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Table 2 Risk of Recurrence (ROR) for the potential discordant sample calls

From: Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

  Sample ID ROR ROR-Group ROR-PS ROR + PS-Group Discordance
NanoString nCounter HCSC-0027 51.10 med 43.42 med NO
HLPR-002 43.57 med 23.44 med YES
HUGM-0022 51.60 med 42.28 med NO
HUGM-0029 73.51 high 68.98 high NO
HUGM-0047 81.24 high 72.48 high NO
INEN-0017 66.66 high 55.051 high NO
INEN-0021 72.50 high 65.40 high NO
RNA-Seq HCSC-0027 35.25 med 33.04 med NO
HLPR-002 16.87 low 10.68 low YES
HUGM-0022 40.68 med 32.44 med NO
HUGM-0029 75.02 high 69.59 high NO
HUGM-0047 73.73 high 69.58 high NO
INEN-0017 62.68 high 52.98 high NO
INEN-0021 66.98 high 64.52 high NO
  1. These measures are extracted from the PAM50 assay outcome (Additional file 1: Table S1). Two measures regarding the risk of recurrence are reported: ROR, which takes into account only the subtype calling; and ROR + PS, which considers also the Proliferation Score. The latter is defined as the mean expression level for the proliferation genes: CCNB1, UBE2C, BIRC5, KNTC2, CDC20, PTTG1, RRM2, MKI67, TYMS, CEP55 and CDCA1. The ROR(+PS)-Group columns gives a categorical classification in terms of risk: high, medium (med) and low