Method Profile
Follow drug-associated changes in individual colorectal cancer organoid models within a shared pool using sequencing and targeted qPCR.
Compare prolonged drug responses across patient-derived models while tracking population-specific signals.
Established, uniquely barcoded colorectal cancer organoids combined into 12- and 15-model pools.
Longitudinal barcode measurements, paired sequencing/qPCR comparisons and a miniaturized 96-well experiment.
Models
Prelabelled patient-derived colorectal cancer organoids with matched tumor/normal molecular information.
Measurements
Nanopore barcode sequencing and barcode-specific qPCR.
Comparators
Drug-treated versus vehicle-treated pools, with targeted genotype–drug test cases.
Estimate model-specific response relative to vehicle in the pooled context; assess detection losses separately from measured drug sensitivity.
Long-term pooled tracking with orthogonal molecular measurement.
Pool 1 contained 12 models; pool 2 contained 15; 12 remained analyzable after miniaturization.
Sequencing versus qPCR and expected TP53–nutlin/RNF43–PORCN relationships.
Sequencing–qPCR correlations were 0.89 for nutlin, 0.79 for LGK-974 and 0.59 for etoposide.
DNA barcode measurements followed individual organoid models within mixed cultures. Sequencing and qPCR captured established genotype–drug relationships, variable drug sensitivity and limitations after assay miniaturization.
