Answers.Body: <p>I think you mean these.  The amino acid numbering has changed, but that happens as we discover more transcript variants.</p>
  <p><a href="http://useast.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=2:21005788-21006788;v=rs5742904;vdb=variation;vf=184237596" rel="nofollow noreferrer">http://useast.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=2:21005788-21006788;v=rs5742904;vdb=variation;vf=184237596</a></p>
  <p><a href="http://useast.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=2:21005696-21006696;v=rs12713559;vdb=variation;vf=186851457" rel="nofollow noreferrer">http://useast.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=2:21005696-21006696;v=rs12713559;vdb=variation;vf=186851457</a></p>
  <p><a href="http://useast.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000084674;r=2:21001429-21044073;v=rs144467873;vdb=variation;vf=251617275" rel="nofollow noreferrer">http://useast.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000084674;r=2:21001429-21044073;v=rs144467873;vdb=variation;vf=251617275</a></p>
  
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Answers.CreationDate: 2023-05-05T21:47:58.210Z
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Answers.UserDisplayName: swbarnes2
Answers.Body: <p>If you are interested in ApoB gene variants you can:</p>
  <ul>
  <li><p>go to <a href="https://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?db=core;g=ENSG00000084674;r=2:21001429-21044073" rel="nofollow noreferrer">https://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?db=core;g=ENSG00000084674;r=2:21001429-21044073</a></p>
  </li>
  <li><p>sort the table by Clin.Sig. column</p>
  </li>
  <li><p>select the name of the variant, i.e. rs5742904</p>
  </li>
  <li><p>search for that variant in your 23andMe file</p>
  </li>
  <li><p>compare the variants from the ENSEMBL with what you got in your result</p>
  </li>
  </ul>
  <p><a href="https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000084674;r=2:21001429-21044073;v=rs5742904;vdb=variation;vf=184237596" rel="nofollow noreferrer">https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000084674;r=2:21001429-21044073;v=rs5742904;vdb=variation;vf=184237596</a></p>
  <p>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?</p>
  
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Answers.CreationDate: 2023-06-07T14:45:45.290Z
Answers.Text: 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.
Answers.UserDisplayName: Paweł Gościcki
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Answers.Text: 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).
Answers.UserDisplayName: darked89
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Answers.Text: 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.
Answers.UserDisplayName: darked89
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Answers.Text: 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 :)
Answers.UserDisplayName: Paweł Gościcki
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Answers.CreationDate: 2023-06-07T19:36:12.933Z
Answers.Text: of course 23andMe won't give you health recommendations.  That would be irresponsible.
Answers.UserDisplayName: swbarnes2
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Answers.Text: @PawełGościcki here are the annotated APOB gene variants from ENSEMBL 109: https://drive.google.com/file/d/1CECqvG_oWDi_MoV_h7GsjL9aqnKPskeC/view?usp=sharing  You just need to check how many  of the Variant_name identifiers are present in your 23andMe file, look at  pathogenic in column 3. I will need to dig into the 23andMe result format to get back to you.
Answers.UserDisplayName: darked89
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Body: <p>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.</p>
  <p>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?</p>
  <p>A single line in my DNA data looks like this:</p>
  <pre><code>rs12567639 1 756268 AA
  </code></pre>
  <p>I have a programming background, but none in the bioinformatics area.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-04T16:06:20.683Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-04T16:48:44.650Z
Comments.Text: Anyway its a good question (in my opinion) and good luck with the analysis. Upvoted.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-07T09:37:15.973Z
Comments.Text: For some reason 23andMe uses genome positions from the previous genome assembly. Anyway, what counts are the identifiers, like: rs12567639
Comments.UserDisplayName: darked89
Tags: <snp>
Title: How can I detect the Apo B gene mutations in my raw dna data?
ThreadText: # How can I detect the Apo B gene mutations in my raw dna data?
  
  (Asked by: username_0 on 2023-05-04)
  
  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.
  
  **Tags:** snp
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_1**: Anyway its a good question (in my opinion) and good luck with the analysis. Upvoted.  
  > **username_2**: For some reason 23andMe uses genome positions from the previous genome assembly. Anyway, what counts are the identifiers, like: rs12567639  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2023-05-05. Score: 3
  
  I think you mean these. The amino acid numbering has changed, but that happens as we discover more transcript variants.
  
  <http://useast.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=2:21005788-21006788;v=rs5742904;vdb=variation;vf=184237596>
  
  <http://useast.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=2:21005696-21006696;v=rs12713559;vdb=variation;vf=186851457>
  
  <http://useast.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000084674;r=2:21001429-21044073;v=rs144467873;vdb=variation;vf=251617275>
  
  
  ---
  
  ### Answer by username_2 on 2023-06-07. Score: 2
  
  If you are interested in ApoB gene variants you can:
  
  * go to <https://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?db=core;g=ENSG00000084674;r=2:21001429-21044073>
  * sort the table by Clin.Sig. column
  * select the name of the variant, i.e. rs5742904
  * search for that variant in your 23andMe file
  * compare the variants from the ENSEMBL with what you got in your result
  
  <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?
  
  > **Comments:**
  > **username_0**: 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.  
  > **username_2**: 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).  
  > **username_2**: 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.  
  > **username_0**: 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 :)  
  > **username_3**: of course 23andMe won't give you health recommendations.  That would be irresponsible.  
  > **username_2**: @username_0 here are the annotated APOB gene variants from ENSEMBL 109: https://drive.google.com/file/d/1CECqvG_oWDi_MoV_h7GsjL9aqnKPskeC/view?usp=sharing  You just need to check how many  of the Variant_name identifiers are present in your 23andMe file, look at  pathogenic in column 3. I will need to dig into the 23andMe result format to get back to you.  
  
  ---
  
  