.00 CC Homozygous
    rs17431071 7 G 1.00 AG
    rs7776772 7 T 1.00 CT
    rs13277026 8 A 1.00 AG
    rs17467721 8 C 1.00 CT
    rs17526980 8 T 1.00 CT
    rs4737570 8 A 1.00 AG
    rs10087163 8 A 1.00 AG
    rs36014856 8 A 1.00 AG
    rs10104551 8 T 1.00 CT
    rs1496753 8 G 1.00 AG
    rs17498168 9 C 1.00 CT
    rs945443 9 T 1.00 CT
    rs16918618 9 G 1.00 AG
    rs35654915 9 G 1.00 AG
    rs17273828 9 A 1.00 AG
    rs3097725 10 G 1.00 AG
    rs2814914 10 A 1.00 AG
    rs41278532 10 T 0.27 AT
    rs45467596 10 A 1.00 AG
    rs11202892 10 C 1.00 CT
    rs11191279 10 T 0.37 CT
    rs284847 10 A 1.00 AG
    rs4647760 11 A 1.00 AC
    rs34584708 11 G 1.00 AG
    rs35809865 11 A 1.00 AG
    rs1800056 11 C 1.00 CT
    rs11605530 11 C 1.00 CT
    rs12801945 11 T 1.00 GT
    rs28370643 12 T 1.00 CT
    rs1250148 12 A 1.00 AG
    rs1313099 12 A 1.00 AG
    rs569254 12 C 1.00 CT
    rs1922744 12 A 1.00 AG
    rs12368829 12 G 1.00 AG
    rs12423375 12 G 1.00 GT
    rs10507477 13 C 1.00 CT
    rs9594505 13 C 1.00 AC
    rs36212784 13 T 0.37 GT
    rs1168999 14 A 1.00 AG
    rs4313770 15 T 1.00 GT
    rs17759504 15 A 1.00 AG
    rs17738933 16 C 1.00 CT
    rs11646402 16 A 1.00 AG
    rs4986970 16 T 1.00 AT
    rs17227403 16 C 0.32 CG
    rs9890964 17 A 1.00 AG
    rs12944954 17 G 1.00 GG Homozygous
    rs2945413 17 A 1.00 AG
    rs3887424 17 C 1.00 CT
    rs3687 17 C 1.00 CT
    rs17799832 18 T 1.00 CT
    rs3218784 18 G 1.00 AG
    rs960491 19 T 1.00 CT
    rs8105775 19 A 0.00 AG
    rs4926123 19 T 1.00 CT
    rs4808647 19 T 0.09 CT
    rs12151353 19 T 1.00 CT
    rs202489 20 T 1.00 CT
    rs235586 20 A 1.00 AG
    rs1205218 20 G 1.00 AG
    rs709046 20 T 1.00 CT
    rs8124453 20 T 1.00 CT
    rs1108458 22 T 1.00 CT
     
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  8. snowathlete

    snowathlete

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    How come these stand out, if you don't mind me asking? Just curious as I have the same result for the second one.
     
  9. snowathlete

    snowathlete

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    I've only searched the really rare results so far - those less than 1.0 - and the two homogenous result, and only one of these SNPs has anything recorded for it in the databases I've looked in online.

    i5002444 2 T 0.27 CT rs121908515

    This one, it says is related to hereditary spastic paraplegia which usually shows up in mid adulthood. The risky result appears to be T;T...I think!
    Would having one of those risk allels present some risk alone? The NHS site says "In most cases, a child with HSP will have inherited the faulty gene from just one of their parents, and this dominates over the corresponding normal gene they inherit from the other parent. This is known as autosomal dominant inheritance. Sometimes, adults will carry a weaker version of the abnormal gene, which means they don't have symptoms but can pass on HSP to their children.
    In some cases, a single copy of the faulty gene does not cause HSP. In these cases, children only develop HSP if they inherit the abnormal genes from both of their parents. This is known as autosomal recessive inheritance.
    About 70-80% of cases of HSP result from autosomal dominant inheritance, and the remainder from autosomal recessive inheritance." which leads me to think the answer can be yes sometimes?

    Help gratefully recieved!
    Best
    Joel
     
    Last edited: Jan 16, 2014
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  10. SickOfSickness

    SickOfSickness Senior Member

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    If you google, there are a few sites that usually come up first. So you can search on those directly, or just google.

    Yes, homozygous (2 bad copies) is much rarer than having only 1 bad copy (heterozygous).

    Not double. It depends on the SNP. Sometimes with 1 bad copy, the person has nothing noticeable, and they are just a carrier. (The carrier's child would have a 50% of getting a bad copy from them.) Sometimes 1 bad copy means the person is sick.
     
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  11. Valentijn

    Valentijn Activity Level: 3

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    My preferred source for SNP info is dbSNP, which has data for this SNP at http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs121908515 . From there you can click on the [detail] link after the red "With pathogenic allele" text. That leads to http://omim.org/entry/604277#0015 which will give very detailed info about that specific SNP.

    Basically that SNP has a definite and more severe impact when homozygous or compound heterozygous. Some people with a simple heterozygous mutation have a milder version, and many are asymptomatic. It's possible that the patients with simple heterozygous mutations also have a second pathogenic mutation which was not detected yet is necessary to cause the problem.
     
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  12. snowathlete

    snowathlete

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    That's super useful. Thanks! I need to read it again later and figure out if there are other SNPs I should check as well if i can, but I have super stiff legs and last year I had an incident where my left leg suddenly clamped up and I couldn't use the muscle properly. This caused a sort of severe limp and I struggled to make it back to the car dragging my foot along. Later it was back to normal. I went to my GP who checked reflexes etc and at first I had no reflex in my knee till he repositioned me and got one. He said he didn't know what was wrong and to come back if it happened again. Perhaps this is related?
     
    Last edited: Jan 17, 2014
  13. Valentijn

    Valentijn Activity Level: 3

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    @snowathlete - Most known pathogenic SNPs have an "i" number from 23andMe instead of the usual "rs" number. So while you might have additional rare SNPs that can cause problems, the "i" numbers are the most obvious suspects.
     
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  14. madietodd

    madietodd Senior Member

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    I've just tried this again, and I'm not even seeing a "genes" file. I've got something called "genes.jar" but I can't open it because it's from an "unknown developer." I never get any of the screens you're talking about - I've just got a bunch of downloads and files that won't open.

    MacBook Air, downloaded Java into Safari, downloaded the program and 23andme files through Chrome (does that matter?).
     
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  15. Valentijn

    Valentijn Activity Level: 3

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    It's the genes.jar file. I'll let my fiance know about the "unknown developer", since that might explain why some Macs won't let it run.
     
  16. madietodd

    madietodd Senior Member

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    Sorry, it actually says "unidentified developer."
     
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  17. snowathlete

    snowathlete

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    I've now run the 10% results. I'm only bothering at the moment to check those that are given i numbers by 23andme, so only 5 results. A few interesting things including one that may affect ATP energy production via mitochondria that I need to look into.
    One of the five is homozygous as well and appears to be the other interesting one. It is on the CYP2D6 gene which has a good wikipedia entry. It seems it is a very important gene for metabolizing xenobiotics, including 25% of clinical drugs. This may be worth me looking into so thanks again for this program which helped me see the wood through the trees! In particular it shows what I already was told by someone in the past, that Rifampicin which I am on to treat Bartonella induces the gene to speed up metabolism of substrates which include amitriptyline which i take for sleep and which has been less effective since I started the rifampicin!

    BTW, looking at a few of my results on 23andme, some of my results have "II" by them instead of a genotype. Does anyone know what that means?
     
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  18. SickOfSickness

    SickOfSickness Senior Member

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    Every "i" number that I Googled has almost no information.
     
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  19. snowathlete

    snowathlete

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    I think that is because only 23andme use the i number, so you need to search for the equivalent rs number given - some still have litle information. you can also search the i number in 23andme and then it will tell you the gene code. You can then google that gene code and at least get an idea of what are that gene is involved in, even if you can't easily discover what your specific mutation might do to it.

    @Valentijn - you know what would be handy? An extra column in the results showing the related gene. This would make it easier to search google for info on it, but more useful than that it would also allow you to order by gene and then see if you have other compound mutations within that gene within the results.
     
  20. SickOfSickness

    SickOfSickness Senior Member

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    I had the same thought. I looked them up manually but for future users it would be nice.
     

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