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Genetic testing: a chance for us to mobilise research


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Just a heads up - there's an additional charge of $79.95 for international shipping if you're not located in the US.

 

In the USA its $9.95 which includes postage-paid return label for the sample.

 

Do you, or anyone, know of gene testing services outside the USA?  The two here are 23andMe and Ancestry

 

 

I will order the test kit in 2 to 3 weeks. Still debating on whether I should go with 23andme or ancestry.

 

I decided to try both and see the difference.  Just got the raw data from Ancestry ... so give me a few days to compare

 

However,

 

Got 701,479 SNPs with ancestry.com

Got 602,353 SNPs with 23andme.com

 

Synth did 23andme with the previous version and got over 900,000 SNPs

 

There are actually many more SNPs but companies don't search them all.  They focus on what they think will be most useful to them.  At this time I can't say which might help us the best.  I'll need to make a little routine to show the difference between the two are.  Was also interested if they report differences for the same SNPs - however, so far both match on mine.  But with so much data, it takes a program to check.

 

Am downloading some massive human genetic data files off of the internet.  Some take more than a day to download even though they are zipped.  Windows would time-out, so made a program to do this.  Then need to extract data out of that.  Since we just have PCs and not huge mainframe computers, the setup for analyzing our data will take weeks to do.  Ordered an additional hard drive since the machine can't hold what we need. 

 

So please be patient and don't loose enthusiasm.  Both tests from the above companies took 4 weeks to get results.  So it takes a little time to get our data collected.

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I share 98.5% of my D.N.A. with Ralph the chimp at the Zoo???   Now I know what is clearly wrong with me!!!   hahaha..                                         There is 10 million Single Nucleotide Polymorphisms in the Human Genome which sculpture different variations of characteristics, functions and individuality in our D.N.A. code. S.N.P.'s is also responsible for the different reactions we have to DRUGS and DISEASES which being analyzed and Identified we could be making a big move in regards to getting some where with this disorder.  Patients is a major virtue here as well as a possible understanding in regards to fighting this disease/disorder once and for all as a nucleus.    Hppd25yearsnow..  :rolleyes:  :rolleyes:  :rolleyes:

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I share 98.5% of my D.N.A. with Ralph the chimp at the Zoo???   Now I know what is clearly wrong with me!!!   hahaha..                                         There is 10 million Single Nucleotide Polymorphisms in the Human Genome which sculpture different variations of characteristics, functions and individuality in our D.N.A. code. S.N.P.'s is also responsible for the different reactions we have to DRUGS and DISEASES which being analyzed and Identified we could be making a big move in regards to getting some where with this disorder.  Patients is a major virtue here as well as a possible understanding in regards to fighting this disease/disorder once and for all as a nucleus.    Hppd25yearsnow..  :rolleyes:  :rolleyes:  :rolleyes:

 

Will have to think of a reply for you ...

 

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Here is a chart of companies doing SNP tests  http://www.isogg.org/wiki/Autosomal_DNA_testing_comparison_chart

 

 

 

There is actually a lot of difference between Ancestry and 23andMe:

 

Ancestry returned 701,479 SNPs -- 308,158 overlapped with 23andme, with 393,320 not found with 23andMe.

Ancestry does not test any mitochondiral DNA (see above chart)

 

23andMe return 602,353 SNPs -- with 286,653 not found with Ancestry

23andMe has a few repeated SNPs (same position but different SNP id)

 

Error rate between them was 25 partial disagreements and 1 full disagreement.  There were also a few missing - don't know if it wasn't able to read or if it is some sort of backward compatability thing.

 

So, we probably should pick just one for now.  The above chart says that Ancestry isn't available outside the US.  If so, we best stick with 23andMe so more can participate.

 

 

Ideal would be to dictate which SNPs we are interested in.  But that would be a custom job and probably cost thousands per test - which we cannot afford.

 

 

Please share your thoughts.

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If someone would take the task to put together a list of people who are in, as well as putting together a to do list it would make things a lot easier. I do not have the time to do this myself. Not sure how these tests works but if someone would be able to collect the data and put it in whatever is needed, it would be even easier.

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This is what is needed:

 

1.  Genetic tests (SNPs) from people with HPPD

2.  Genetic tests from people without HPPD (control group)

3.  A detailed survey filled by each member submitting genetic data

4.  Then this data will be analyzed for patterns that might relate to HPPD symptoms.

 

Current status:

 

We only have raw genetic data from two members.  This project was suggested May 6th ... so is just starting.

 

We have a survey started by Synth but needs to be complete

 

For control, we have various databases on the internet (1000genome, Alfred, etc...) to compare with.  Ideally, would like the control group to be people who used recreational drugs but didn't develop HPPD - but this can come later.  You might enjoy reading about how one company asked Ozzy Osborne for DNA to study because he did lethal amounts of drugs yet is alive and basically healthy.

 

 

This is an informal start ... and a broad sweep.  It is self funded so each member needs to get tested and send in raw genetic data file.  Currently, I am the only one active on this project, though several said they want to get the test done and send the raw data files.

 

Regardless of whether there is enough interest in the project for it to proceed, it would also be good for all members who did the drug trial with Dr A to get tested and email him the results for rs4680 which was the basis of his theory for the trial.

 

This project is only viable if many samples are sent in.  Without that it can't get off the ground.  Several have expressed interest, but at this time only 2 tests are in.  With Statistical Process Control, a minimum of 32 samples are needed.  But even Dr A's test had value with just 20 patients.

 

 

If members continue to submit data files, then we can proceed with evaluations.  While this type of evaluation would highlight genetic weaknesses, knowing these is important in finding treatment ... just as it is in any disorder.

 

Ideally such a test should be preformed with a large budget, large sample size, and complete SNP testing.  That is not likely to be done soon or if at all.  But a small budget study can still have value and lead to important information now. 

 

I will continue to work on finding data and methods for evaluating tests.  As data files come in, they will compose a spreadsheet.  If enough sample come in to start, then I will start analysis.  The raw data files supplied by the above 2 companies do not have personal information in them, so members will remain anonymous.

 

So, its up to volunteers ...

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No need for promises.  This is all volunteer including self.  What is needed is the "raw genetic data" file.  You just download it and send.  So it can be done lazy, lol.

 

When you have a little time, you may want to run your data through programs like Prometheaus which matches your data to SNPedia so you can see health related stuff more quickly.  Its cool ... but you need time to read stuff and think, so do that part later.  As it is, it takes several weeks just to get the saliva test done.  So it won't interfere with summer plans.

 

Sounds like you are having fun with your life.  That is good.  Never been sailing yet.

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Due to unforeseen circumstances, I have to delay in taking the test. Money problems but nothing serious.

I think I rather do ancestry because I don`t like that article on 23andme. Does prometheus and geneticgenie analyze raw genetic data from ancestry.com as well?

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Promethease says it loads ancestry.  However, genetic genie says it needs 23andMe.

 

 

Unlike the National Geographic test, both Ancestry and 23andMe don't state the entire goal of what they may do with the data.

 

Ancestry has avoided FDA scrutiny by not stating any health related values of their test.

 

23andMe has actually been open about health value and is actively trying to learn more about certain diseases.  Parkinson's and a host of neurological diseases are part of what they are trying to research.  So in spite of that article, 23andMe has been fairly open about their goals ... and neurological research is right up our alley.

 

Again, you don't need to give your identity and you don't really need to answer their surveys.  23andMe has zillions of question that you may choose to answer that help their research.

 

Until more companies become available, these are the options for now.  There are some companies that do entire genome sequencing (6 billion) but that is expensive.  Initially around $40,000 but soon will be $1000.  For most, that is beyond what we can do.  Perhaps in another decade the price will be reachable.  Also, these companies don't seem to be available for private testing of individuals ... probably more for studies.

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That is great!  Then I presume you don't need Promethease ... is the 23andMe health reports as extensive (or more extensive)?

 

 

BTW, since this thread was started last May, I've only received 2 samples from members (total = 4) ... so there is clearly lack of interest.  I will still collect sample for any who wish to send them, however, until there are a lot more samples, the project is on hold.

 

Don't let that discourage any from getting tested since the information can be helpful for each person.

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