Tumor organoid culture compositions, systems, and methods

A method for culturing a tumor organoid cell line, the method comprising:

• a) obtaining a tumor sample from a subject, wherein the tumor sample is an anal cancer, a basal cell skin cancer, a squamous cancer, a breast cancer, a bladder cancer, a cervical cancer, an endometrial cancer, a head and neck cancer, a hepatobiliary cancer, a kidney cancer, a gastric cancer, a lung cancer, a mesothelial cancer of the pleural cavity, a mesothelial cancer of the peritoneal cavity, an ovarian cancer, or a prostate cancer;
• b) isolating nucleic acids from the tumor sample and sequencing a plurality of alleles for a plurality of loci of interests from the isolated nucleic acids of the tumor sample to identify a plurality of tumor sample somatic variants, wherein the sequencing is performed by next-generation sequencing;
• c) culturing the tumor organoid cell line comprising at least one tumor organoid in an organoid culture medium substantially free of R-spondins, wherein each respective tumor organoid in the tumor organoid cell line is derived from one or more cells of the tumor sample;
• d) isolating nucleic acids from the tumor organoid cell line and sequencing a plurality of alleles for a plurality of loci of interests from the isolated nucleic acids to identify a plurality of tumor organoid somatic variants, wherein the sequencing is performed by next generation sequencing;
• e) determining a reference genomic variant profile, wherein the reference genomic variant profile comprises, for each respective somatic variant in the plurality of tumor sample somatic variants identified in step b), a variant allele fraction for the respective somatic variant of the tumor sample;
• f) determining a first organoid genomic variant profile of the tumor organoid cell line, wherein the first organoid genomic variant profile comprises, for each respective somatic variant in the plurality of tumor organoid somatic variants identified in step d), a variant allele fraction for the respective somatic variant;
• and
• g) confirming at least a 65% concordance in the clonal diversity of the tumor organoid cell line and the tumor sample by comparing each variant allele fraction for each respective somatic variant of the tumor sample to the corresponding variant allele fraction for the corresponding somatic variant of the tumor organoid cell line, across a plurality of somatic variants found in both the reference genomic profile and the first organoid genomic variant profile.