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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Inquiry Regarding Suitability of PennCNV for CNV Detection with Low-Resolution Array Data #118

Open jeff665547 opened 4 months ago

jeff665547 commented 4 months ago

We need to determine whether PennCNV is appropriate and effective for analyzing data generated from low-resolution arrays (such as array-CGH with an overall median probe genomi spacing of 40-60 kb).

  1. Can PennCNV effectively handle data from this kind of low-resolution arrays?
  2. What are the limitations and challenges associated with using PennCNV for CNV detection in datasets with larger probe spacings?
  3. Are there any recommended adjustments or alternative approaches for analyzing CNVs in low-resolution array data?
  4. Are there any known studies or experiences demonstrating the effectiveness (or lack thereof) of PennCNV in this context?
kaichop commented 3 months ago

1 some people have used PennCNV for low resolution array such as the IBC array with 50k markers. 2 depending on whether it is evenly spaced array, or whether it is a candidate gene based array, some post-calling adjustment are needed 3 I do not have other recommendations, except to manually examine the data and calling results to know what is reasonable 4 as I mentioned in 1

On Wed, Mar 27, 2024 at 6:11 AM jeff665547 @.***> wrote:

We need to determine whether PennCNV, a popular tool for CNV detection, is appropriate and effective for analyzing data generated from low-resolution arrays (such as array-CGH with an overall median probe genomi spacing of 40-60 kb).

  1. Can PennCNV effectively handle data from this kind of low-resolution arrays?
  2. What are the limitations and challenges associated with using PennCNV for CNV detection in datasets with larger probe spacings?
  3. Are there any recommended adjustments or alternative approaches for analyzing CNVs in low-resolution array data?
  4. Are there any known studies or experiences demonstrating the effectiveness (or lack thereof) of PennCNV in this context?

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