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My SNPs

Why Doesn’t StrateGene Report on APOE SNPs?

StrateGene does not report the APOE genotype. APOE SNPs present unique challenges for genotyping analysis using array technology. This leads to discrepant results from multiple assays. First, if we are not confident in our accuracy of a specific rsid

My notable variation for a haplotype says "indeterminate" - what does this mean?

An "indeterminate" haplotype will appear when the SNPs that make up the haplotype could not be called. For example, it will state "indeterminate COMT haplotype". One or more SNPs will show a call of "-", meaning that the lab was unable to report that

How come the StrateGene SNP list is so different from what I am reading elsewhere online?

The StrateGene report only includes SNPs that reach significance based on evidence that shows potential dysregulation in biochemistry, has known disease associations, causes diseases in many different ethnic populations and has clear enzymatic change

How accurate are the COMT Haplotype speeds?

In short, they're accurate 90-97% of the time depending on the population. This means that 3-10% of the time they are classified as 'unknown'. The COMT haplotypes are gamete phase-dependent. This is a fancy way of saying the series of 4 possible base

How important is MAT1A in the SAM/methionine story?

There are several isoforms of MAT (MAT1aI/III) and MAT2a and there is a complicated switching mechanism back and forth for them depending on the nutritional status at any given moment. In low methionine/fasting conditions both BHMT and MAT1aI/III get

My COMT speed (specifically V158M/RS4680) was different in a previous StrateGene report than what is being reported here in my new StrateGene. Why is this?

Short answer: In many nutrigenomic reports the COMT V158M was seen as 'slow' if +/+ and ‘fast” if -/-.   In vitro/test tube results do show this result when you focus on only the one SNP rs4680.  Researchers now know this isn’t an accurate portrayal

What does “increased risk” mean?

In medicine, risk is defined several ways: relative vs. absolute, for example. In short, increased risk is the probability of an outcome in an affected group compared to the probability of an outcome in an unaffected (control) group. You can read mor

How can I find more information about a particular SNP?

Go to Scholar.Google.com and type in the rsid number of the variant you would like to learn more about (e.g.: rs7412). Google Scholar will return a list of any research including that search term. This search is often more helpful than Pubmed, as Pub

I see results reported as NA, NC, or "indeterminate". What does this mean?

When you see an "indeterminate" SNP on your report, or "Note: Unfortunately, the presence of this SNP could not be determined from your saliva sample. This prevents its use in the assessment of this gene.", this means the SNPs could not be called due

What is meant by "tag SNP"?

Scientists have discovered over 100 million SNPs that occur across the world's population. There is no genetic testing technology that can detect that many potential variants in a single test array. Therefore the genome is sampled initially by geneti

Why are alleles for SNPs in genes such as SOD2, COMT, and MAO reported differently from other services such as Genetic Genie?

These genes and their mutations are somewhat special cases, since any allele, be it wild or variant, has risks and benefits. This quality makes the assignment of risk allele difficult. We decided to represent the wild type as (-) and the variant type

My report is showing a COMT haplotype, however the "Advanced Tables" are missing my COMT SNPs. Where are they?

The link to the haplotype explanation is directly below the dopamine Advanced Tables if there is a haplotype present, as shown in the example below:. The SNPs for the COMT haplotype will not show up in the table, but are present in the notable variat

Why is your SNP list is so different from what I am reading in another report/online elsewhere?

The StrateGene report only includes SNPs acknowledged to be true functional variants. This means they reach significance based on solid evidence that shows potential dysregulation in biochemistry, has known disease associations, may cause disease in

I am heterozygous for a SNP and it seems better/worse than being homozygous for the mutation. Is this a mistake?

No, it is not a mistake. What you are witnessing is called ""molecular heterosis" and it appears counter-intuitive at a molecular level. For example, if homozygous wild type (AA) has “normal” gene expression, and a mutation (B) decreases that express

What is the difference between wild, ancestral and risk allele? How is that related to variant, minor(ity) or major(ity) allele?

Wild allele typically references the majority allele in a specific population although the term major allele is often used too. Major allele commonly references the most common allele across all populations (but not always, it may only be referencing

I have several bad SNPs, but no evidence of disease, what does this mean?

This may be explained by phenotype: expression of traits and characteristics that arise with interaction with diet and environment. Phenotype thus differs from genotype which is simply your genetic code, not its subsequent potential expression (pheno

How many RSIDs are included in the raw data?

The raw data contains 660,199 RSIDs spread across the entire human genome. StrateGene uses a microarray which looks at targeted variations on all genes. It is not a full genome genetic test.

Why does StrateGene not evaluate GAD1 SNPs?

In a review of the literature, it becomes apparent that single GAD1 SNPs in isolation do not play a major role in many mental health conditions. While it is well established that lower GAD1 expression is found to exist with bipolar disease or schizop

What is a proxy rsid#?

A proxy rsid# is a surrogate or stand in for a rsid# that fails to meet quality control and/or cannot be successfully called by the microarray. A proxy rsid# is detectable by the array and has extremely high linkage disequilibrium (D prime) as well a

I cannot find a gene in StrateGene raw data, but I know it is there, what now?

Currently, raw data browsing is available only using rsID’s. In the future, we will add the ability to browse by gene abbreviations.

What are kinetics, and what does "contradictory"/"controversial" labeling mean?

In a perfect world, research to understand how genetic mutations change enzyme expression and/or activity would be solid and reproducible. In fact, very few enzymes fall into this category. Those tend to be enzymes involved in drug metabolism and, ev

Throughout my StrateGene report, individual SNPs are reported as (+/-) or (-/-), however for haplotypes I see report speed only, and no "(+/-)". Why is this?

Haplotypes represent combinations of (+/-) or (-/-) spread over two or more SNPs, sometimes in more than one gene. This makes for a more challenging way to represent the findings in shorthand form of "(+/-)". We choose aliases or titles that follow t

I have several SNPs, but no evidence of disease. What gives?

This may be explained by phenotypic expression, which differs from genotype. Perhaps that patient has an excellent diet and lifestyle that minimizes the effects of the SNP. Many mutations also have low penetrance, meaning few individuals carrying tha

My patient has all the signs and symptoms of a MTHFR defect but no SNP, what gives?

Even a "normal" gene can express altered enzyme activity. Look at the regulatory factors for that gene: Perhaps your patient has heavy metal toxicity, lack of cofactors, chronic infection, etc that are affecting the gene, even in lieu of a SNP. Anoth

Some of the gene names in the report do not correspond with other names I have seen listed elsewhere: what does this mean?

The literature for genetic mutations spans several decades now and over that time different names have been used to identify the same gene. Strategene uses the standardized name as identified by genecards.org. We have chosen however to use the most p

What are haplotypes?

There are many definitions for haplotype, see here for more: https://en.wikipedia.org/wiki/Haplotype. For the purposes of this PDF, a haplotype is a group of single-nucleotide polymorphisms (SNPs) on one chromosome that are statistically shown to be

Can you tell me more about SNP kinetics? (Indicated with arrows in the report.)

In a perfect world, research to understand how genetic mutations and polymorphisms (e.g., SNPs) alter enzyme expression or activity would be robust and reproducible. Unfortunately, very few enzymes fall into this reasonably well researched category.