Hi again Kobe,
I am pretending that you know how to search your raw data and how to interpret.
Disclamer: Please know that I am not an expert but this below is how I interpret what I have read.Will start with this paper that I found the other day,
From (Sep 2016)
Capecitabine Therapy and DPYD Genotypehttps://www.ncbi.nlm.nih.gov/books/NBK3 ... rt=classicIt has info about 3 important DPYD SNPs and & rsid# are included.
All 3 of them can be found in my 23andme raw data ! Direct link to a table in the paper
https://www.ncbi.nlm.nih.gov/books/NBK3 ... objectonlyThese are the SNPs DPYD*2A rs3918290 Alleles G or A Risk allele A
Note: 23andme Alleles C or T - Risk allele
T* DPYD*13 rs 55886062 Alleles T or G Risk allele G
Note: 23andme Alleles A or C - Risk allele
C* (2846A>T) rs 67376798 Alleles A or T Risk allele T
Note: 23andme Alleles A or T - Risk allele
A* ("Note that the "A>T" term in the name used in the literature for this SNP can be confusing, since the gene is in reverse orientation to the chromosome strand on the reference genome." https://www.snpedia.com/index.php/Rs67376798
Plus see below * * = “Genes are read (transcribed) in either the forward or reverse direction, as numbered along the chromosome. If a new build comes along that flips a large segment of a chromosome, the gene direction will change. As a result, at different times, as well as in different publications or different databases, the same SNP can be defined as being on the forward (plus) or as being on the reverse (minus) strand. In terms of the nucleotides for that SNP, the pairing of A with T, and C with G, in the DNA double helix means that an A on the plus strand by definition is a T on the minus strand, and vice versa, and a C on the plus strand means a G on the minus strand (and vice versa).” “Companies follow their own protocols, which are often different. 23andMe currently reports all genotype data based on the plus strand of GRCh37, whether or not dbSNP defined the SNP as being on the plus strand (in that build or any other build); they explain this for their customers … here (
https://customercare.23andme.com/hc/en- ... -Genotypes ).
This often leads to confusion since a 23andMe customer may see a genotype in their raw data that will not match the genotypes defined by dbSNP, in SNPedia, or in their Promethease report. This will most often happen when the StabilizedOrientation is minus. In these cases, the alleles need to be "flipped" to match:
A->T
T->A
C->G
G->C
” Reference:
https://www.snpedia.com/index.php/OrientationLinks to Snpedia for these 3 SNPs for more research reading/info about them:
https://www.snpedia.com/index.php/Rs3918290https://www.snpedia.com/index.php/Rs55886062https://www.snpedia.com/index.php/Rs67376798-------------
Here is another recent paper from 2017 that mention
5 SNPs, the first 3 are the same as the above. I have not looked/found rsid# for the last two yet.
Pharmacogenetic testing through the direct-to-consumer genetic testing company 23andMehttps://bmcmedgenomics.biomedcentral.co ... 017-0283-0“
For 5-FU toxicity, the frequency of DPYD*2A is low in all populations. It is almost non-existent in African-American and Japanese populations, and has frequency of 0.91% and 0.47% in Dutch and German populations respectively [26].”
“For 5-FU, 23andMe tests only for the *2A variant, but as 23andMe state on their website, further variants in the gene are associated with 5-FU toxicity. For example, recent studies have shown that DPYD*13, rs67376798, c.1679 T > G and c.1236G > A/HapB3 are also associated with 5-FU toxicity [28, 29, 30].”
Kind regards /L
DH @ 65 DX 4/11/16 CC recto-sigmoid junction
Adenocarcenoma 35x15x9mm G3(biopsi) G1(surgical)
Mets 3 Liver resectable
T4aN1bM1a IVa 2/9 LN
MSS, KRAS-mut G13D
CEA &
CA19-9:
5/18 2.5 78 8/17 1.4 48 2/14/17 1.8 294 Folfox 6/15-7/30 (b4 liver surgery) 8 after
CT: 8/8 no change 3/27/17 NED->Jan-19 mets to lung NED again Oct-19
Steroid induced hyperglycemia dx after 3chemo
Surgeries 2016: 3/18 Emergency colostomy
5/23 Primary+gallbl+stoma reversal+port 9/1 Liver mets
RFA 2019: Feb & Oct lung mets