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Data for: Neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER+/HER2- breast cancer: a randomized phase II trial

https://doi.org/10.48723/j14a-6r76
The dataset contains whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) FASTQ files derived from tumor tissue samples collected in the PREDIX Lum B clinical trial (prospective randomized phase II, ClinicalTrials.gov ID: NCT02603679) conducted at three hospitals in Sweden. In total, the dataset includes 166 WES samples and 163 RNA-Seq samples. For WES, matched normal blood samples are also included. Metadata file containing patient anonymized ID, treatment arm, gender, and the corresponding WES and RNA-seq sample anonymized IDs. Files are organized by sequencing type (WES and RNA-Seq), plus a metadata table listing all variables: trial ID, gender, treatment arm, and associated file paths. No specialized software is required to open the FASTQ files or metadata. Downstream analysis requires related bioinformatics tools. The dataset consists of: - 4,974 FASTQ files, compressed as GNU zip files - 3 CSV files - 1 readme file in TXT format The total size of the dataset is approximately 7.6 TB
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Documentation files

Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Data contains personal data:

Yes

Type of personal data:

The dataset does not contain direct identifiers such as names, personal identity numbers, social security numbers, contact details, or other directly identifying information. Each patient is represented by a repository-specific anonymized study ID generated from the original trial-specific patient ID using a salted SHA-256 hashing procedure. The original trial-specific patient IDs are not included in this repository, and the private salt used for ID generation is not shared. The repository-specific study IDs cannot, on their own, be used to identify individual patients. Linkage between the original trial-specific patient IDs and individual identities is possible only at the local study sites by the principal investigator and designated site staff, using site-specific key files that are not included in this repository and are not shared. The metadata include limited clinical variables, including gender and treatment arm, which may constitute indirect identifiers. The sequencing data, consisting of WES and RNA-seq FASTQ files, represent individual molecular and genetic profiles and therefore qualify as sensitive health-related and genetic data. Although direct identifiers have been removed and study IDs have been anonymized using a cryptographic hashing procedure, genomic data may be inherently identifiable and should therefore be handled and protected in accordance with applicable regulations for sensitive personal data, genetic data, and health data.

Code key exists:

Yes

Sensitive personal data:

Yes

Citation:

Language:

Method and outcome

Population:

The study was conducted at three hospitals in Stockholm, Sweden (Karolinska University Hospital, Södersjukhuset, and Capio S:t Göran Hospital). Between March 18, 2016, and July 29, 2021, 181 patients were enrolled. Two patients were excluded from all analyses, leaving 179 patients in the intention-to-treat (ITT) population. The study population consisted of women and men aged ≥35 years with ER-positive (≥10%) and HER2-negative breast cancer, Eastern Cooperative Oncology Group (ECOG) performance status 0–1, tumor size >2 cm and/or node-positive disease. Patients with up to two distant metastases treatable with curative intent were eligible. All participants had adequate cardiac, renal, and hepatic function and no other malignancy within the past five years. Tissue biospecimens were collected from the patients prior to the initiation of the neoadjuvant therapy, as specified in the study protocol. Up to five 14-gauge ultrasound-guided core needle tissue biopsies were collected. Three fresh-frozen (FF) tissue samples were stored directly at −80 °C after collection. The remaining two samples were directly immersed into 10% neutral-buffered formalin for preparation of formalin-fixed paraffin-embedded (FFPE) tissue blocks. Biopsies at baseline and on-treatment were obtained after the PET/CT scan. Whole peripheral blood was also collected before the initiation of neoadjuvant therapy in 4ml EDTA tubes and stored at –80 °C. Plasma and serum samples were collected at baseline and every six weeks during treatment, as well as during follow-up. After all quality control and preprocessing steps, biopsy samples available for translational analysis comprised 166 for RNA sequencing (RNA-Seq) and 166 for whole exome sequencing (WES).

Study design:

  • Experimental study
  • Randomised controlled trial (RCT)
  • Cross-over

Data format/​data structure:

Geographic coverage

Geographic location:

Administrative information

Responsible department/​unit:

Department of Oncology-Pathology [K7]

Ethical Review

Reviewer:

  • Stockholm Ethical Review Board

Registration number:

2014/1492-31/4

Funding

Funding agency:

Award number:

2020-00636_VR

Award title:

Randomized Trials on Biology-Driven De-escalation of Neoadjuvant Treatment for HER2-positive Breast Cancer: ARIADNE master protocol

Funding information:

Abstract (1446/1500 chars)ARIADNE is a multicenter, open-label, randomized, comparative phase IIB trial which consists of two separate sub-studies. The main aim is to evaluate whether neoadjuvant therapy for HER2-positive breast cancer can be safely de-escalated while maintaining efficacy, based on biology-driven management decisions. Eligible patients will have early or locally advanced breast cancer (cT2-4, N0-3, M0) with confirmed HER2-positive status. Patients with ER-positive disease will be randomized 1:1 to receive standard of care therapy (docetaxel, carboplatin, trastuzumab, pertuzumab (TCHP) for six cycles) or T-DM1 in combination with ribociclib and letrozole for six cycles. Patients with ER-negative disease will be randomized 1:1 to receive TCHP x6 or treatment according to PAM50 molecular intrinsic subtype: HER2-enriched patients will be treated with T-DM1 x6; tumors in other subtype groups will be treated with dose-dense epirubicin and cyclophosphamide x4, followed by TCHP x4. In both studies, patients progressing after two cycles with de-escalated therapy will crossover to standard of care. Further adjuvant therapy will be given depending on assigned arm and residual disease. The primary endpoint is rates of pathological complete response (pCR), defined as ypT0/Tis, ypN0, as determined at the surgical specimen. Fewer adverse events, improved quality of life and similar outcomes compared to standard therapy are the expected benefits for the study participants.

Topic and keywords

Swedish Standard Classification of Research Subjects 2025:

Keywords:

Relations

Is part of:

Clinical Trial, EUCT number:2024-519019-32-00

Publications

Citation:

Matikas A, Tzoras E, Sarafidis M, Sifakis EG, Bjöhle J, Barnekow E, Margolin S, Isaksson-Friman E, Kessler LE, Zouzos A, Johansson H, Hellström M, Agartz S, Grybäck P, Salgkamis D, Zerdes I, Wang K, Hartman J, Acs B, Sun W, Boyaci C, Villacampa G, Pascual T, Gavila J, Prat A, Perou C, Brandberg Y, Bergh J, Hatschek T, Foukakis T. Neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER + /HER2- breast cancer: a randomized phase II trial. Nat Commun. 2026 Apr 8;17(1):3403. doi: 10.1038/s41467-026-71452-6. PMID: 41951647.

Citation:

Matikas, A., Bjöhle, J., Barnekow, E., Isakssonfriman, E., Zouzos, A., Tzoras, E., Johansson, H., Margolin, S., Acs, B., & Boyaci, C. (2024). 122P Primary results and biomarker analysis from PREDIX LumB: A prospective randomized phase II trial investigating sequence of neoadjuvant chemotherapy and palbociclib/endocrine therapy for luminal breast cancer. In ESMO OPEN (Vol. 9, pp. 103110–103110). https://doi.org/10.1016/j.esmoop.2024.103110

SwePub:

oai:swepub.ki.se:868305

Contact

Metadata

Version 1
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