TY - JOUR
T1 - Building flexible and robust analysis frameworks for molecular subtyping of cancers
AU - Pedersen, Christina Bligaard
AU - Campos, Benito
AU - Rene, Lasse
AU - Wegener, Helene Scheel
AU - Krishnan, Neeraja M.
AU - Panda, Binay
AU - Vitting-Seerup, Kristoffer
AU - Rossing, Maria
AU - Bagger, Frederik Otzen
AU - Olsen, Lars Rønn
N1 - Publisher Copyright:
© 2023 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
PY - 2024
Y1 - 2024
N2 - Molecular subtyping is essential to infer tumor aggressiveness and predict prognosis. In practice, tumor profiling requires in-depth knowledge of bioinformatics tools involved in the processing and analysis of the generated data. Additionally, data incompatibility (e.g., microarray versus RNA sequencing data) and technical and uncharacterized biological variance between training and test data can pose challenges in classifying individual samples. In this article, we provide a roadmap for implementing bioinformatics frameworks for molecular profiling of human cancers in a clinical diagnostic setting. We describe a framework for integrating several methods for quality control, normalization, batch correction, classification and reporting, and develop a use case of the framework in breast cancer.
AB - Molecular subtyping is essential to infer tumor aggressiveness and predict prognosis. In practice, tumor profiling requires in-depth knowledge of bioinformatics tools involved in the processing and analysis of the generated data. Additionally, data incompatibility (e.g., microarray versus RNA sequencing data) and technical and uncharacterized biological variance between training and test data can pose challenges in classifying individual samples. In this article, we provide a roadmap for implementing bioinformatics frameworks for molecular profiling of human cancers in a clinical diagnostic setting. We describe a framework for integrating several methods for quality control, normalization, batch correction, classification and reporting, and develop a use case of the framework in breast cancer.
KW - Bioinformatics workflows
KW - Clinical bioinformatics
KW - Molecular subtyping
KW - Sample classification
U2 - 10.1002/1878-0261.13580
DO - 10.1002/1878-0261.13580
M3 - Journal article
C2 - 38158740
AN - SCOPUS:85181494510
SN - 1574-7891
VL - 18
SP - 606
EP - 619
JO - Molecular Oncology
JF - Molecular Oncology
IS - 3
ER -