"I" is an insertion and "D" is a deletion.BTW, looking at a few of my results on 23andme, some of my results have "II" by them instead of a genotype. Does anyone know what that means?
Welcome to Phoenix Rising!
Created in 2008, Phoenix Rising is the largest and oldest forum dedicated to furthering the understanding of, and finding treatments for, complex chronic illnesses such as chronic fatigue syndrome (ME/CFS), fibromyalgia, long COVID, postural orthostatic tachycardia syndrome (POTS), mast cell activation syndrome (MCAS), and allied diseases.
To become a member, simply click the Register button at the top right.
"I" is an insertion and "D" is a deletion.BTW, looking at a few of my results on 23andme, some of my results have "II" by them instead of a genotype. Does anyone know what that means?
The location data (chromosome # and position on that chromosome) can be used to look up the rs number, but the rare allele program also includes the rs number "translation" when 23andMe uses an i number.Every "i" number that I Googled has almost no information.
Yeah, it's something I've been thinking about. But it would mean another database which needs to be downloaded and added complexity to the program. I'll talk to the programmer about it@Valentijn - you know what would be handy? An extra column in the results showing the related gene. This would make it easier to search google for info on it, but more useful than that it would also allow you to order by gene and then see if you have other compound mutations within that gene within the results.
So the double II means both base pairs got inserted?"I" is an insertion and "D" is a deletion.
Yup. It's pretty common to have insertions and deletions, and it's usually not indicating anything interesting.So the double II means both base pairs got inserted?
Well, it will pick up heterozygous mutations where the minor allele is at 10% prevalence. That means that the heterozygous genotypes would be reported going up to a (calculated) 18% prevalence rate for that genotype.@Valentijn - does your program have a report for those mutations that are greater than the 10% rarity? I'm thinking specifically of those which are labeled with an "i" code by 23andme. I'm thinking these might also be interesting to identify?
My preferred source for SNP info is dbSNP, which has data for this SNP at http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs121908515 . From there you can click on the [detail] link after the red "With pathogenic allele" text. That leads to http://omim.org/entry/604277#0015 which will give very detailed info about that specific SNP.
Basically that SNP has a definite and more severe impact when homozygous or compound heterozygous. Some people with a simple heterozygous mutation have a milder version, and many are asymptomatic. It's possible that the patients with simple heterozygous mutations also have a second pathogenic mutation which was not detected yet is necessary to cause the problem.
Yeah, those are probably not important. Similarly, known missense mutations are a lot more interesting as well.Genome analysis is fun. I have three homozygous SNPs (no clinical data available). All three are located in intron regions of my genome. Can we therefore conclude, that their importance is probably minor? I'd love to have my whole genome sequenced and run through this analysis tool.
Probably, but I've never looked for it. I'd start with dbSNP, 1000 genome project, and/or OMIM.Val - Is there a database somewhere accessible that lists known missense mutations?
SNPedia is a good start. I prefer dbSNP, where I can easily see missense mutations and such, plus links to more of the research. Basically SNPedia is more user friendly, but contains less data and fewer SNPs.this is neat, i analyzed my genome - now what? is there an easy way to interpret the SNPs? should we use SNPedia?
I am, but only for patients who have CCC/ICC-defined ME with post-exertional malaise if they exceed their limitations.This is such a great program. Thank you for creating it @Valentijn and for all you do to help others learn how to navigate their 23andMe data. Are you still collecting people's data and compiling it?
I forgot to mention - it will also fully support the newer V4 23andMe chip. The older version was designed only around the V3 chip (960,000 SNPs), though the SNPs did overlap quite a bit with the V4 chip and gave quite a few results for patients with V4 data.As a heads-up to those who are interested, there should be a major update to the Analyze My Genes program in the next week or two. It's been nearly two years since it was created, so I guess it's somewhat overdue