RNA sequencing data processing
RNA sequencing processing for baseline frozen biopsy samples in the two trials has been previously describedWhen evaluating the potential technical differences between NeoALTTO and CALGB 40601 in terms of number of normalized BCR and TCR reads and clones, we considered the difference in read length as potential cause of such differences, and explored whether and how BCR/TCR read/clone counts would be impacted in NeoALTTO by trimming reads from 100-bp to 50-bp (Supplementary data The “tximport” R package (v1.16.1)Intrinsic subtypes were obtained from RNAseq gene expression data in both studies by applying a HER2/estrogen receptor subgroup-specific gene normalization method