Details
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Type:
Task
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Status: To-Do (View Workflow)
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Priority:
Minor
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Epic Link:
Description
Situation: I talked to a researcher at GCC2024 who was working with calculating copy numbers. Using IGB's thresholding functionality, we should be able to create a demo that walks through the steps to isolate parts of the chromosome with copy numbers greater than 1, then create a new track with just those loci and export it as a new file for further analyses.
Task: Find data suitable for the thresholding/copy number demo I've briefly described above. This will likely involve some investigative work as to what kind of data is often used for calculating copy number/when that's scientifically meaningful.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2809 [ 19325 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 6 [ 200 ] | Summer 7 [ 201 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Dylan Marrotte [ dmarrott ] |
| Sprint | Summer 7 [ 201 ] | Summer 6 [ 200 ] |
| Priority | Major [ 3 ] | Minor [ 4 ] |
| Sprint | Summer 6 [ 200 ] | Summer 7 [ 201 ] |
| Sprint | Summer 7 [ 201 ] |
| Assignee | Dylan Marrotte [ dmarrott ] |
I found a study that we may want to look into for this demo: https://doi.org/10.1038/s41598-024-66021-0
It investigated copy number variants (CNVs) in schizophrenia pedigrees, and in the abstract it mentions a well-established reference sample (NA12878) as well as a rare deletion/CNV at the gene (PITRM1) which has been implicated in a complex phenotypes associated with affected adults. This makes for a really cool story! I bet we could track down that reference sample and visualize the CNV in IGB.