How to learn about your individual Single Nucleotide Polymorphisms (SNPs) related to Cannabis (or anything else).
Disclaimer: The information found on this website is for educational and scientific purposes only. It is to help you inquire about what is in your DNA. It is not for interpretation. For detailed questions on how any genetic marker may be related to your health, please consult a licensed genetic counselor. Any questions on specific medical, or lifestyle changes, should be directed to your doctor, a certified genetic counselor or other health care professional.
*Remember that these SNPs are not in the human genome because of cannabis. They are there for all kinds of reasons, mostly related to basic neurological, biochemical, or metabolic functioning. Please read the sections on Genetics in the book to put this type of genetics into perspective.
If you have taken a whole genome genetic test from direct to consumer genetic companies like Ancestry.com or 23andMe or other companies, you have most likely spit in a tube and mailed it back to the company. They typically extract the DNA from your sample and perform a test with a whole genome genotyping chip. This is not whole genome sequencing.
These are tests that often identify millions of Single Nucleotide Polymorphisms (SNPs). A few weeks later you get a report about the results. If you did this, it was probably not that exciting or informative, since most SNPs code for changes that have very small effects or are neutral with no effect at all. With most SNPs, we don’t know anything about any effect they may have. Also, the tests these companies do only test a small subset of all the known SNPs and other genetic variants in the human genome.
In the results the company sends you, including the associated data files, you should look for a text file, or CSV file with the words “raw data” in the name. The data files may be in a zipped format and you may have to unzip them with an unzip utility program such as WinZip or 7-Zip. The file names may change over time. The raw data file from 23andMe may have the word “genome” in the name. The Ancestry.com file may be called something like “AncestryDNA raw data download”. You can contact third party companies to analyze these files for additional analysis beyond what 23andMe or Ancestry.com provides. Here are descriptions for the raw data download for 23andMe and Ancestry.com.
You can open these raw data text files in a spreadsheet program like MS EXCEL or in a text editor such as EditPadLite. This file may be very long, between 500,000 or over a million lines. Excel may not be able to open a file over 1 million lines long. You may be able to open the raw file in a text editor first, and cut and paste it into smaller files less than 1 million lines each. Excel can handle over 1 million lines each if you copy and paste less than 1 million lines into different worksheets in the same file. A convenient way to chop up this data is by chromosome. Human chromosomes get smaller as the chromosome number goes up. Chr 1 is the biggest, Chr 23 is the smallest. You can probably get all the data for Chr1 and 2 in one Excel worksheet, then all the other chromosomes on one or two other worksheets.
You may want to remove the information in the header lines if they are at the top of the file. These header lines may start with a hash tag #, meaning they are not part of the raw data, just informational stuff. Once you have removed the header lines, the data should look something like this.
There should be a small number of columns and a long number of rows, 500,000 to over 1 million. You should see the rsid# (or SNP id #), what human chromosome it is found on, the nucleotide position of the SNP, and your 2 variants at each SNP. One on each chromosome. One from Mom and one from Dad.
When you open the file in a spreadsheet program it may look like this.
How to lookup SNPs in SNPedia.
Go to: SNPedia at this web address: https://www.snpedia.com (I am not affiliated with SNPedia in any way). Search for the word Cannabis (or anything else you may be interested in)
These are the current records (12-12-2020) or RS-ID numbers in SNPedia that mention Cannabis. If you can’t focus in on the relationship of that SNP to cannabis, do a search with the SNP RSID# and the word Cannabis at the same time (or anything else). Some SNPs have a lot of info, others don’t. On many SNP description pages on the upper right, you will see the nucleotides that are important in different traits (A,A; A,G;G,G, etc) for that SNP. Here is a good example: Rs4680
Click through any SNP record in SNPedia to learn about that SNP. Then search your raw data file for each SNP. Your particular raw data file may not have all SNPs. Some may be missing. Different companies may provide different or conflicting results. Be careful of upper or lower case. On the right hand side of each SNP record in SNPedia there are also many links to other public databases that have information about that SNP such as dbSNP, ClinGen, etc. Endless hours of fun.
Copy any important RS# in SNPedia, go to your prepared EXCEL file of raw data, highlight the column of RSIDs. Hit CTRL F, to activate the search or find window. Search for that individual RS#. Look in the Allele1 and Allele2 column for your allele types. That is what is in your DNA for that SNP. Such as A,A or C,C, or T,G, etc.etc. There may be ambiguity codes such as I, or other letters rather than the standard A,T,C,G.
Be careful to match the RS# exactly. Some smaller RS#s may be contained in a larger one; such as rs6277 is contained within rs627705, they are two different SNPs. Then go to SNPedia and search for that SNP. Read the record in SNPedia for each SNP you are interested in. Read about what nucleotide A, T, C or G may be associated with different traits. Remember that certain traits may also be modified by other SNPs you may carry.
IMPORTANT: In almost all cases, the large majority of SNPs are not useful in determining that you will get a disorder or a disease. They are more likely to be relevant to predispositions to certain traits. Most SNPs are neutral or of unknown function. Something more to think about rather than something to act on.
If you have any questions about the information on this page, drop me a line.
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