What are the considerations for the spike-in cell population for CNV detection?

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  1. Is a diploid cell population required for analysis?
    1. Yes, a spike-in cell population with a known genomic profile is required.
  2. What is the recommended spike-in percentage? 
    1. The recommended spike-in percentage for these runs is at least 5% of the total input. The diploid cells must be spiked into the test sample. 
  3. Can my spike-in cells have non-diploid genomic regions?
    1. It is recommended that this spike-in is diploid, but a spike-in with a known ploidy other than 2 can be used. The ploidy locations must be known and detailed in the spike-In CNV file, detailed here. If the diploid cell population has only one copy of chrX, this file type is needed to indicate that the X chromosome is haploid.
    2. Information on recommended spike-in cell lines can be found here. We recommend the GM12878 cell line (available here).
      1. Please note this is a B-cell line and expresses cell-surface antigens that are common targets of CAR-T cells (e.g., CD19, CD22). If the test material is CAR-T cells, please consider an alternative diploid cell population.
    3. Healthy PBMCs can also be used as your spike-in for these experiments, but the genome should be confirmed to be diploid. Further details about recommended spike-ins can be found here.
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