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Table 1 Computational and microscopic methods used for estimation of overall infiltration and calculation of specific cell populations

From: Comprehensive evaluation of methods to assess overall and cell-specific immune infiltrates in breast cancer

MethodApproachDescriptionOverall immune scoreCell populations
H&E whole slide (WS)Microscopy basedPathology TIL scoresTIL scoresNA
IHC whole slide (WS)Microscopy basedPathology scores with IHCSummed lymphocyte fractionsYes
Whole slide digital (digWS)Microscopy basedVisiopharm digital scores IHCNAYes
H&E tissue microarray (TMA)Microscopy basedPathology TIL scoresTIL scoresNA
IHC tissue microarray (TMA)Microscopy basedPathology scores IHCSummed lymphocyte fractionsYes
TMA digital (digTMA)Microscopy basedVisiopharm digital scores IHCSummed lymphocyte fractionsYes
Absolute CIBERSORT (aCBS) [20]DeconvolutionCell fractions, absolute mode usedSummed lymphocyte fractionsYes
quanTIseq, lsfit (qSEQ) [21]DeconvolutionCell fractions, absoluteSummed lymphocyte fractionsYes
MCP-counter (MCP) [22]Gene markerArbitrary unitsNAYes
xCell [23]Gene markerArbitrary unitsNAYes
EPIC [24]DeconvolutionCell fractions, absoluteSummed lymphocyte fractionsYes
MethylCIBERSORT (metCBS) [25]DeconvolutionCell fractions, absoluteSummed lymphocyte fractionsYes
TIL rna score (TILrna) [26]Gene markerTIL associated gene signatureTIL signatureNA
meTIL [27]Gene markerTIL methylation profileTIL signatureNA
Cell signatures Davoli et al. [28]Gene markerComputed gene signatureNAYes
Cell signatures Danaher et al. [29]Gene markerComputed gene signatureNAYes