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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

Method Approach Description Overall immune score Cell populations
H&E whole slide (WS) Microscopy based Pathology TIL scores TIL scores NA
IHC whole slide (WS) Microscopy based Pathology scores with IHC Summed lymphocyte fractions Yes
Whole slide digital (digWS) Microscopy based Visiopharm digital scores IHC NA Yes
H&E tissue microarray (TMA) Microscopy based Pathology TIL scores TIL scores NA
IHC tissue microarray (TMA) Microscopy based Pathology scores IHC Summed lymphocyte fractions Yes
TMA digital (digTMA) Microscopy based Visiopharm digital scores IHC Summed lymphocyte fractions Yes
Absolute CIBERSORT (aCBS) [20] Deconvolution Cell fractions, absolute mode used Summed lymphocyte fractions Yes
quanTIseq, lsfit (qSEQ) [21] Deconvolution Cell fractions, absolute Summed lymphocyte fractions Yes
MCP-counter (MCP) [22] Gene marker Arbitrary units NA Yes
xCell [23] Gene marker Arbitrary units NA Yes
EPIC [24] Deconvolution Cell fractions, absolute Summed lymphocyte fractions Yes
MethylCIBERSORT (metCBS) [25] Deconvolution Cell fractions, absolute Summed lymphocyte fractions Yes
TIL rna score (TILrna) [26] Gene marker TIL associated gene signature TIL signature NA
meTIL [27] Gene marker TIL methylation profile TIL signature NA
Cell signatures Davoli et al. [28] Gene marker Computed gene signature NA Yes
Cell signatures Danaher et al. [29] Gene marker Computed gene signature NA Yes