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single-cell-genetics / XClone

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
https://xclone-cnv.readthedocs.io/en/latest/
Apache License 2.0
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Unable to Use Prior Whole Genome Sequencing Information #17

Open DarioS opened 2 months ago

DarioS commented 2 months ago

Numbat has Using Existing CNV Calls for borrowing information from sample-matched whole genome sequencing. Such a prior could make whole genome duplicated samples results more reliable if overall ploidy could be incorporated into the calculation.

Rongtingting commented 2 months ago

Hi @DarioS,

Thank you for raising this issue and for the suggestion!

In XClone, the robust BAF module can help distinguish different types of CNAs. We have a WGD warning strategy (e.g, XClone infers complex CNA states with whole genome duplication in astrocytoma).

You are right, incorporating prior information about ploidy from whole-genome sequencing (WGS) could indeed improve the reliability of CNA results, especially for samples with whole-genome duplications. We are actively testing some WGD simulations in XClone now and will consider how to integrate prior information if a matched WGS exists.

We will keep you updated on any progress made in this issue. In the meantime, please don't hesitate to share any further thoughts or suggestions. Thank you!

Bests, Rongting