Complex genotypes, especially multiple single nucleotide variances, that may differentially distributed among alleles can be efficiently mapped in each allele of the gene using next generation sequencing of RNA transcripts from the alleles and the allele fraction information of RNA transcripts. Such reconstructed single nucleotide variances among alleles can be associated with the expected effectiveness of the cancer therapy to update or generate the patient's record or adjust the dose and schedule of the cancer therapy to reduce the undesirable effect of the cancer therapy.
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