Help to research and organise genetic info

[Sea]

Does anyone have any suggestions?

I know how to browse my raw data at 23andme and look up individual snps. Is there a way to find out which are the major/minor alleles of a whole list (say a particular gene) rather than one by one?

If I search my raw data by a particular gene then sometimes I miss relevant information about the intergenic region nearby. So far I have only been able to overcome that by listing an entire chromosome, but that is almost endless pages of info to scroll through to get to what I want to look at.

If only 23andme had a search by chromosome position that would be easier. I can search my downloaded text file by chromosome position but then it doesn't have the other helpful stuff that 23andme has like being able to click directly to dbsnp.

How do people organise the info that you find out about your snps so that you can go back to it easily?

 

[Critterina]

How do people organise the info that you find out about your snps so that you can go back to it easily?

Sea, that's such a good question! I've been trying to figure that out myself.

What I've done is create a spreadsheet with each investigation on a new tab. I called it "mutation map" and I started it before I got my 23andme results, guessing from symptoms and other lab results. It's not really consistent, but I usually put the gene, rs number, risk allele, and my SNP in different columns, then a +/+ or +/- column like genetic genie, and color it. I sometimes post the PubMed article in the next column, or notes about what the mutation means. It's not the best, but it's workable. I'm hoping others have better ideas.

 

[SOC]

Just sent away for my 23andme spit kit. Now y'all are scaring me I'll have a major crash from mental exertion trying to figure out all this genetic info. I don't even recognize half the words you are using, much less their meaning! What have I gotten myself into!
<----- Not sure if this is laughing at my poor ME brain or hysteria.

 

[Critterina]

Just sent away for my 23andme spit kit. Now y'all are scaring me I'll have a major crash from mental exertion trying to figure out all this genetic info. I don't even recognize half the words you are using, much less their meaning! What have I gotten myself into!
<----- Not sure if this is laughing at my poor ME brain or hysteria.

SOC,
You will get a lot of help here. Start with the basics and run your 23andMe data through a program like genetic genie. Post that and you may get some conflicting opinions, but you'll know where to start.

 

[Critterina]

Meanwhile, you can start learning the vocabulary. I read the heartfixer page over and over for about two months, and finally it started to make sense. It has good diagrams. It's incorrect about the CBS mutation, but that's another issue.

http://www.heartfixer.com/AMRI-Nutrigenomics.htm

Also, look at the links in some people's signatures as you browse the site. A lot of people have very helpful references.

 

[PDXhausted]

I wrote myself a program to do this automatically. It takes your whole raw data, then looks up the gene in dbsnp by rs# and and looks up the genotype frequency in hapmap and then sorts the whole thing by gene and flags which snps have the least common frequency. Then I can just search the text file and browse for how many snps in a gene are mutated. There are some improvements I want to make on it the program (like fixing to look up by chromosome loc# instead of rs# in order to include the i snps, and switching to 1000 genomes instead of hapmap) but I'm too crashed out right now to work on it. If you feel comfortable emailing me your data, I'll run it through and give you back the results with what I have so far. Just PM me.

 

[Critterina]

I wrote myself a program to do this automatically. It takes your whole raw data, then looks up the gene in dbsnp by rs# and and looks up the genotype frequency in hapmap and then sorts the whole thing by gene and flags which snps have the least common frequency. Then I can just search the text file and browse for how many snps in a gene are mutated. There are some improvements I want to make on it the program (like fixing to look up by chromosome loc# instead of rs# in order to include the i snps, and switching to 1000 genomes instead of hapmap) but I'm too crashed out right now to work on it. If you feel comfortable emailing me your data, I'll run it through and give you back the results with what I have so far. Just PM me.

PDX, that sounds great. What genes/SNPs does it analyze?

 

[PDXhausted]

It doesn't actually analyze anything in the sense of drawing conclusions about the data-- it essentially just takes your whole 23andme raw data file and appends the gene and frequency info, as well as flags indicating less frequent genotypes. It just makes the raw data file much more useful to look at.

 

[Valentijn]

I know how to browse my raw data at 23andme and look up individual snps. Is there a way to find out which are the major/minor alleles of a whole list (say a particular gene) rather than one by one?

One way is with rare allele analyzers. These won't get the more common minor alleles, but the 10% database from http://sourceforge.net/projects/analyzemygenes/ gets alleles with 10% or lower prevalence. Because everyone (mostly) has two alleles per SNP, it's effectively getting alleles present in 20% or less of the general population.

How do people organise the info that you find out about your snps so that you can go back to it easily?

I have my full results in an excel file. Excel can be used to import a text file (like your 23andMe results), then create columns based on tab-separation. Then I deleted the 23andMe header info in Excel, added a column for "Gene Name", Function, Mutation (missense, stop-gain, pathogenic), etc.

 

[Aileen]

Just sent away for my 23andme spit kit. Now y'all are scaring me I'll have a major crash from mental exertion trying to figure out all this genetic info. I don't even recognize half the words you are using, much less their meaning! What have I gotten myself into!
<----- Not sure if this is laughing at my poor ME brain or hysteria.

I think we are all having that problem to one degree or other. I sure am! So, what to do?

I have been trying various free on-line courses (called MOOCs) offered by major universities. I've tried and dropped out of a couple genetics courses and started a couple new "introductory" genetics courses this week. My definition of "basic" seems to be different than theirs. I need genetic kindergarten!
But, the course I have found the most helpful by a mile is the introductory biology class from MIT. I thought it looked like a beginner course. It is on the edX site and is called 7.00x Introduction to Biology - The Secret of Life

I didn't realize this when I signed up but it is taught by a geneticist who played a MAJOR role in the Human Genome Project. It goes over the basics slowly enough that you can actually understand and learn. He takes you back to the very beginning of genetics (now I know who Mendel was) and gives a history lesson as he goes along. Just as a comparison, what Prof Lander takes approx 6 hours to explain is presented in 15 minutes or so in the genetics courses I'm trying!!

We are now in week 8 of the Intro Biology class but it doesn't matter. You can sign up still. Don't be put off by exams. You don't have to take them. The first 2 weeks are basics of biochemistry (yuck). Genetics starts at week 3. Week 6 starts to show how genetics and biochemistry come together (molecular biology). He's a really good teacher!

If you want to listen to a very entertaining short talk he gave click here. Then click the yellow "listen" box near the bottom of the page. Even if you are not interested in taking a course it is worth a listen. I laughed my way through it and so did the audience. How DNA got started in US courts.

 

[Waverunner]

Does anyone know any other useful DNA tools? I heard, that Promethease is good. Can anyone confirm this? http://snpedia.com/index.php/Promethease

 

[Sea]

Does anyone know any other useful DNA tools? I heard, that Promethease is good. Can anyone confirm this? http://snpedia.com/index.php/Promethease

Yes Promethease is very good. Lots of information and well organised

 

[Sea]

Just sent away for my 23andme spit kit. Now y'all are scaring me I'll have a major crash from mental exertion trying to figure out all this genetic info. I don't even recognize half the words you are using, much less their meaning! What have I gotten myself into!
<----- Not sure if this is laughing at my poor ME brain or hysteria.

Haha, you'll be fine SOC. It does take a while to get your head around the whole thing but I've found just taking my time has been helpful. You don't have to understand it all at once.

 

[Aileen]

It would be really nice if we could find a geneticist who could point us in the right direction. We have some limited data (23andMe) and now need to know how to go about trying to figure out what is important. Perhaps it is time to consider approaching someone?

If we could get someone to think of us as a student group project and act as a sort of mentor/overseer. Give us some idea of what we should be looking for and how we can best use the info we already have. What pitfalls to avoid. How to organize things. Someone we can contact and ask "Does this mean what we think it does?" or "We think we found something useful. Is it?"

It could be a rather interesting experiment from a geneticist's point of view I would think. Give a group of non-scientists some genetic data and see what they can do. After all, with 23andMe and similar companies offering this, would it not be to everyone's advantage to see what can and cannot be done? More and more people will be doing this sort of thing individually (and as we are) so why not use us as a "test"? And if we can get some help to figure out our illness(es) then so much the better. Win/win situation.

And we paid for the data and work for free! We have already organized ourselves and are pretty good at working together. Cheap and helpful lab rats who analyse their own data. Work well with minimal supervision. Innovative. Surely we can find some curious scientist who will adopt us as a side project to watch over from a distance? Genetics is a new frontier requiring original approaches ... and we are definitely original!!

I'd love to hear people's thoughts on this. I'm using these on-line courses to see who might be good to approach and who to definitely avoid in addition to learning genetics.

 

[Waverunner]

@Aileen: Excellent idea. I would put a lot of effort into this project. If we could do the interpretation ourselves, we could save around $8,000 but another huge advantage would be, that we could pool CFS data and compare it to healthy people. I'm 100% sure, that we, the patients, have to take action ourselves. Right now I'm waiting for a reliable company to offer full genome sequencing for a reliable price, without interpretation and without the requirement to have a doctor sign up for you.

A geneticist was asked about what software he would use to analyze his genome and he said, that the best way would be to use GenomeStudio. Most of the professionals use it. He even said, that it could be used for 23andMe raw data but I have no clue how this should work and I couldn't find any reference, that would support his view. GenomeStudio can be found here:

http://support.illumina.com/array/array_software/genomestudio/downloads.ilmn

Illumina is one of the market leaders or even the leader in producing sequencing systems.

 

[Aileen]

I may have found an already existing way to make some sense out of our raw data. Well, I should say the lecturer in one of my courses told us about it Encyclopedia of DNA Elements (ENCODE)
Maybe someone with some computer programming knowledge and/or a slightly more advanced knowledge of genetics could take a look.

From: http://www.genome.ucsc.edu/ENCODE/
"The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

ENCODE data are now available for the entire human genome. All ENCODE data are free and available for immediate use via ... [ list of different methods on their site]

--------
And from: http://www.genome.gov/Pages/Research/ENCODE/ENCODE_UsersGuide.pdf

"... to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and health. ENCODE is ... a collective effort to discover and define the functional elements encoded in the human genome including genes, transcripts, transcriptional regulatory regions, chromatin states and DNA methylation patterns. ..."