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Familial defective apolipoprotein B-100 (FDB) is an autosomal dominant disorder associated with increased plasma cholesterol concentration and may thus increase the risk of premature coronary heart disease. To date, three apo B mutations, apo B R3500Q, apo B R3531C and apo B R3500W that cause defective apo B, have been reported.

I have my raw DNA data from 23andMe (where each line corresponds to a single SNP). How can I search it for those related Apo B gene mutations?

A single line in my DNA data looks like this:

rs12567639 1 756268 AA

I have a programming background, but none in the bioinformatics area.

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    $\begingroup$ There are a fair number of members that could answer this. They might think this is too difficult to easily explain because this is an easy answer, but it's alot of explaining given your background. It would be helpful to try and provide the key information, a couple of lines of the output placed into the answer - you've probably got a simplified VCF. The reference genome used is really important (the company should supply and the original VCF). If there's no answer then VarSome is one company that could do this (no affiliation). I'm no longer involved in eukaryotes apart from immune stuff. $\endgroup$
    – M__
    May 4, 2023 at 16:06
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    $\begingroup$ Anyway its a good question (in my opinion) and good luck with the analysis. Upvoted. $\endgroup$
    – M__
    May 4, 2023 at 16:48
  • $\begingroup$ For some reason 23andMe uses genome positions from the previous genome assembly. Anyway, what counts are the identifiers, like: rs12567639 $\endgroup$
    – darked89
    Jun 7, 2023 at 9:37

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If you are interested in ApoB gene variants you can:

https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000084674;r=2:21001429-21044073;v=rs5742904;vdb=variation;vf=184237596

But I assume all of this is moot since 23andMe should give you some summary of the results and not just the raw file, right?

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  • $\begingroup$ 23andMe doesn't give any health recommendations to their clients outside of the US. All I got was the raw file, some ancestry data and human traits probabilities. $\endgroup$ Jun 7, 2023 at 14:45
  • $\begingroup$ OK, just to make sure: did they send you any non high cholesterol related potentially pathological trait probability? Anyway, if you want to extract relevant markers/sequence variation from your results or rather intersect these the above ApoB pathogenic markers not one by one you probably should start with getting either command line on Mac or WSL (Windows Subsystem for Linux). $\endgroup$
    – darked89
    Jun 7, 2023 at 15:32
  • $\begingroup$ To give you some idea about the task: one can obtain all variants for the human APOB gene and their putative clinical significance using BioMART from ENSEMBL and ENSG00000084674 gene id. The result is a TSV (tab separated file). Selecting the column with variant IDs and getting the relevant lines from your 23andMe text file is trivial on Linux/Mac command line (awk and grep commands). I am not familiar with Power Shell but looks like Select-String does not have the same functionality as grep. $\endgroup$
    – darked89
    Jun 7, 2023 at 15:55
  • $\begingroup$ No pathological traits from 23andme whatsoever. I'm fairly proficient with the command line. Just need to devote a couple of hours analysing your answer :) $\endgroup$ Jun 7, 2023 at 19:12
  • $\begingroup$ of course 23andMe won't give you health recommendations. That would be irresponsible. $\endgroup$
    – swbarnes2
    Jun 7, 2023 at 19:36

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