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I am reading a journal paper about the relationship between NCAM2 and autism. I have come across the following statement in the paper:

Based on analysis utilizing the UCSC Genome Browser (hg18, build 36), there are a total of 19 genes deleted (Table I). The proximal deletion breakpoint falls within the NCAM2 gene, deleting 17 out of 18 exons, and the distal deletion involves 16 out of 17 exons of the GRIK1 gene.

I am not sure what is meant by a 'proximal deletion breakpoint'. I have tried searching for the definition online but I have not found anything useful. Any insights are appreciated.

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    $\begingroup$ Just break it down: look up "breakpoint" for chromosomes, look up "deletion" if you have to, and look up "proximal" and "distal". $\endgroup$
    – mgkrebbs
    Nov 17, 2020 at 0:24
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    $\begingroup$ This paper is not very helpful with understanding the role of NCAM2 in Austism, as the patient had chromosomal translocations in addition to the deletion. $\endgroup$
    – Polypipe Wrangler
    Nov 17, 2020 at 2:49

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Let's break down the phrase as one of the commenters mentioned:

  • "proximal": in the context of chromosomal position, this means closer to centromere, whereas "distal" means further from the centromere (the middle part of the chromosome).
  • "deletion": referring to the genes that were deleted as a result of the chunk of the 21st chromosome being missing.
  • "breakpoint": points at which the chromosomes was broken leading to the deletion.

Putting it all together, this says that the deletion breakpoint closer to the centromere falls within the NCAM2 gene, whereas the deletion breakpoint further from the centromere falls within the GRIK1 gene, with the other 17/19 genes falling between the two.

To verify this interpretation, we can use the USCS Genome Browser as mentioned. We can see that if we compare the position of the NCAM2 gene and the GRIK1 gene on the 21st chromosome, the former is closer to the centromere than the latter. We can also do a spot check to verify that ADAMTS1 one of the other 19 deleted genes, lies between the two of them.

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