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I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where they have family members with the disease-causing mutations.

enter image description here

For the BMC family, they found using a SNP array that a deletion of ~200 kb between intron 5 and 6 of the IL1RAPL1 gene results in an in-frame deletion of exon 6.

I am having trouble interpreting the graph in Figure D, which is the results of the SNP array analysis. Aren't SNP arrays used for detecting single nucleotide polymorphisms? I am confused because in this paper they are using a SNP array to detect a gene deletion.

Any insights are appreciated.

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In the materials and methods of the paper, you will observe the following statement regarding the CNV (deletion) analysis:

CNV analysis was performed using CNV-WebStore (38).

That citation points to this paper, a software package designed to infer CNVs such as deletions from array data.

Recall that SNP arrays are essentially asking "how much DNA from the sample is sticking to each of N probes against specific sequences". The SNP is inferred by comparing how much DNA sticks to one allele vs the other allele on the array. If a specific sequence assayed by the array is simply missing, then you will observe a corresponding decrease in signal.

This is signified by panel D of the figure that you include, where signal in the pink region is dramatically lower.

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  • $\begingroup$ The OP has asked many questions that could have been similarly answered by doing a little work — I think you are encouraging them to ask low quality questions by rewarding their lack of effort. $\endgroup$
    – tyersome
    Commented Apr 26, 2022 at 4:36
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    $\begingroup$ @tyersome perhaps a different aesthetic preference. OP has linked to a source, clearly stated their confusion, and pointed to specific items that confused them. They didn't know that "CNV" could mean "deletion", which I interpret as simple unfamiliarity with subject domain. They could probably get the answer with a ton of effort, but same could be said for many questions. I'm not a fan of question "quality" evaluation, but I'd still say it's upper 50% at least. I worry more about stifling curiosity than about encouraging low quality questions. Maybe I'm wrong; feel free to downvote. $\endgroup$
    – Maximilian Press
    Commented Apr 27, 2022 at 0:16
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    $\begingroup$ It is possible that I'm being too strict based on the OPs failure to respond to past suggestions for improvements and frequent posting of questions that show no evidence of prior research. ——— As for downvoting, I only do that for answers that are actually bad (e.g. contain significant factual errors) and usually only if the poster fails to respond constructively to suggestions. $\endgroup$
    – tyersome
    Commented Apr 27, 2022 at 1:45

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