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bobh

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Everything posted by bobh

  1. 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.
  2. Cross-post: I have completed a final phase of analysis of 23andMe and AncestryDNA data contributed by parents of kids with PANS or PANDAS, and found 5 SNPs statistically significant in these disorders: SNP _______ risk _ Odds Ratio rs10493812 __ A ___ 9.13 rs115521555 _ T ___ 9.33 rs6896998 ___ T ___ 8.42 rs5029936 ___ A ___ 9.06 rs76298532 __ T ___ 17.0 You can read and download the brief report at https://osf.io/53yve/ . There is also a spreadsheet with more details at https://osf.io/br2kh/ (that is best viewed in excel after downloading).
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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.
  9. 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.
  10. 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
  11. 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
  12. 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
  13. 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.
  14. 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
  15. More Q & A from elsewhere: Q: Can you use DNA date from another source ... or do you need the raw data? A: Because the frequencies of risk alleles can vary quite a bit by ethnicity, I use the full raw data to give an ethnicity report (at GEDmatch, where I load only de-identified data - this is mentioned in the post above that doubles as a "consent form"). I use the frequencies associated with 6 main ethnicities to effectively create a control group from dbSNP (a database of allele frequencies). So, sorry - I do use a good chunk of the raw data.
  16. I am going to post here paraphrased questions and answers from other private places where this post was also placed. Q: I can't remember - Can you tell me if I participated in the original study? A: ... I can't tell you right now because I don't have a list of the names on my computer where the de-identified data is. I've never had a computer hack or theft or break-in at my house, but just in case any of that happens, I kept the list of names identifying which data belonged to whom written on an (unhackable) piece of paper locked in a completely different place, and I am not there ri
  17. If you or your child have a PANS or PANDAS diagnosis from a licensed medical practitioner, and you have 23andMe genetic data for that person, you are invited to participate in a follow-up research study titled “Replication of a Genetic Association Among Patients with PANDAS or PANS”. This study is being conducted by Bob Horvath, Michaela Holden and Sam Keating. We are "citizen scientists” with some qualifications in statistics and data manipulation, and direct experience (ourselves or family members) with PANS and other autoimmune or immunological conditions, as well as autism. The p
  18. A report on the pilot study of this post has (finally) been uploaded at Open Science: https://osf.io/pf7q2 . The new files are the last one (the report), and the first one (the spreadsheet). I am wanting to replicate the finding, and am working towards that. There is no earth shattering new results there that weren't posted above. For example, the SNP that is statistically significant is still not revealed (because doing so could bias the replication study). The report is several pages of methodology details (the whole thing is 5 pages), so, I don’t recommend people read it unless th
  19. Sorry I didn't notice your response until now. Well, we are wanting to replicate for good measure, but as a first approach, we are trying to partner with folks that have existing data sets. They don't know the SNP, and I don't see their data in advance, so I feel that blindness protects us from a certain kind of p-hacking criticism for already-collected data. If working with others falls down, I might consider doing the replication with data collected as we did in this first round. I would be happy to let you know if you wanted to contribute. As to your 2nd question, the simple bonfer
  20. After checking 10,417 SNPs in the PANS genetics data sets that were donated for the above study (from this and other groups), we finally found one that does have a "statistically significant difference" in incidence between 68 PANS kids (who are mostly of European ethnicity), and a representative general population. This is not at all like Huntington's, where if you have the mutation, you've got the disease, and if you don't, you are clear, 100%. Rather, it is like what we know so far of many immune disorders, where there are many gene mutations (even hundreds of them) that are associated
  21. I committed to feed results back as they trickle in, so here is one such result: For MTHFR A1298C (rs1801131), there were 70 sets of data: - 5 were homo for the risk allele (i.e., +/+) - 23 were heterzygous (+/-) - 42 of them did not have the risk allele at all (-/-) For MTHFR C677T (rs1801133), there were 71 sets of data: - 5 were homo for the risk allele (i.e., +/+) - 26 were heterzygous (+/-) - 40 of them did not have the risk allele at all (-/-)
  22. Note: This has been approved for posting by Forum administration. For any that contributed to this genetic study that we posted here (and elsewhere) - thank you so much! The cutoff was last night, and we had a great result - 71 sets of data. I will post some tidbits of "aggregate" results here (and in the other groups this was put in). I am wary of posting full results on facebook, because then facebook could claim some ownership. Instead, full analysis results (data in aggregate form only) will eventually be posted here: https://osf.io/pf7q2/?view_only=ba9efeabb38e4a22adced3
  23. If anyone is still interested in participating, there is only one more week until the cutoff for this pilot study. I am not sure if anyone from this group has uploaded data (it would be some work for me to check where non-anonymous donors are from, and of course I won't know for anonymous donors), but there are 40 participants so far from other groups. It is exciting work for which there has not been (to the best of my knowledge) anything published to date. We intend to publish publicly only at Open Science Foundation, not (at least at this time) formally in any peer-reviewed journal.
  24. Ibuprofen (aka advil, motrin) is for some (not all) a "resuce med" in a flare (you can't keep giving it indefinitely). It is definitely the case that some abx work and others not, and it varies from kid to kid and (likely?) by particular sickness for a child.. Haven't had the vomiting experience, but have had our fair share of mystery stomach aches. I have no experience with Colorado docs - am far away.
  25. Sorry to hear about you and your grandaughter's struggles. For several years, it was impossible for our child to get to school, because of his severe OCD. We chose to homeschool (mostly using online resources) - it was that or nothing. Different parents, and situations, have made for different coping mechanisms (e.g. type schooling in the search box at top right, once you are in this forum). If the issue is just October, you might approach the school for some kind of leniency/temporary school at home option. Many parents have had discussions with schools, with varying success wit
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