SCAN-B Early Breast Cancer Cohort (2010–2020)
Description
Data for the SCAN-B Early Breast Cancer Cohort (2010–2020), including clinical and follow-up metadata, RNA-sequencing metadata, and RNA sequencing-based gene expression data, as described and presented in the preprint "Population-scale integration of tumor transcriptomics into breast cancer care: a decade of the SCAN-B initiative" by Saal LH et al., medRxiv 2026.08.20.26360879 (for link see bottom of page). RNA-seq libraries were prepared using either a stranded dUTP mRNA protocol or the Illumina stranded TruSeq mRNA protocol. Gene expression estimates (Fragments Per Kilobase of transcript per Million mapped reads, FPKM) were generated using analysis pipelines based on HISAT/StringTie, with the GRCh38 human genome primary assembly and GENCODE Release 27 transcript and gene definitions. Gene expression data are summarized by GENCODE gene identifier, with gene and transcript definitions and annotations from GENCODE Release 27. Detailed descriptions of the cohort, study material, RNA-seq methods, and HISAT/StringTie analysis pipelines are provided in the source reference: Saal LH et al. Population-scale integration of tumor transcriptomics into breast cancer care: a decade of the SCAN-B initiative. medRxiv. 2026.08.20.26360879. doi: 10.64898/2026.08.20.26360879. Please cite the source reference and acknowledge the SCAN-B project in any use of these data.