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PMID: 28679399 Published · epublish English Journal Article Comment

Data normalization considerations for digital tumor dissection.

Genome biology ·Vol. 18 ·No. 1 ·2017-00-05 ·Pages 128

Newman AM, Gentles AJ, Liu CL, Diehn M, Alizadeh AA

Abstract

In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The Cancer Genome Atlas. Methods to characterize TIL biology are increasingly important, and the authors offer several arguments in favor of their strategy. Several of these claims warrant further discussion and highlight the critical importance of data normalization in gene expression deconvolution applications.Please see related Li et al correspondence: www.dx.doi.org/10.1186/s13059-017-1256-5 and Zheng correspondence: www.dx.doi.org/10.1186/s13059-017-1258-3.

MeSH Terms
Humans Lymphocytes, Tumor-Infiltrating Neoplasms
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Newman Aaron M
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA. amnewman@stanford.edu. | Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA. amnewman@stanford.edu.
Gentles Andrew J
Center for Cancer Systems Biology, Stanford University, Stanford, California, 94305, USA. | Department of Radiology, Stanford University, Stanford, California, 94305, USA.
Liu Chih Long
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA. | Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA.
Diehn Maximilian
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA. | Department of Radiation Oncology, Stanford University, Stanford, California, 94305, USA. | Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA.
Alizadeh Ash A
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA. arasha@stanford.edu. | Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA. arasha@stanford.edu. | Center for Cancer Systems Biology, Stanford University, Stanford, California, 94305, USA. arasha@stanford.edu. | Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA. arasha@stanford.edu. | Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA. arasha@stanford.edu.
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/s13059-017-1257-4
Email
amnewman@stanford.edu
arasha@stanford.edu
Published
2017-00-05
Epub
2017-00-05
Pages
128
Language
English
Region
England
NLM ID
100960660
PMCID
PMC5498978
Subset
IM
Grants
NCI NIH HHS · P30 CA124435 · United States
NCI NIH HHS · U01 CA194389 · United States
Corrections
CommentOn
PMID: 27549193
CommentIn
PMID: 28679386
External Links
PubMed source DOI: 10.1186/s13059-017-1257-4 PMC Full Text View journal details
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