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Table 1 Concordance of the two BC signatures, and gene expression, between matched FFPE and FF samples. Gene Expression refers to individual gene measurements, for which values in the table are medians over all genes. The combination of protocol (NEW vs OLD) and data summarization of mapped counts (UMI groups vs reads). Bold font indicates higher value for given signature

From: Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Signature Protocol CCC CCC
low CI
CCC
high CI
Rho Bias Scale Location
PIK3CA OLD_reads 0.861 0.680 0.943 0.946 0.910 0.729 0.313
NEW_reads 0.980 0.934 0.994 0.984 0.995 0.956 0.089
NEW_UMIs 0.982 0.941 0.994 0.985 0.996 0.950 0.072
SET_ERPR OLD_reads 0.956 0.871 0.985 0.968 0.987 0.881 0.103
NEW_reads 0.901 0.764 0.960 0.984 0.916 0.953 −0.425
NEW_UMIs 0.901 0.766 0.960 0.985 0.915 0.977 −0.432
Gene Expression OLD_reads 0.785 0.888 0.907 0.967 0.018
NEW_reads 0.911 0.977 0.951 0.997 −0.015
NEW_UMIs 0.921 0.966 0.958 1.019 −0.027