How to Search Raw DNA Data Files for BCHE Variants

A few years ago, I was lucky enough to find a gene variant that greatly impacts my life. The BCHE variants. Learning this information changed my life and I found the relief I had been searching for.

BCHE variants can reduce butyrylcholinesterase enzyme activity. These enzymes are involved in detoxing pesticides, herbicides, the alkaloids in nightshades, and more. BCHE is also involved in regulating the hunger hormone ghrelin, and involved in fat accumulation. BCHE also metabolizes certain drugs. 

I found the BCHE variants using my Ancestry raw DNA data and uploading it to Promethease. 

Unfortunately in 2019, the gene variant disappeared from my Promethease report. In November 2018, the FDA banned Pharmacogenetic genes from displaying on consumer DNA reports. Promethease had to pull them from their reports. Ancestry removed the gene from their RAW DNA data. Completely hidden....WHY???

The FDA does not want people to stop taking their medications. They prefer hiding the important information from people. Why not a simple warning - to talk to your doctor before stopping medications? I mean we are adults, and we should be able to make our own decisions. 

The FDA is also concern that the discoveries by geneticists have not been backed up by studies. Geneticists are WAY ahead of the studies. These studies are normally paid for by drug companies.  Getting funding for a study, and then actually doing the study can take several years. Even if you found funding today, it could be 10 years before we have the results. I'd actually like to live my life and enjoy it - NOW. I don't have YEARS to wait for studies to be done to tell me what I should or shouldn't be feeling. Figuring out a nightshade and cholinesterase inhibitor sensitivity, without knowing this information, is extremely difficult. It shouldn't be hidden from us.

For now they are hidden. However, we have figured out a way to find them. 23andMe has special permission from the FDA to include the pharmacogenetic genes in their RAW data. I did another DNA test to confirm this and my BCHE variants are in the raw data as of 2022.

You still need to know how to find them because they are not included in their simple health reports. You don't need to pay for the full $200 fee for the "health" report. You can find these genes by ordering their less expensive 23andMe Ancestry report. You just want the raw data....not their fancy reports telling you what color of eyes you may have or that you may prefer chocolate over vanilla. You already know that right?

You can view the 12 Cholinesterase Inhibitor Sensitivity genes on SNPedia. Cholinesterase Inhibitors are pesticides, herbicides, certain foods including nightshades, caffeine, some prescription drugs and street drugs, and nerve gas. Yep that's right, chemicals that can kill people, are in low levels in the foods we eat and products we put on our bodies. If your body has a gene variant that causes a CI sensitivity, low levels of CIs in foods may make you sick. Trust me, this is a thing and nobody knows about it.

Do you want to find out if you have any of these gene variants?

You'll need your raw DNA data from one of these site:

• 23andMe
• Ancestry - but raw data must be from 2018 or earlier.
• Genes for Good - but raw data must be from 2018 or earlier. My report had less variants than the others.

These companies put your raw DNA data into a text file when you download them. Visit their sites and find those instructions. 

Instructions for 23andMe:

If you have 23andMe, from their web-site, go to the upper right corner where your name is. Click on your name, then click "Search Raw Data". From there you can download your raw data or browse the data.

If you browse the date, search for BCHE and it will list ALL of the BCHE genes. Or you can search each SNP individually to find the the 4 cholinesterase inhibitor sensitivity genes. Searching the 4 SNPs is easier. 

Here are the SNPs to search for:

• rs1799807 
• CT (A-Typical BuChE)
• CC (A-Typical BuChE)
• TT (Normal, Typical)
• rs1803274
• CT (K Variant)
• TT (K Variant)
• CC (Normal)
• rs28933389
• AA (BCHE FLOURIDE 1)
• AG (BCHE FLOURIDE 1)
• GG (Normal)
• rs28933390
• AA (BCHE FLOURIDE 2)
• AC (BCHE FLOURIDE 2)
• CC (Normal)

Click each SNP listed above to read more about it on SNPedia. If you compare your raw data to SNPEDIA, the genotypes are flipped. If your raw data says rs1799807 TC in 23andMe, it's Rs1799807 AG in SNPEDIA. 

Flipping Genotypes from 23andMe to SNPedia:

• A->T
• T->A
• C->G
• G->C

PON1 - Paraoxonase 1 Gene (Update with genotypes)

• rs854560
• rs662
• rs705379
• rs705381

If you search for a SNP and nothing comes up, the SNPs have been omitted from your raw data. I found that some my PON1 SNPs were missing from 23andMe, but found one in my older Ancestry data.

Ancestry or Genes for Good Instructions:

If you have Ancestry data, prior to 2019 or Genes for Good, follow these steps to find the variants:

1. Locate the raw data on their web-site and download.
2. Open the text file and open Excel. I find it's easier to search for the gene variants in Excel.
3. Copy the text file and paste into Excel.
4. Delete the header data.
5. Then you need to search the Excel file for the SNPs listed above.
6. If you have a match, you click on the SNP and read the genotypes and compare above.

Genetic Genie GenVue:

If you've downloaded your raw DNA data, you can upload it to Genetic Genie, GenVue Discovery. If you have A-Typical BuChE, it will be displayed under "Other Risks" and look for BCHE (image below). This is the only Cholinesterase Inhibitor sensitivity gene in Genetic Genie.

Livewello

For a small fee, you can also upload your raw DNA data to Livewello. From there you can do a search for each of the SNPs listed above. 

Remember the genotypes are flipped in Livewello, if you view these SNPs in SNPedia.

• A->T
• T->A
• C->G
• G->C

What if my cholinesterase inhibitor sensitivity genes are all normal?

If you don't have the variants, but still suffer from pain, fatigue, anxiety, headaches, spasms, and more; you can still have reduced cholinesterase enzymes. Pregnancy, birth control, a stressed liver or kidneys, malnutrition, eating a lot of nightshades, pesticide exposure, etc. - Can all cause reduced cholinesterase enzymes.

You can get your cholinesterase enzyme levels tested through a simple blood test. You can ask your doctor to order, or order testing through Ulta Labs and locate a local facility to do the blood draw. I have two of the BCHE variants listed above and my cholinesterase enzyme levels are low.

RESOURCES:

The genotype is flipped in the raw data. This explains it:

https://www.snpedia.com/index.php/Orientation 

Statement from the FDA

MORE INFORMATION:

Cholinesterase Inhibitors by Anne Wright

Nightshade Sensitivity & Anesthesia Risk

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