Tumor Characterization and Profiling

ER status, as well as other tumor characteristics (tumor grade, stage, and size) were obtained from the medical records. RNA and DNA were extracted for transcriptional and genomic profiling on the Illumina Human v3 microarray and Affymetrix SNP 6.0 platforms, respectively^{36 (link)}. Tumors were classified for TP53 functional status (mutant-like/wildtype-like) using the RNA-based TP53 signature^{32 (link)} and for PAM50 intrinsic subtype (basal-like/non-basal-like) using a research version of the PAM50 predictor^{30 (link),33 (link)}.

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Hurson A.N., Abubakar M., Hamilton A.M., Conway K., Hoadley K.A., Love M.I., Olshan A.F., Perou C.M., Garcia-Closas M, & Troester M.A. (2022). Prognostic significance of RNA-based TP53 pathway function among estrogen receptor positive and negative breast cancer cases. NPJ Breast Cancer, 8, 74.

Publication 2022

Human v3 microarray SNP 6.0

Human Microarray Tp53 Transcriptional Tumors

Corresponding Organization :

Other organizations : University of North Carolina at Chapel Hill, National Cancer Institute

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Variable analysis

independent variables

ER status
Tumor grade
Tumor stage
Tumor size

dependent variables

Transcriptional and genomic profiling on the Illumina Human v3 microarray and Affymetrix SNP 6.0 platforms
TP53 functional status (mutant-like/wildtype-like)
PAM50 intrinsic subtype (basal-like/non-basal-like)

control variables

Medical records

positive controls

TP53 signature
Research version of the PAM50 predictor

negative controls

Not explicitly mentioned

Annotations

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