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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