Answers.Body: <p>Why not just good old qPCR? That's (A) quick, (B) cheap and (C) easy to analyze. If you care about the exact location of the break point (I'm guessing from the context that you don't), then targeted sequencing with a custom capture kit would work.</p>
  
  <p>Regarding validating the biological relevance of this, there are multiple (parallel) routes one can take. Firstly, screen unaffected family members for this same alteration. If you find this in unaffected individuals then it's obviously not the causative alteration. Ideally, one would also do either a cell-line experiment or a mouse (or other model organism) experiment to see if you can reconstitute at least some component of the clinical phenotype. This may not always be possible, of course.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-05-31T21:28:07.403Z
Answers.LastActivityDate: 2017-05-31T21:28:07.403Z
Answers.UserDisplayName: Devon Ryan
Body: <p>We have arrayCGH (aCGH) results for one sample. There is a 0.5 Mb terminal duplication on chromosome 19 (62995490-63407936, according to NCBI36/hg18). The duplication is rare: a literature review suggests there are only 3-4 samples with clinical information.</p>
  
  <p>What are the steps to validate the results? How do we ascertain that this duplication is the cause of the clinical symptoms?</p>
  
  <p>I have some ideas:</p>
  
  <ul>
  <li>aCGH the parents. Not sure how this would help.   </li>
  <li>whole genome exome sequencing. Worried this might make it more difficult to pinpoint genetic cause.</li>
  <li>whole genome sequencing?</li>
  <li>other ideas?</li>
  </ul>
  
  <p><strong>Note:</strong> I am new to aCGH and high-throughput sequencing, any advice is welcome.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T21:15:01.933Z
Comments.Text: Is the duplication in the telomere or before it?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T21:25:33.180Z
Comments.Text: @DevonRyan I think, it is before, on the last band of chr19. Does it matter, sorry not being ignorant, just no clue about it.
Comments.UserDisplayName: zx8754
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T21:26:26.800Z
Comments.Text: Telomeric sequences are highly repetitive, so yes it matters :)
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T21:28:12.110Z
Comments.Text: Telomere starts at the end of the last band, or is it part of chromosome?
Comments.UserDisplayName: zx8754
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T21:43:14.580Z
Comments.Text: If you look at the UCSC genome browser, the telomere is the `GGGTTA` simple repeat at the end. In others it's just a stretch of NNNN in the reference (no clue how this looks in hg18).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-02T05:09:32.010Z
Comments.Text: Just as a little suggestion, especially in the beta you should take the recommendations of the SE interface very seriously and always leave a comment when down-voting, or you demonstrate just the prejudice of hostility! Also be a little open minded, questions about omics data and how to validate omics results are typically very relevant. Otherwise you will notice that nothing can be asked anymore. Just saying, from and old bs mod. P.S.: I have the feeling that people down-vote because they do not understand, that's not always the fault of the Op.
Comments.UserDisplayName: Michael
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-02T05:17:56.620Z
Comments.Text: Another observation, this question might be ethically questionable! You are putting forward info on a real case to diagnosis, possibly identifying information is revealed.
Comments.UserDisplayName: Michael
Tags: <ngs><array-cgh><exome>
Title: How do I validate a single sample ArrayCGH result?
ThreadText: # How do I validate a single sample ArrayCGH result?
  
  (Asked by: username_0 on 2017-05-31)
  
  We have arrayCGH (aCGH) results for one sample. There is a 0.5 Mb terminal duplication on chromosome 19 (62995490-63407936, according to NCBI36/hg18). The duplication is rare: a literature review suggests there are only 3-4 samples with clinical information.
  
  What are the steps to validate the results? How do we ascertain that this duplication is the cause of the clinical symptoms?
  
  I have some ideas:
  
  * aCGH the parents. Not sure how this would help.
  * whole genome exome sequencing. Worried this might make it more difficult to pinpoint genetic cause.
  * whole genome sequencing?
  * other ideas?
  
  **Note:** I am new to aCGH and high-throughput sequencing, any advice is welcome.
  
  **Tags:** ngs, array-cgh, exome
  
  > **Comments:**
  > **username_1**: Is the duplication in the telomere or before it?  
  > **username_0**: @username_1 I think, it is before, on the last band of chr19. Does it matter, sorry not being ignorant, just no clue about it.  
  > **username_1**: Telomeric sequences are highly repetitive, so yes it matters :)  
  > **username_0**: Telomere starts at the end of the last band, or is it part of chromosome?  
  > **username_1**: If you look at the UCSC genome browser, the telomere is the `GGGTTA` simple repeat at the end. In others it's just a stretch of NNNN in the reference (no clue how this looks in hg18).  
  > **username_2**: Just as a little suggestion, especially in the beta you should take the recommendations of the SE interface very seriously and always leave a comment when down-voting, or you demonstrate just the prejudice of hostility! Also be a little open minded, questions about omics data and how to validate omics results are typically very relevant. Otherwise you will notice that nothing can be asked anymore. Just saying, from and old bs mod. P.S.: I have the feeling that people down-vote because they do not understand, that's not always the fault of the Op.  
  > **username_2**: Another observation, this question might be ethically questionable! You are putting forward info on a real case to diagnosis, possibly identifying information is revealed.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-05-31. Score: 2 | Accepted answer
  
  Why not just good old qPCR? That's (A) quick, (B) cheap and (C) easy to analyze. If you care about the exact location of the break point (I'm guessing from the context that you don't), then targeted sequencing with a custom capture kit would work.
  
  Regarding validating the biological relevance of this, there are multiple (parallel) routes one can take. Firstly, screen unaffected family members for this same alteration. If you find this in unaffected individuals then it's obviously not the causative alteration. Ideally, one would also do either a cell-line experiment or a mouse (or other model organism) experiment to see if you can reconstitute at least some component of the clinical phenotype. This may not always be possible, of course.
  
  
  ---
  
  