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Doing a Whole Genome Sequencing (WGS)

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99
Basically the new version can label genes, pull out and/or flag rarer SNP alleles, flag missense mutations, flag known pathogenic SNPs, and calculate BLOSUM62 scores (4 to -4, with 4 being no difference and -4 being the most drastic) to help to predict if a missense mutation is pathogenic.]

It sounds really great!

I had a notice today that the new version is available on SourceForge. I am a little spooked by downloading a zip file from SourceForge, though, because of their bad press regarding adware and malware since 2013. i.e. http://www.howtogeek.com/218764/warning-don’t-download-software-from-sourceforge-if-you-can-help-it/ , http://www.information-age.com/indu...google-discovers-588-pages-malicious-software

Is the program available on another site?
 
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Is the program available on another site?
Nope. And it sounds like the SourceForge problem went away shortly after that article was published, based on the update at the bottom.

The extra data file is downloaded separately, to keep the basic program bundle nice and small for people with downloading or other limits. It's the "remarks.zip" file at https://sourceforge.net/projects/analyzemygenes/files/Databases/ and just needs to go into the same folder with the other files from the program.
 
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Nope. And it sounds like the SourceForge problem went away shortly after that article was published, based on the update at the bottom.

You mean the update on the bottom of the SourceForge landing page? Yes, I see that they've changed management in Jan 2016... https://sourceforge.net/blog/sourceforge-acquisition-and-future-plans/ So presumably downloads are clean again, since they've been bitten once.

I took a quick look at the java and I can see someone spent a lot of time on this! It's great you created this resource and offer it free to the world. Many thanks to you and Jan.
 
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My results will be ready in around 2 months from Gene by gene.
Correct me if im wrong, finding information related to my disease is like finding a needle in haystack pretty much?
And if my symptoms are from an infection or something i wasn't born with, this information wont be in the data at all?

When the data is ready, could you teach me what i can do myself to find anything useful from this?
 
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15,786
Correct me if im wrong, finding information related to my disease is like finding a needle in haystack pretty much?
Yes ... but there are ways to search through the haystacks more efficiently. Mythbusters had a fun episode on that :D
And if my symptoms are from an infection or something i wasn't born with, this information wont be in the data at all?
Even if it's not a strictly genetic disease, there could still be a genetic susceptibility. For example, there are missense mutations in the genes involved in innate immunity which can result in reacting poorly to a few specific infections. But unless/until someone with one of those mutations runs into one of those infections, everything is going to be pretty normal.
When the data is ready, could you teach me what i can do myself to find anything useful from this?
Yes. Currently I'm working on getting the 23andMe files for Analyze My Genes to include more of the rare SNPs (some were omitted from earlier versions due to being difficult), but after that my next project is to attempt something similar for at least the exome, maybe the genome depending on how huge the data files get.

But even without that sort of program you can probably still manually focus on the genes which are most likely to contribute to your disease/symptoms.
 
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Hello again,

My results are now ready, not sure which one of these i should upload for you tho?

https://www.dropbox.com/s/uhbnait3ythnhz1/Namnlös.png?dl=0

Very much looking forward to begin searching for any clues in this data. I know its just a small chance that we find anything related to my symptoms but im willing to spend time each day looking as long as you teach me how and what im suppose to look for. :)
 
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My results are now ready, not sure which one of these i should upload for you tho?
The files are zipped, so I can't tell what the file extensions are :p The interesting ones should be in .vcf format, but the visible exome.vcf file is too small to contain much data.

Based on the naming, the "post" files probably all go with the "post.bam" file. .bam is basically the raw string of alleles.

So the more useful ones are probably "exome.vcf" and the files after it are probably .vcf files too, but broken into smaller parts so the files aren't too large to be copied or downloaded. So I'd like to see the "exome.vcf" file and at least the first two following it, so we can get a version of the Analyze My Genes program working with the specific formatting and multiple files.

I'll send you a PM (conversation) with my contact info.
 

OkRadLakPok

Senior Member
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124
I did what is almost that at a University. I do have a large duplication over 8 genes, one of which is PACSIN1. They say it is clinically sig in terms of my hyper sensitivity. It makes me happy to have that dx after YEARS of hell, telling me I a crazy.

Now when I go to Dr and tell them, and tell them it is NOT 23 and Me which they laugh at ( I do NOT know why because 23 and me showed my some stuff!!) then they perk up and stop making me feel like crap

Yes, I will do WGS soon. It is worth every thousand I will spend . It may show nothing more, but if you are dumped in that psych boat, you will n otice how differently they treat you when you really do have a genetic issue.
 
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Sounds good, for me it doesn't matter if your software can read the results now or in 3 months as long as it works. :)

I don't know if you are aware of my history but basically i will take this "medicine" which cured me 10 years ago (Accutane) again and before i start with this i will do a bunch of tests because i obviously cant search for my disease through tests during this time (which will take 2 years). Will that be the same with WES or my gene information wont be affected when i take this?
If it wont be affected i can do WES anytime during these 2 years and it will be the same results anyway?
Im also wondering if its possible to look at specific genes with your software?

what do you mean when you used accutane you are cured , i took it and i got CFS in the 3rd month
 
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The files are zipped, so I can't tell what the file extensions are :p The interesting ones should be in .vcf format, but the visible exome.vcf file is too small to contain much data.

Based on the naming, the "post" files probably all go with the "post.bam" file. .bam is basically the raw string of alleles.

So the more useful ones are probably "exome.vcf" and the files after it are probably .vcf files too, but broken into smaller parts so the files aren't too large to be copied or downloaded. So I'd like to see the "exome.vcf" file and at least the first two following it, so we can get a version of the Analyze My Genes program working with the specific formatting and multiple files.

I'll send you a PM (conversation) with my contact info.

you seem knowledgeable in the field of genetic analyzing , i would ask you if you have done any genetic testing WGS or WES ?
 

wastwater

Senior Member
Messages
1,270
Location
uk
Arnt people with me/cfs going in for these genome projects and making data public to see what can be learnt from this if anything
They are studying rare diseases and cancer I think so it might not be easy to get in
 
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Hi all,

I'm doing a WGS with Dante Labs. Still waiting on my results, so can't recommend them just yet, but their Customer Service is very good. You also get the raw data files (I'm going to use mine with Promethease).

Thought I'd point it out as it doesn't require a physician's order. I paid £575 for it.