Reference Genome Choice Shapes RNA-Seq Quantification and Downstream Interpretation in Chinese Breast Cancer Patients

Background/Objectives: Reference genome choice can introduce systematic bias into cancer transcriptomic analyses, particularly for populations underrepresented in standard references. However, its impact on downstream biological interpretation remains insufficiently characterized.

Methods

We compared GRCh38, T2T-CHM13, and the East Asian-matched T2T-YAO using bulk RNA-seq data from 148 Chinese breast cancer patients and single-cell RNA-seq data comprising 65,968 cells from paired primary tumors and lymph node metastases. We assessed reference-dependent differences in read mapping, gene expression, and downstream transcriptomic analyses.