23andme Patient Data Analysis

Community Projects
#22

Is it closing??

#23

Will you be able to check with 23andme whether we have DNA methylation?

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#24

Mr Dubya why it is last call? I thought there is no time limits

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#25

The first round of analysis is beginning now. There was a TON of preparation preceding starting from scratch doing a GWAS to make sure it is being performed with minimal error.

@airforlife
Itā€™s never too late to submit a 23andMe file.
Once complete, an option could be to repeat the steps annually to include the new data and increase the statistical power of the results.

Ideally, we would have around 1,000 genotypes to begin with. As of now, we have a little over 60.

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#26

1000? But where do we get so many samples from?

#28

It would be best if everyone viewed every single submission as adding a little to the quality of the results and not despair about having relatively few at this point.

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#29

No. Methylation are epigenetic changes. It just checks your DNA. Methylation tests are unfortunately more difficult and also vary due to the specific tissue (you may have methylation in brain DNA, but not blood etc.)

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#30

Approx how long until we get results from the first round of analysis?

Thanks

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#31

Approximately 2 weeks to 2 months, as things are going now.

An update regarding future submissions will be posted to the main topic very soon.

Youā€™re welcome!

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#32

Analysis of the current 23andMe data set has begun and acceptance of new submissions is on hold until further notice.

First, letā€™s get the bad news out of the way:

  • There were only 70 submissions, including data provided by the PSSD forum, and only 63 of these are usable files. We have only 1 submission pending.

  • GWAS projects to identify disease-associated SNPs typically analyze sets of 1,000 to 10,000+ samples all genotyped using the same chip and these often fail to yield reproducible results.

  • The low statistical power provided by so few samples makes it unlikely that a significant association will be found, especially if this condition is dependent upon small contributions from many genes. This was corroborated by a geneticist friend from the PSSD community and a scientist who some of our staff were in contact with.

  • The usable files are spread across 3 different chips 23andMe has used over the years, meaning 3 different analyses will need to be run and the results compared across the different chips.

The good news:

  • Despite the current shortcomings of this project, we said there would be 23andMe patient data analysis, so there will be 23andMe patient data analysis.

  • There is still the possibility an association will be found if there is one or few uncommon genoptypes that contribute to some attribute of this post-drug syndrome phenotype.

  • Spurious associations are a true concern. The 23andMe data is being subjected to a stringent quality control procedure and any findings will be heavily scrutinized prior to being reported to the community to prevent anyone from being misinformed or misled in error.

  • Given the decreasing costs and increasing availability of full-genome sequencing, some of our staff members are considering pursuit of a full-genome sequencing study of post-drug syndrome patients to be performed by professional researchers. This is comparable to reading an entire book, rather than skimming pages, and would require far fewer participants for sufficient statistical power.

  • Our staff and involved members are implementing several projects, including the Youtube Video project, aimed at increasing awareness of PFS and the greater post-drug syndrome, and garnering scientific interest in investigating this condition.

Bottom line, as appears to always be the case for us, is to not get your hopes up but not give up.

The least that will be performed is a basic association analysis of autosomal SNPs (chromosomes 1-22) of v4 and v5 chip data.

Time permitting, and somewhat contingent on significant results in the basic analysis; analysis of v3 chip data, mitochondrial and sex chromosomes, and imputed genotypes will be performed, probably in that order of increasing difficulty.

There is an upcoming series of meetings being held by the MHRA to review the safety of Accutane/Isotretinoin in early February that may end up consuming %100 of my involvement in the near future. Other than that, this is priority #1, so donā€™t expect to still be waiting 6 months from now.

And thanks again to all those who participated in this project!

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#33

It is very unfortunate to find this subject in the forum now. Iā€™d like to participate but I think it is late now.

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#34

Btw I did full exome then full genomeā€¦ and now trying to read 125 gigabyte bam file to check my ar gene promptersā€¦

#35

The analysis can always be repeated in the future once enough additional files have collected.

Getting the procedures from 23andMe data -> analysis -> graphical information is the hard part.

I donā€™t have the computing power, storage capacity, or knowledge, at my disposal at the moment to do anything with sequencing data.

Someone managed to submit a file in Variant Call Format, which would probably take an additional day to figure out how to properly add to the current analysis.

So, the first round will be as vanilla as possible for the sake of getting it done.

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#36

I recommend you to check known stuff first, like Hla types for autoimmunity serotonin receptor snpā€™s comt gene and Ar I have high hopes for correlation on these areas.
Then we need to check rare snpā€™s and hope that we might see a connection.
I am also curious about apoE4 variant frequency it usually produce worst out come in brain inflammation/damage.
We just need a good statistician and mathematician.

For example, I have high susceptibility for ms, celiac and ankylosing spondylitis because of my hla types and interleukin genes.
I also have some mutations in htr2a gene causes changes n antidepressant, antipsychotic response and increase susceptibility to rheumatoid arthritis.
Yet I did not develop any of them.

#37

@Dubya_B how much is needed in funds for the full analysis?

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#38

Donā€™t know yet. It is only a consideration at this point.

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#40

I have my results in the next week had to send it back a few times because I didnā€™t do it right.

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#41

You can try www.dantelabs.com too

#42

I just received my test now, but is it to late for me to participate?

#43

If you havenā€™t sent the kit in to 23andMe yet, it will be too late to submit for this round of analysis by the time you receive the data.