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The CSiN score and the other neoantigen-based metrics used for comparison

TW Tao Wang

Last updated date: Apr 8, 2022 Views: 584 Forks: 0

original An abbreviated version of this protocol was published in Science Immunology in Feb, 2020
Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes
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Hello!

 

The CSiN score calculation script is called automatically, as part of the detect_neoantigen.pl pipeline

 

https://github.com/tianshilu/QBRC-Neoantigen-Pipeline/blob/master/detect_neoantigen.pl

 

I suggest you to run our pipeline for detection of neoantigens, and also calculation of CSiN, which may be more accurate

 

Modifying your neoantigen/mutation data for input into CSiN.R is a little difficult. If you insist on doing this, I suggest you to run our mutation calling and neoantigen calling pipelines on some example data, and check the output format of everything before the point of CSiN.R. Then mimic that format for your data.

 

Thanks!
 

Tao

 

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Wang, T(2022). The CSiN score and the other neoantigen-based metrics used for comparison. Bio-protocol Preprint. bio-protocol.org/prep1610.
  2. Lu, T., Wang, S., Xu, L., Zhou, Q., Singla, N., Gao, J., Manna, S., Pop, L., Xie, Z., Chen, M., Luke, J. J., Brugarolas, J., Hannan, R. and Wang, T.(2020). Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes . Science Immunology 5(44). DOI: 10.1126/sciimmunol.aaz3199

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