Summary of novel technologies
| Technology | Suggestions and potential biomarkers | Sample preparation | Bioinformatic tools | References and recommended reading |
|---|---|---|---|---|
| Whole exome sequencing for neoantigen discovery | • Mutation load for CTLA-4 and PD-1 blockade therapy• Neoantigen-specific T cell response | DNA from tumor and normal cells | EBcall, JointSNVMix, MuTect, SomaticSniper, Strelka, VarScan 2, BIMAS, RNAKPER SYFPEITHI, IDEB, NetMCHpan, TEPITOPEpan, PickPocket, Multipred2, MultiRTA | Van Buuren et al., 2014 [248]; Duan et al., 2014 [130]; Snyder et al., 2014 [62]; Snyder et al., 2015 [131]; Rizvi et al., 2015 [104]; Le et al., 2015 [105]; Van Allen et al., 2015 [63] |
| Gene signature and pattern | • MAGE-A3 gene signature• Chemokine expression in melanoma• Neoantigen signature | DNA and RNA from tumor, lymph node and PBMCs | BRB-ArrayTools, LIMMA, SAM, PAM, Partek, Genomic Suite, GSEA, Ingenuity IPA | Quackenbush et al., 2002 [231]; Simon et al., 2013 [249]; Simon et al., 2007 [250]; Subramanian et al., 2005; Smyth et al., 2005; Tusher et al., 2001 [251]; Tibshirani et al., 2002 [252]; Leek et al., 2010 [243]; Gaujoux et al., 2013 [245]; Ulloa-Montoya et al., 2013 [142]; Brown et al., 2014 [148] |
| Epigenetic-differentiation based immune cell quantification | • Immune cell lineage specific epigenetic modification• Leukocyte ratios in blood and tissue | Genomic DNA from fresh or frozen whole blood, PBMC, lymph node and fresh tissue or FFPE tissue and blood clots | HOMER package Motif Finder algorithm findMotifGenome.pl, MatInspector (Genomatix), Mendelian randomization | Wieczorek et al., 2009 [154]; Sehouli et al., 2011 [155]; Schildknecht et al., 2015 [253]; Steinfelder et al., 2011 [156]; Lavin et al., 2014; Gosselin et al., 2014; Liang et al., 2015 |
| Protein microarray (seromics) | • TAA antibody response• Broad antibody signature• New antigen discovery | Fresh or frozen serum and plasma | Prospector, LIMMA package, PAA package, Spotfire package | Gnjatic et al., 2009 [254]; Kwek et al., 2012 [56]; Turewicz et al., 2013 [175]; Graff et al., 2014 [27] |
| Flow Cytometry and Mass Cytometry | • Use best flow practices and recommended flow panels• Multimers for T cell epitope screening• TAA-specific T cell response for CTLA-4 blockade therapy• CD4+ICOS+ T cells for CTLA-4 blockade therapy• Baseline MDSC for CTLA-4 blockade therapy | Whole blood; Fresh or frozen PBMCs and TILs; Fresh or frozen cells from ascites or pleural effusion | Computational algorithm-driven analysis for MDSC, Cytobank, FlowJo, SPADE, PhenoGraph, PCA, viSNE, Citrus, ACCENSE, Isomap, 3D visualization | Maecker et al., 2010 [176]; Maecker et al., 2012 [177]; Streitz et al., 2013 [178]; Kvistborg et al., 2012 [255]; Chang et al., 2014 [190]; Yuan et al., 2011 [57]; Carthon et al., 2010 [50]; Kitano et al., 2014 [72]; Levine et al.,2015 [189] |
| T and B cell receptor deep sequencing | • CD3 T cell count• T Cell clonotype stability for CTLA-4 blockade therapy• Baseline T cell clonality in tumor in PD-1 blockade therapy | DNA from FFPE; Frozen cells from tumor, lymph node or PBMCs; Fresh or frozen cells from ascites or pleural effusion | Shannon Entropy, Morisita’s distance, Estimated TCR gene rearrangements per diploid genomes, Clonality, ImmuneID, Adaptive ImmunoSeq software | Cha et al., 2014 [205]; Tumeh et al., 2014 [103]; Howie et al., 2015 [202] |
| Multicolor IHC staining | • CD3 Immune score• CD8/FOXP3 ratio for tumor necrosis• PD-L1 expression on tumor in PD-1 blockade therapy | FFPE tissue; Fresh or frozen tissue | TissueGnostic system, PerkinElmer system | Galon et al., 2006 [10]; Hodi et al., 2008 [54]; Taube et al., 2014 [110] |
Abbreviations: PBMC peripheral blood mononuclear cells, TAA tumor associated antigen, MDSC myeloid derived suppressor cells, TILs tumor infiltrating lymphocytes, IHC immunohistochemical staining, TCR T cell receptor, FFPE formalin-fixed, paraffin-embedded, PD-1 programmed cell death-1, PD-L1 programmed cell death ligand −1