README
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Dataset title:
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Longitudinal Multi-Omic Characterization of Patient Responses to Neoadjuvant HER2-Targeted Therapy

Recommended Citation:  
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Wang, K., Sifakis, E., & Foukakis, T. (2026). Longitudinal Multi-Omic Characterization of Patient Responses to Neoadjuvant HER2-Targeted Therapy (Version 1) [Data set]. Karolinska Institutet. https://doi.org/10.48723/js80-sx29
See the Researchdata.se catalogue entry for this dataset - accessible via the DOI link above - for compete metadata, including the dataset description, contact information and information about how to obtain the dataset. 

Responsible organization:
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Karolinska Institutet

Description: 
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This dataset contains longitudinal multi-omic profiles derived from patients with early HER2-positive breast cancer enrolled in the randomized phase II PREDIX HER2 clinical trial (NCT02568839). The study compared neoadjuvant treatment with docetaxel, trastuzumab, and pertuzumab (DHP) versus trastuzumab emtansine (T-DM1). The primary aim of this data collection was to monitor tumor evolution and tumor microenvironment dynamics during HER2-targeted therapy.
Data Material and Collection:
The dataset comprises multi-omic data from patient samples collected at different timepoint: on-treatment (after two cycles of neoadjuvant therapy) and post-treatment (after six cycles of neoadjuvant therapy).
Methodology and Assay:
Comprehensive molecular characterization was performed using multiple high-throughput technologies. This includes whole-exome sequencing (WES) to identify somatic mutations and genomic alterations, RNA-sequencing (RNA-seq) for bulk transcriptomic profiling, and proteomics to monitor protein abundance. Additionally, imaging-based spatial transcriptomics was performed using the Xenium In Situ platform to map the spatial organization of the tumor microenvironment; note that the Xenium spatial data is exclusively available for the on-treatment time point.

Access restrictions: 
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This dataset can be requested from the Researchdata.se research data catalog using the link above.

Library preparation and Sequencing:
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RNA libraries: Illumina Stranded Total RNA with Ribo-Zero Plus.

DNA libraries:Twist Comprehensive Exome Kit (Cat. No. 102031, Twist Bioscience).

Sequencing: Conducted at the National Genomics Infrastructure (NGI), SciLifeLab, Uppsala, Sweden using NovaSeq6000 system (150 bp paired-end, S4 flowcell, v1.5 reagents).

Xenium 5K: In situ hybridization performed using the Xenium In Situ Gene Expression Human Breast 5K Probe Panel (10x Genomics). Tissue sections underwent standard dewaxing, decrosslinking, and probe hybridization, followed by rolling circle amplification (RCA). Fluorescence-based, high-throughput imaging was executed on the Xenium Analyzer (10x Genomics) with automated cycle chemistry to decode spatial transcripts at subcellular resolution.

Dataset organization
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The dataset consists of the following:

1) RNA-seq/sequencing_batch/Sample.fastq.gz
Folder containing raw paired-end FASTQ files from RNA-seq. 
Each tumor sample was multiplexed across sequencing sample/lane index combinations. 
File names begin with the project-sample ID and include R1 or R2, denoting forward and reverse reads, respectively.

2) WES/sequencing_batch/Sample.fastq.gz
Folder containing raw paired-end FASTQ files from RNA-seq. 
File names begin with the project-sample ID and include R1 or R2, denoting forward and reverse reads, respectively.

3) Xenium_5k
Each subfolder contains the standardized, uncompressed output directory generated by the Xenium Ranger analysis pipeline for an individual tissue section.