This blog is a way of sharing the information and resources that have helped me to recover my son Roo from an Autism Spectrum Disorder. What I have learned is to view our symptoms as the results of underlying biological cause, which can be identified and healed. I say "our symptoms" because I also have a neuro-immune disorder called Myalgic Encephalomyelitis.

And, of course, I am not a doctor (although I have been known to impersonate one while doing imaginative play with my son)- this is just our story and information that has been helpful or interesting to us. I hope it is helpful and interesting to you!

Monday, August 25, 2014

SNP testing

The term SNP stands for Single Nucleotide Polymorphism, and refers to variation in genes that arise from a single substitution of one nucleotide for another at a specific point along a gene.  Genes are segments of our DNA that are coposed of long sequences of base pairs, which are two of these nucleotides, one from each side of the DNA double helix, that "fit together" like the teeth on a zipper.  A SNP (pronounced "snip") is a variant of a gene that alters the function of the protein that is coded for by the gene.  These proteins can be enzymes, in which case the SNP will alter the rate at which the enzyme works in many cases,  or can be components of cells and tissue, in which case the function of the cell or tissue can be altered.  

Dr Amy Yasko pioneered the use of a person's SNP profile to guide biomedical intervention, which allows dietary, supplement, and other interventions to be more customized and to avoid many potential side effects or poor outcomes.  This testing was very expensive however so not accessible to many.  The company 23andMe has brought the cost way down and provides information on many more SNPs than Yasko testing has.  23andMe has stopped giving out what they call "health info" due to an order from the FDA.  This DOES NOT affect your access to your SNP data which is usually the reason to do the testing.  You can order the test here.  For some basic FAQs about suing 23andMe go here.  Many people feel uncomfortable about having this information about them "out there" so they choose to submit the test kit under a false name.  Forbes has just run an article giving an update about 23andMe's business plan and a possible sale to Genentech, which provides a little more information about what is being done with the data they are collecting.  Once the test is processed, you are sent a link to access your information online.  To find out your SNPs, download your raw data from the 23andMe website, and then run it through one of a number of apps available to generate a SNP report.

Here are some options:

Genetic Genie is free with a suggested donation of $10.  It provides a modest report with some good information about the SNPs found.  You can choose a methylation report or a detox report.

Promethease is another option, it costs $5.  There is a video on the site that gives more information about the service.

I prefer an app called LiveWello, that is more expensive at $19.95 (these costs are all per person, so if you are running 3 people's data from your family you will have to pay for each person).  LiveWello generates a much more comprehensive report, and has a sandbox feature where you can look up your SNPs in any of the raw data by typing in the gene name or rs number (a tutorial for using this feature can be found here).  You also have access to smaller reports made by other users that identify SNPs associated with specific issues, such as Parkinson's, Crohn's Disease, allergies, even production of oxytocin.  If you don't see a template that fits your needs, you can go to google and search for "risk alleles associated with ___" whatever you are interested in.  Then you can copy and paste the rs number into the sandbox feature and find out which SNPs you have for that gene.


There are a lot of tools available online to help you understand the meaning of your SNPs.  Honestly, I have found Wikipedia to be one of the most helpful resources.  The first step is often to figure out what the gene does, the second step is figure out what affect your variation has on it's function.  In addition to these sources, you can simply google your SNP and look for scientific articles that mention it.

A Catalog of Published Genome-Wide Association Studies

Genetics Home Reference

Tales From The Human Genome is a class presented by Udacity and 23andMe for beginners






Basic map from Heartfixer

Basic map from Dr Yasko

Dr Yasko's methylation maps

Methylation basics from Wikipedia

The Role of Methylation in Gene Expression


Know Your Genetics will provide a Yasko Methylation Protocol Analysis

This sample MPA (from above) can help you begin to process your SNP information

Amy Yasko's book Autism: Pathways to Recovery

The workbook for Pathways to Recovery

Genetic Bypass by Dr. Amy Yasko

Articles by Dr Yasko

Videos of presentations by Dr Yasko

Slides from Dr Yasko's presentations