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bobh last won the day on January 28 2019

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  1. The post of this thread was edited for an important revision. Also, my co-author Sam Keating and I recently completed another genetic study about P/P, that is unusual in that it is quite different than a typical genetic association study. The work is done, and with exciting results, but it is not yet formally or informally published - we need some more time for some additional checking. So we can't show results, but you can read what the study is about via its registration plan, here: https://osf.io/ck5un .
  2. I just finished another study, checking whether the risk alleles of SNPS for elevated uric acid occur more commonly in PANDAS and PANS. It looks like the answer is no. The report I did is here: https://osf.io/35sx6/ This idea to check out uric acid genetics came from a P/P mom. I think it was a great idea, that is why I spent a lot of time getting that "no" answer. If anyone else has any good ideas, let me know! I am motivated to make use of this data.
  3. Edited: A final phase of analysis of 23andMe and AncestryDNA data contributed by parents of kids with PANS or PANDAS initially found 5 SNPs statistically significant in these disorders, but only 2 replicated in additional work recently completed (and uploaded as a revision to the report): SNP _______ risk _ Odds Ratio rs10493812 __ A ___ 4.1 rs5029936 ___ A ___ 2.0 You can read and download the brief report at https://osf.io/53yve/. If you want to look up these SNPs, it would be good for you to read the 3 short paragraphs of Section 2 of the report. The spreadsheet wi
  4. If anyone is interested in participating in this project by contributing data, I will be taking extra data until the end of this month (Jan/20). This time, I will be taking AncestryDNA data too. I have decided to go ahead with a 3rd (and final) phase of this genetic association study, where I check all the SNPs called in 23andMe and AncestryDNA, not just a small, predetermined list. Well, not quite all, because some aren't reported on in databases, or don't have an rsID, but it is huge chunk of work. For those interested in technical details, the plan for this study can be found here: http
  5. We did find one other statistically significant SNP when combining data from the previous pilot study and this replication study: rs1042098. The tallies for both significant SNPs are: AA AG GG rs1042098 66 28 5 (there were 99 calls) expected# 42 45 12 TT CT CC rs2811178 23 21 10 (there were 54 calls) expected# 8 25 21 Although there are 138 participants (pilot + replication studies combined), not all versions of 23andMe and AncestryDNA called both SNPs
  6. I have received the 70th data set (the goal for this replication study), and of course I couldn't resist checking the results. I was very surprised to find that the main SNP we were trying to replicate (the one related to MS that was unusually common in the pilot study) was not in fact unusual among this newest 70 PANDAS/PANS patients. I will be doing some checks around this, but it should be concluded that that SNP is not associated with PANS or PANDAS. But another SNP, rs2811178 (on the DPYD gene, 97981242T>C) has been shown in this study to have me
  7. It has been a long road, but I am in the "home stretch" of data collection for this study: I need only 10 more participants to reach the goal of 70 data sets. So, this is an appeal to any of you that have 23andMe data for your PANS or PANDAS child, to consider participating. Also, I am taking the opportunity to link to a good podcast on what has been called the "replication crisis". This genetic study I am doing is partly a replication of an initial result in a pilot study. Successful replication is very important because up until recently, half or more of all peer-review, published studi
  8. More Q&A from elsewhere: Some of you have looked at or downloaded the report for the previous pilot study at https://osf.io/pf7q2/ (there have been 174 downloads to date). Recently, I did an important update to that report. It was unfortunately a disappointing update to do, because it was to include statements (and corresponding analysis) about a Turkish genetic association study (the one presented at the Common Threads conference last year) that didn't replicate amongst our kids. It could be the case that genetics among Turkish P/P kids are not the same as among the mostly
  9. It has been a while since I used it, and I don't fully remember. I don't recall struggling, though. I also used Promethease, and that was more difficult, but with much more results. I recently had recommended to me SelfDecode (www.selfdecode.com), but I haven't used it.
  10. Oh - I did use my credit card, so they have my name - but it wasn't my data. So, I need to admit that I was not completely hidden from them. it would have been slightly smarter to use my wife's (she kept her different last name), but that wouldn't have been totally bullet-proof either. I wonder if a paypal account can be temporarily setup. I think not answering health questions is important. I used a fake name for genetic genie, and it was free.
  11. Another paraphrased Q&A from one of the 10 or so FB groups this is also posted in: Q: I'm happy there is research being done but ppl need to be careful where u r sending your child's identity and genetics! ... This doesn't sound safe and not sure results would be publishable. A: The publishing is less formal, in a different arena than most researchers publish, which is at Open Science Framework. If you don’t know me, you can always upload anonymously. ... If data is completely anonymous (the first thing I do is anonymize it anyway), I can’t fathom any danger. I persona
  12. For those that may not have 23andMe raw data on their own computer, here are some instructions for re-downloading from 23andMe: 1. Sign into your account at www.23andMe.com (the sign-in button is near the top right). 2. On the right hand side click on the arrow beside your name and scroll down to "browse raw data" 3. Click on "browse raw data" and on the page that opens just under 'Your Raw Data' there is a note "You can view or download your data at anytime". Click on the word download which is highlighted in blue. At the bottom of the page that appears (read, and
  13. Q: So are you looking at genetic vulnerability? What are the long term goals of your study and how might it affect kids with these conditions in the future? A: Yes. The “holy grail” of a genetic study would be an “if and only if” genetic variation as has been found for Cystic Fibrosis (CF), where if you have the genetic variation you have the disease, and if you don’t have the defective gene, you don't have the disease. But autoimmune diseases don’t seem to be like that. Instead, dozens or hundreds or maybe even more than a thousand genetic variations seem to incr
  14. Q: Can you use AncestryDNA raw data? A: We did use ancestry for the pilot study, but it doesn't call 7 of the 10 SNPs I am looking at this time around. Because I am going to stop when I get 70 data sets, getting Ancestry data sets will mean less data for those 7 SNPs, which means weaker results for them. So, we won't be taking AncestryDNA data sets this time.
  15. Q: Will participants get to see the final results of the research? A: Most definitely! You can see most of the results from the original pilot study at a link quoted near the beginning of the post (which actually serves as a consent form). We are hiding the identity of the SNP of significance so that this replication study cannot be accused of collecting data from people that knew they had they risk allele for that SNP! ... you (and everyone else) will be able to see results at an Open Science Framework website. It will be somewhat similar to the results shown for the pilot study.What I
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