At Home Genetic Testing

[Libby]

Those at home genetic testing kits have always interested me for a number of reasons. Ancestry, to a point, but mostly because of the wealth of medical information that would result. It's not for everyone; we still don't know enough about genetics, except in certain cases, to say anything definitively. Knowing can create a lot of unnecessary stress (or a false sense of security). But I like this kind of thing. .

I finally decided to take the plunge a few months ago with 23andme. The FDA slapped them with a cease and desist a few years ago, preventing them from providing medical information, so I had to jump though the added hoop of uploading the raw data into another site (Promethease) for a minimal fee. But wow! Over 18k individual bits of info detailing specific points in your genome, your genotype at those points, and in many cases what research has said regarding what that gene codes for and what your genotype suggests. I've learned that I'm meant to have breast cancer, prostate cancer, and be morbidly obese. lol. Like I said, it needs to be taken with a grain of salt.

I've always suspected that I might have a mutation in the FBN1 gene. My dad's side of the family seems to have some marfanoid traits. Not classic Marfans syndrome - we're not that bad off - but there are a few things. I have stretch marks when I've never had a BMI of even 21, MVP, my arm span is slightly longer than my height, and of course POTS - my brother has a slightly sunken chest (pectins excavatum) - there have been significant heart valve problems all through the my dad's side. Nothing that's prevented anyone from living relatively long lives, but something to suggest there's something there.

And it looks like I do have a few mutations in the FBN1 gene. One in particular, rs2118181, seems to be associated with the vascular component of Marfans, but without many of the other symptoms Marfans patients show (eye problems, scoliosis, etc). Bingo.

Now, I'm not thrilled to have a higher risk of aortic dissection. But I'm feeling super vindicated right now, haha. I had a pompous EP basically tell me that I was an idiot when I suggested something like this to him a few years ago.

Anyway. It doesn't change anything, knowing. But despite the obvious physical symptoms, I've always wondered if I was...not making it up, but maybe exaggerating? Not that I couldn't be exaggerating now. But at least I know that there definitely is something genetic going on here.

[MightyMouse]

I found my own dwarfism gene on the X chromosome a few years ago using 23andMe as well. I ran it through free gene processing on NIH's gene database and then wen through the snp's myself (an snp is a segment of genetic material), segment by segment. About a year later, I did the same thing you did to check my work, running through the Promethease system for a small fee, which replicated my own findings, but also showed me a few other things--for example, I carry a bunch of mutations for hemochromatosis--and now it makes perfect sense why my blood iron readings have always been high. I've shared my findings with my physicians.

For dwarfism genes I carry at least 9 pathogenic alleles for SHOX, a bunch of probable pathogenic alleles, and a bunch with unknown outcome. "Pathogenic" means the genes cause problematic outcomes. You may recall dominant versus recessive genes from your basic biology classes--the problem with my pathogenic genes is that all them fall in a location that's called "pseudo autosomal dominant region" of X. This means genes in this area are expressed as if they're dominant... SHOX, like EDS and Marfans, causes bone and collagen tissue defects, from fragility of blood vessels, hypermobile joints, etc.

When I went to my doctor with my info, I printed out a screen shot of each of the SHOX related gene's location on X, the associated report from NIH for each individual pathogenic and probable pathogenic SHOX gene, along with the general SHOX gene report from NIH, here http://ghr.nlm.nih.gov/gene/SHOX

I am curious. How have your current medical team members responded to your findings?

[sue1234]

MightyMouse, I looked up the SHOX gene in my 23andme data, and it just tells me I have "Your data includes 0(zero) SNPs on this gene, located on the x chromosome". What did you type in in the gene box to look at your SNPs? I typed in SHOX.

[MightyMouse]

Here's how to check accurately:

first, go to the gene broswer, and open up gene x by clicking on the link for it. Then, open the any of the intergenic sequences you see listed under the "gene" column.

Click on the reference link for dbSNP lookup, which takes you to NIH's gene library to cross search your own data.

Scroll down to the integrated maps section, where there is a search box that has the word "find" on it.

Type in the gene you're looking for.

When I type in SHOX, a pop up search window shows from 624344 to 659411 are positive for SHOX.

I have 14 pathogenic sequences (show up as purple blocks). To see the details aobut them, you close the pop up window

go back to the top of the gene map, immediately left of search box you used, mouse over the letter and number sequence right of the blue left facing arrow, which will open it up to "full view" (entrez view is the standard view).

Once the map displays, If you mouse over blocks that are purple, blue, green, it will give you the exact alleles that are pathogenic, suspected pathogenic, benign and unknown outcomes.

Entering SHOX in 23andMe's search box comes up with nothing for me too, but I am most definitely positive for SHOX

[MightyMouse]

So, if I follow all those steps, here's what I see:

http://s85.photobucket.com/user/ninaismighty/media/DINET%20Photos/Screen%20Shot%202015-06-13%20at%208.53.25%20AM.png.html

[sue1234]

How irritating...I got all the way to the screen like you put a picture of, and when I have my cursor hover over the purple areas, nothing pops up. When I bring my cursor to anything outside of the red-lined area, it does show pop-ups. But, bring it back in where all the purple boxes are, and nothing happens. Even clicking on them, nothing happens. I was so close!

[sue1234]

Ok, I finally had to zoom in on the area for the cursor to let the info pop up. So, then that pops up, and I get the "rs" numbers. I type them into my 23andme SNP box, and it won't show anything for them. So, my hopefully last question is, how do you find your A or G data to compare to the data at the purple boxes?

I forgot to mention that I first looked up the location #s, such as 664052(example) instead of SNPs against the X chromosome list I had listed with all the intergenic SNPs. Nothing from the purple dots match any of the numbers, so I couldn't match them up that way.

[ramakentesh]

The problem with diy genetics is that it doesnt tell you which genes are actually expressed and which are epigenetically suppressed