RT Journal Article
SR Electronic
T1 Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 146795
DO 10.1101/146795
A1 Zeya Wang
A1 Jeffrey S. Morris
A1 Shaolong Cao
A1 Jaeil Ahn
A1 Rongjie Liu
A1 Svitlana Tyekucheva
A1 Bo Li
A1 Wei Lu
A1 Ximing Tang
A1 Ignacio I. Wistuba
A1 Michaela Bowden
A1 Lorelei Mucci
A1 Massimo Loda
A1 Giovanni Parmigiani
A1 Chris C. Holmes
A1 Wenyi Wang
YR 2017
UL http://biorxiv.org/content/early/2017/06/08/146795.abstract
AB We develop a novel method DeMixT for the gene expression deconvolution of three compartments in cancer patient samples: tumor, immune and surrounding stromal cells. In validation studies using mixed cell line and laser-capture microdissection data, DeMixT yielded accurate estimates for both cell proportions and compartment-specific expression profiles. Application to the head and neck cancer data shows DeMixT-based deconvolution provides an important step to link tumor transcriptome data with clinical outcomes.