Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

Finotello, Francesca; Mayer, Clemens; Plattner, Christina; Laschober, Gerhard; Rieder, Dietmar; Hackl, Hubert; Krogsdam, Anne; Loncová, Zuzana; Posch, Wilfried; Wilflingseder, Doris; Sopper, Sieghart; E. Ijsselsteijn, Marieke; P. Brouwer, Thomas; B. Johnson, Douglas; Xu, Yaomin; Wang, Yu; E. Sanders, Melinda; V. Estrada, Mónica; I. González-Ericsson, Paula; Charoentong, Pornpimol; M. Balko, Justin; F.C.C. de Miranda, Noel; Trajanoski, Zlatko

doi:10.1186/s13073-019-0638-6

Public

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

Published in Genome Medicine • May 24, 2019

Authors:

Francesca Finotello

Clemens Mayer

Christina Plattner

Abstract

We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, and immunohistochemistry data.quanTIseq analysis of 8000 tumor samples revealed that cyto...

Subject

Immune system

Flow cytometry

Cancer research

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