This was copied from a Facebook post made by the Founder and Lead Developer of Livewello who is also an M.D. and has a son on the #Autism Spectrum
"I'd like to share with you the reason why 23andMe Gene results sometimes differ depending on the App used. This is because of the Minor Allele used:
All of LiveWello's Minor Allele information is retrieved directly from dbSNP. A link to dbSNP is added to every SNP in a Livewello Gene Variance Report. That way, a user and their Practitioner can verify minor allele information for themselves.
At Livewello, we only use the forward strand for interpreting all our SNPs. This is because it is the same strand that is used by 23andMe where the Gene Tests are done. Be aware that other reporting authorities/ Apps do not consistently do this, and will sometimes report minor alleles from the minus strand.
Our goal at Livewello is to make our Gene App reporting more consistent and reproducible by using the same methodology for analyzing each and every SNP, rather than by using ad hoc techniques.
We have chosen to use a more consistent approach which shows a person’s actual phenotype, to be based on the presence or absence of a minor allele.
For example the Risk Allele for MAO B (rs1799836) is ‘C’ in Livewello's Gene Report. It is listed in dbSNP/1000Genomes as the MAF or Minor Allele Frequency (occurring with 43% frequency in the default global population).
dbSNP(NCBI) also lists the refSNPs as "A/G". (The ref SNPs, unlike the MAF, is supposedly only reported on the plus strand).
This would mean that only either "A" or "G" is found at this location on the plus strand of the genome. Conversely, only "T" or "C" can be at this location of the minus strand. So since "C" always pairs with "G" and "C" is being reported as the MAF, it means that we should be using "G" as the MAF instead because your 23andMe raw data is reported on the plus (forward) strand, and not on the minus strand.
We realize that there will still be those who would prefer to alter the allele information to suit their needs. For this, we have added the SNP Sandbox feature which is free with your Livewello Gene App. It gives users the ability to edit minor alleles to see what their phenotype would look like using different values. The intent of this feature is to offer flexibility as users utilize their Variance Application.
It also offers users access to their results beyond the 300 SNPs in standard variance reports. Using SNP Sandbox, users can access their results for up to 300,000 SNPs:
Finally, as always, every Gene in your Livewello report comes with LIVE hyperlinks to the very latest research information from PubMed, dbSNP, Ensembl, SNPedia and Google Scholar. Just log in any day, any time, to view it.
As the genetics community learns more about SNPs, the interpretation of genetic raw data, will likely change. As it is, nearly everyday, new research is being added. This is why your Livewello Gene App is designed to offer users free App updates. For me personally, as the father of a child on the Autism Spectrum, I think it is crucial that we are all able to have easy access to such important information.
If you have further questions regarding this or another issue, please do not hesitate to contact us at: firstname.lastname@example.org
I wish you and your family all the best.
Kwame Iwegbue M.D
Founder and Lead Developer
Navigating the research resources in your Livewello Gene Report:
Since making this video, you can click on each Gene in your LiveWello Gene Report and it pulls up LIVE Research information on each Gene from PubMed, SNPedia, dbSNP, Ensembl and Google Scholar: https://vimeo.com/73068158
Sample Standard Livewello 23andMe Gene App Report:
[ This is just the Standard report. Livewello's Gene App also allows you to generate your report with up to 297,000 SNPs which is the actual number of SNPs in your 23andMe Raw Data ]
Link to post: https://www.facebook.com/kw...
Q: What is a "strand”?
A: Strand refers to DNA strand. There are 2 of these for every gene location. Plus (or forward) strand and minus (or reverse) strand. Both of these have complementary information i.e. they have the opposite nucleotide of a pair of nucleotides: A, T, C, G, such that if one has ‘A’ the other will have ’T’, and if one has ‘C’, the other will have ‘G’. This is usually the way in which nucleotides pair up on a person’s chromosome. So chipsets used by personal genomic data companies like 23andMe, will only read from one of these two chromosome strands, because they can reasonably deduce what should be on the opposite strand.
Q: Why does 23andMe use the plus strand
A: https://customercare.23andm...- "
About The Livewello Gene App: https://Livewello.com/23andMe
#SNP #Gene #23andMe #MTHFR #MAOA
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