biostudies-literatureZhao YNational Cancer InstituteNCI NIH HHSNational Institutes of Health269https://www.ebi.ac.uk/biostudies/studies/S-EPMC8220791biostudies-literatureUnknown19(1)<h4>Background</h4>In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Several methods have been proposed and continue to be used. However, a consensus has not been reached regarding the best gene expression quantification method for RNA-seq data analysis.<h4>Methods</h4>In the present study, we used replicate samples from each of 20 patient-derived xenograft (PDX) models spanning 15 tumor types, for a total of 61 human tumor xenograft samples available through the NCI patient-derived model repository (PDMR). We compared the reproducibility across replicate samplJournal of translational medicineTPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository.PMC8220791HHSN261200800001EWilliams PMDoroshow JHDas BLi MCChen LKarlovich CKonate MMEvrard YAZhao YMcShane LMfalseTPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository.<h4>Background</h4>In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Several methods have been proposed and continue to be used. However, a consensus has not been reached regarding the best gene expression quantification method for RNA-seq data analysis.<h4>Methods</h4>In the present study, we used replicate samples from each of 20 patient-derived xenograft (PDX) models spanning 15 tumor types, for a total of 61 human tumor xenograft samples available through the NCI patient-derived model repository (PDMR). We compared the reproducibility across replicate sampl2021-01-01T00:00:00Z2021 Jun2026-05-08T00:29:09.864Z2022-02-10T15:58:31.158ZS-EPMC82207913415806010.1186/s12967-021-02936-w