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sorry for the naive question, but how do I determine what the copy number is in GRCh37 for a gene with multiple CNVs? (e.g. DRD4).

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    $\begingroup$ Can you give some indications of things that you've tried or what kind of data you have access to? $\endgroup$ – Maximilian Press Jun 25 '20 at 17:17
  • $\begingroup$ Thanks for the reply! I was poking around this page: grch37.ensembl.org/Homo_sapiens/Gene/… but I don't know enough to understand a lot of it. I also tried looking at DRD4 within GRCh37 in the NCBI variation viewer. $\endgroup$ – krstn Jun 26 '20 at 22:00
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A very naive approach would be to simply ask how many copies of the sequence in question are in the hg38 sequence, at some level of homology. You could do this using a tool such as BLASTN (which has a web interface that you can use to search against a human genome) or, if you have the sequences downloaded somewhere where you can work with them, using a tool such as minimap2 (which will be faster) as long as you're comfortable using command-line tools.

If you choose to do this, you will have to be comfortable setting thresholds for what counts as a copy of the gene in question.

A more involved solution would be to obtain DNA sequencing reads for the sample you're interested in and use them to quantify the copy number of the gene based on the number that map to a given sequence of interest. An older approach would be to use microarrays.

I am guessing that since you are interested in the reference genome that you are not interested in going to that kind of trouble.

Is this a homework question? If so, you should add the "homework" tag.

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  • $\begingroup$ Thank you so much for the detailed answer. Minimap2 looks great. (This isn't a homework question, just a question I am pursuing to try and learn more.) $\endgroup$ – krstn Jun 29 '20 at 4:59
  • $\begingroup$ Ok, gotcha. Minimap2 is an excellent tool by Heng Li, who is also the author of the ubiquitous short-read mapper bwa and a million other projects. I strongly recommend using him and his blog as a starting point if you're getting started in bioinformatics etc.: lh3.github.io $\endgroup$ – Maximilian Press Jun 29 '20 at 16:52
  • $\begingroup$ Ah perfect, I've been looking for something like this. I definitely will! $\endgroup$ – krstn Jul 3 '20 at 20:31

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