In LiveWello, is minor allele always +? Can I override?

[shoponl]

As far as I can tell, LiveWello always assigns "+" (and a red code) to the minor allele. This is misleading when the minor allele is the better one to have, or there is no clearly advantageous allele.

Is there a way to override the minor = + designation when making a template?

Thanks

 

[FightingCFS]

The Minor Allele is one of 4 nucleotides: A, T, C or G not + or -. I think you are referring to the DNA strand which is always on the plus strand which as I understand, is the same strand used by 23andMe, dbSNP, 1000 Genomes and the GWAS Project.
If what you want to do, is to edit the minor allele, I finally figured this out. Make sure the Gene report is a template, then click the edit button to edit the minor allele. This is what I found in their FAQ:
"The SNP Sandbox feature 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 & Gene Library, users can access their results for up to hundreds of thousands of SNPs..." http://bit.ly/1jGMprx

 

[Valentijn]

@FightingCFS - The impression I'm getting is that @shoponl is saying that Livewello is marking the minor (rarer) allele as being the risk (+) allele, even when it's a beneficial rarity, or when there is insufficient data to determine if there's any risk allele for that SNP.

@shoponl - Do you have an example of where they're doing that?

 

[FightingCFS]

Ohhhh! as far as I know, Livewello doesn’t use the term “risk allele”. From what I see at the bottom of my report, I think they just mark a pair of minor alleles as homozygous for a trait. And sometimes they also provide studies relating to it if they're available. But I haven’t seen that they suggest that a SNP will cause or protect against a disease. My assumption was that the coloring system used by all these Apps was referring to Homozygous (red), Heterozygous (yellow) and green for absence of the variant allele. Variant allele meaning rarer form of an allele i.e wild type or more common phenotype. Thanks for clarifying the question though Valentijn. Ugh! so much to learn.

 

[shoponl]

@Valentijn and @FightingCFS,

Yes, that's it exactly, Valentijn.

For example-- in this post, nandixon lists the alleles associated with inflammation from vitamin E:
http://forums.phoenixrising.me/inde...-to-inflammatory-cytokines.19377/#post-556000

"TNF rs361525
GG = pro-inflammatory (increases TNF-α)
AG = anti-inflammatory (decreases TNF-α)
(AA is rare)"

But LiveWello shows the rs361525 GG variant as "-/-" or green (favorable) on all its reports. For this SNP, the best versions to have (at least as far as vitamin E is concerned) are the rarer AG or AA alleles. So the red/yellow/green colors shown on the report don't reflect the true effect of this SNP. https://livewello.com/library/vitamin-e-pro-inflammatory-snps?author=momhill

The red/yellow/green color coding system on LiveWello and elsewhere just isn't always helpful. In some cases a rare SNP allele is beneficial. In other cases, a SNP variant would be positive in some situations, but negative in others... for example, with SNPs influencing cholesterol metabolism, SNPs leading to low plasma cholesterol should be green from the perspective of heart disease, but red when evaluating the risk of stroke and depression.

It would be great to be able to choose the color (red/yellow/green) for each template. Most of the time the rare variant is the negative one, but not always.

 

[Valentijn]

The red/yellow/green color coding system on LiveWello and elsewhere just isn't always helpful. In some cases a rare SNP allele is beneficial. In other cases, a SNP variant would be positive in some situations, but negative in others... for example, with SNPs influencing cholesterol metabolism, SNPs leading to low plasma cholesterol should be green from the perspective of heart disease, but red when evaluating the risk of stroke and depression.

Agreed. It's not applied thoughtfully in many cases, such as when +/- results in completely normal gene function. Why would that be yellow? It sounds like they're trying to cut corners, and are probably just including each SNP which is mentioned as being researched anywhere, but using Minor Allele Frequency instead of actually reading the research to see if 1) the SNP is actually relevant, and 2) which genotypes are actually associated with risk.

It would be great to be able to choose the color (red/yellow/green) for each template. Most of the time the rare variant is the negative one, but not always.

Usually it's pretty straight-forward where the risk is, so this shouldn't be necessary. It gets complicated with psychological SNP research, but that might because most of that research is very low quality and fishing for connections where there might not be any. This can happen when they increase the number of SNPs or number of "personality traits", etc, which are being considered, but they fail to account for increased rate of false positive results.