Gene Expression Profiling in Immuno-Oncology

Gene expression data were generated using the HTG EdgeSeq Precision Immuno-Oncology Panel (HTG Molecular Diagnostics, Inc., Tucson, AZ, USA), per the manufacturer’s instructions. The library was sequenced on the Illumina Nextseq 500 platform (Illumina, Inc., San Diego, CA, USA) and data were processed by HTG EdgeSeq parser software. Read count was normalized by library size to obtain count per million, which was then log transformed for downstream analysis [26 (link)]. “High” and “low” gene expression subgroups were defined using the median expression as the cutoff between groups.

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Ye D., Desai J., Shi J., Liu S.Y., Shen W., Liu T., Shi Y., Wang D., Liang L., Yang S., Ma X., Jin W., Zhang P., Huang R., Shen Z., Zhang Y, & Wu Y.L. (2023). Co-enrichment of CD8-positive T cells and macrophages is associated with clinical benefit of tislelizumab in solid tumors. Biomarker Research, 11, 25.

Publication 2023

Illumina Nextseq 500 platform

Gene expression Library Molecular diagnostics Oncology

Corresponding Organization : Guangdong Provincial People's Hospital

Other organizations : Fudan University Shanghai Cancer Center, Peter MacCallum Cancer Centre, University of Melbourne, BeiGene (China), First Affiliated Hospital of Jinan University

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Variable analysis

independent variables

Gene expression data

dependent variables

Gene expression levels used to define 'high' and 'low' subgroups

control variables

Sequencing platform (Illumina Nextseq 500)
Data processing (HTG EdgeSeq parser software)
Normalization method (count per million, log transformed)

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