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• A New CA19-9 Cut-Off Value Identifies Lewis Antigen Status and Refines Prognostic Stratification in PDAC

  This study investigates the clinical utility of serum CA19-9 levels in pancreatic ductal adenocarcinoma (PDAC), with a focus on identifying patients with Lewis antigen–negative status due to germline FUT3 variants. Using data from multicenter prospective cohorts in Taiwan, we analyzed CA19-9 classification, FUT2/FUT3 genotypes, and clinicopathological annotations. The goal of this study is to refine prognostic stratification and reduce false-negative interpretation of CA19-9 in PDAC patients. All participants provided informed consent, and the study was approved by the relevant institutional review boards.

  Study EGAS50000001575

• Acute lymphoblastic leukemia in children produces endogenous T-cells targeting tumor associated antigens and neoantigens in peripheral blood

  In this study we investigated the presence of endogenous T-cells recognizing private tumor-associated antigens and predicted neoantigens. To this end, HLA-I and HLA-II restricted tumor associated antigens (TAAs) and neoantigens were respectively identified and predicted from matched tumor and germline (PBMCs) in three acute lymphoblastic leukemia patients. Circulating T-cells targeting both Mass spectrometry (MS)-identified TAAs and predicted neoantigens were identified in virtually all pediatric BCP-ALL patients, extending up to two years on remission.

  Study EGAS50000000925

• Nurminen et al ("GP2Men") Study Primary and Metastatic Prostate Cancer Whole Genome Sequence Data

  We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones.

  Study EGAS50000000005

• Whole exome sequencing of pediatric soft tissue sarcoma PDX models

  Childhood cancer remains one of the leading causes of death in pediatric patients in Europe. Pediatric sarcomas, comprising soft tissue sarcomas and malignant bone tumors, are a heterogenous group of malignancies, with more than 50 subtypes (WHO classification). Due to low case numbers, studying pediatric sarcomas requires accurate and reliable preclinical models. Here, we established 18 soft tissues sarcoma PDX models, including Ewing Sarcoma, Rhabdmyosarcoma and Osteosarcoma. We characterized these models by Whole Exome Sequencing and assessd the response to a wide range of drugs.

  Study EGAS50000000048

• Papua New Guinean Lowlanders Dataset

  High-coverage whole genome sequences were collected to study patterns of genomic variation across the southern lowland of Papua New Guinea. This region has experienced an extremely complex demographic history, including repeated bouts of admixture with archaic and modern human groups. This dataset reports whole genome sequences for 41 individuals from this region. Particular attention has been paid in the original study to genomic signals that are informative for population history, including admixture with archaic hominins and the role of modern human admixture during the late Pleistocene and Holocene.

  Study EGAS50000000033

• Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in cancer patients

  The lack of comprehensive diagnostics and consensus analytical models for evaluating the status of a patient’s immune system has hindered a wider adoption of immunoprofiling for treatment monitoring and response prediction in cancer patients. To address this unmet need, we developed an immunoprofiling platform that uses multiparameter flow cytometry and RNA-seq to characterize immune cell heterogeneity in the peripheral blood of healthy donors and patients with advanced cancers. Using unsupervised clustering, we identified five immunotypes with unique distributions of different cell types, and gene expression profiles.

  Study EGAS50000000286

• Paired Biopsy Project: West Coast Dream Team

  This project aims to analyze the paired metastatic biopsy samples from patients with metastatic castration-resistant prostate cancer (mCRPC), collected before the initiation of the first-line androgen receptor signaling inhibitor (ARSI) for mCRPC and after radiographic disease progression on that ARSI, to understand the resistance mechanisms. We generated both whole genome sequencing (WGS) and RNA-seq data on these samples. A majority of these samples have been deposited in the public domain along with prior publications, and this project contains the 16 WGS samples that have not yet been deposited.

  Study EGAS50000000327

• Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

  Gastric cancer (GC) is a major cause of global cancer mortality with high levels of heterogeneity, and intratumoral heterogeneity (ITH) represents a significant barrier to GC patient outcomes. In this study, we applied GeoMx DSP technology to identify ITH in GC. We found spatially colocalized RNA-based intratumor subgroups within samples, each correlated with distinct spatially oriented TME and immune profiles. The findings broadening our understanding of the spatial and molecular complexity of GC ITH and offering a valuable data resource for future exploration and discovery.

  Study EGAS50000000345

• Gene Expression Signature in Normal Mammary Gland from 83 Breast Cancer Patients Indicates Pre-tumorous Changes and Adverse Outcomes

  This study assessed the transcriptomic profiles of 242 samples from 83 breast cancer patients with unfavorable outcomes, including paired uninvolved mammary gland samples collected at varying distances from primary lesions. As a reference, control samples from 53 mammoplasty individuals without cancer history were studied. A custom panel of 634 genes linked to breast cancer progression and metastasis was employed for expression profiling (targeted RNA sequencing), followed by whole-transcriptome (RNA sequencing) verification experiments and statistical analyses to discern molecular signatures and their clinical relevance.

  Study EGAS50000000011

• cfDNA Methylomes for HCC Detection and Postoperative Monitoring

  To overcome the limitations of current ctDNA-based HCC detection, specifically mutational profiling, we propose quantifying cfDNA methylation levels using cfMeDIP-seq and evaluating its capacity for HCC detection and post-surgery recurrence monitoring. This approach aims to reveal the clonal dynamics of HCC during surgery and upon relapse. Our preliminary data and analyzed results demonstrate that tumor-agnostic cfDNA methylomes can accurately detect HCC and predict recurrence after liver resection or transplantation. This method could have significant implications for the diagnosis, treatment, and monitoring of HCC.

  Study EGAS50000000450