A method for ensuring that gene products used in cell therapy do not carry a risk of reduced efficacy or toxicity due to production of unintended variants. The method includes performing an in-silico analysis on the gene construct to identify and alter sequences likely to cause variants. Also, the method includes performing an in-vivo analysis consisting of RNA-sequence of construct based products. Variant detection may then be performed based on gapped reads from the RNA-sequence to determine variant expression levels, variant significance. The method may include repeating the in-silico analysis if identified variants are unacceptable.