A5091194323- HER2/EGFR in Cancer Research
- Breast Cancer Treatment Studies
- Lung Cancer Treatments and Mutations
- Advanced Breast Cancer Therapies
- Cancer Cells and Metastasis
- Click Chemistry and Applications
- Cancer Genomics and Diagnostics
- Synthesis and biological activity
- Multiple and Secondary Primary Cancers
- Single-cell and spatial transcriptomics
- Cancer Immunotherapy and Biomarkers
- Cell Image Analysis Techniques
- Gene expression and cancer classification
- Genetic factors in colorectal cancer
- Monoclonal and Polyclonal Antibodies Research
- Prostate Cancer Treatment and Research
- RNA modifications and cancer
- RNA Research and Splicing
- Digital Mental Health Interventions
- Lymphoma Diagnosis and Treatment
- Esophageal Cancer Research and Treatment
- Lung Cancer Diagnosis and Treatment
- Cancer-related molecular mechanisms research
- Intensive Care Unit Cognitive Disorders
- Lung Cancer Research Studies
Roche (Switzerland)
2018-2025
University Hospital of Lord’s Transfiguration
2020-2023
Poznan University of Medical Sciences
1997-2023
Nicolaus Copernicus University
2020-2022
Metropolitan University
2020
University of Zurich
2014-2019
SIB Swiss Institute of Bioinformatics
2014-2019
Instytut Matki i Dziecka
2013
Centralny Szpital Kliniczny
2013
Central Clinical Hospital
2013
<ns4:p>High-dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high-throughput interrogation characterization cell populations. Here, we present an updated R-based pipeline differential analyses HDCyto data, largely based on Bioconductor packages. We computationally define populations using FlowSOM clustering, facilitate optional but reproducible strategy manual merging algorithm-generated clusters. Our workflow offers different analysis paths,...
High dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high throughput interrogation characterization cell populations.Here, we present an R-based pipeline differential analyses HDCyto data, largely based on Bioconductor packages. We computationally define populations using FlowSOM clustering, facilitate optional but reproducible strategy manual merging algorithm-generated clusters. Our workflow offers different analysis paths, including association...
Abstract High-dimensional flow and mass cytometry allow cell types states to be characterized in great detail by measuring expression levels of more than 40 targeted protein markers per at the single-cell level. However, data analysis can difficult, due large size dimensionality datasets as well limitations existing computational methods. Here, we present diffcyt , a new framework for differential discovery analyses high-dimensional data, based on combination high-resolution clustering...
<ns4:p>There are many instances in genomics data analyses where measurements made on a multivariate response. For example, alternative splicing can lead to multiple expressed isoforms from the same primary transcript. There situations differences (e.g. between normal and disease state) relative ratio of may have significant phenotypic consequences or prognostic capabilities. Similarly, knowledge single nucleotide polymorphisms (SNPs) that affect splicing, so-called quantitative trait loci...
RNA-seq has been a boon to the quantitative analysis of transcriptomes. A notable application is detection changes in transcript usage between experimental conditions. For example, discovery pathological alternative splicing may allow development new treatments or better management patients. From an perspective, there are several ways approach data unravel differential usage, such as annotation-based exon-level counting, percentage spliced in, assembled transcripts. The goal this research...
<ns4:p>There are many instances in genomics data analyses where measurements made on a multivariate response. For example, alternative splicing can lead to multiple expressed isoforms from the same primary transcript. There situations total abundance of gene expression does not change (e.g. between normal and disease state), but differences relative ratio may have significant phenotypic consequences or prognostic capabilities. Similarly, knowledge single nucleotide polymorphisms (SNPs) that...
Abstract Purpose: We retrospectively assessed prognostic value of circulating cell-free DNA (cfDNA) using data from the phase III ALEX study in treatment-naïve, advanced ALK+ non–small cell lung cancer (NSCLC). Patients and Methods: were randomized to receive twice-daily alectinib 600 mg (n = 152) or crizotinib 250 151). cfDNA was quantified baseline plasma samples, with patients stratified into ≤median &gt;median biomarker-evaluable populations (BEP). Effect concentration on outcomes...
In KATHERINE, adjuvant T-DM1 reduced risk of disease recurrence or death by 50% compared with trastuzumab in patients residual invasive breast cancer after neoadjuvant therapy (NAT) comprised HER2-targeted and chemotherapy. This analysis aimed to identify biomarkers response differences biomarker expression before NAT.Exploratory analyses investigated the relationship between disease-free survival (IDFS) HER2 protein expression/gene amplification, PIK3CA hotspot mutations, gene HER2, PD-L1,...
Abstract Purpose: Despite extensive genomic and transcriptomic profiling, it remains unknown how signaling pathways are differentially activated tumors sensitized to certain perturbations. Here, we aim characterize AKT activity its association with other or IHC-based PI3K/AKT pathway biomarkers as well the clinical of ipatasertib (AKT inhibitor) in FAIRLANE trial. Experimental Design: In FAIRLANE, 151 patients early triple-negative breast cancer (TNBC) were randomized 1:1 receive paclitaxel...
<ns4:p>High dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high throughput interrogation characterization cell populations.Here, we present an R-based pipeline differential analyses HDCyto data, largely based on Bioconductor packages. We computationally define populations using FlowSOM clustering, facilitate optional but reproducible strategy manual merging algorithm-generated clusters. Our workflow offers different analysis paths, including...
502 Background: The phase 3 KATHERINE study (NCT01772472) compared adjuvant T-DM1 versus H in patients with residual invasive breast cancer after neoadjuvant chemotherapy plus HER2-targeted therapy. Here we report exploratory analyses of the relationship between disease-free survival (IDFS) and biomarkers potentially related to response. Methods: Formalin fixed paraffin-embedded tissue samples were collected before treatment and/or at surgery. Surgical used for analyses, except when only...
13 Background: In IPATential150 (NCT03072238), ipatasertib (ipat) + abiraterone (abi) as first-line treatment for metastatic castration-resistant prostate cancer (mCRPC) significantly reduced the risk disease worsening or death vs placebo (pbo) abi in patients (pts) with tumors PTEN loss by immunohistochemistry (IHC; HR, 0.77 [95% CI: 0.61, 0.98]; P = 0.0335) but not intention-to-treat population (de Bono, ESMO 2020). IHC, median radiographic progression-free survival (rPFS) was 16.5 mo (95%...
<ns4:p>High-dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high-throughput interrogation characterization cell populations. Here, we present an updated R-based pipeline differential analyses HDCyto data, largely based on Bioconductor packages. We computationally define populations using FlowSOM clustering, facilitate optional but reproducible strategy manual merging algorithm-generated clusters. Our workflow offers different analysis paths,...
Abstract Background This phase 1b study (ClinicalTrials.gov identifier NCT03695380) evaluated regimens combining PARP and MEK inhibition, with or without PD‐L1 for BRCA wild‐type, platinum‐sensitive, recurrent ovarian cancer (PSROC). Methods Patients PSROC who had received one two prior treatment lines were treated 28‐day cycles of cobimetinib 60 mg daily (days 1–21) plus niraparib 200 1–28) atezolizumab 840 1 15). Stage assessed safety before expansion to stage 2, which randomized patients...
Numerous data indicate that polymorphism of estrogen receptor alpha (ERalpha) may predict lipid levels, response to hormone replacement therapy (HRT), myocardial infarction risk, bone fracture mineral density (BMD) and changes in BMD over time. In this study we aimed evaluate distribution ERalpha PvuII XbaI genotypes population Polish postmenopausal women qualified different protocols HRT. Subject the were 64 consecutive aged from 45 65 years (mean 56.6) assigned was determined by...
182 Background: IPATential150 is a randomized trial comparing Ipat + Abi vs placebo in patients (pts) with 1L mCRPC (NCT03072238). We evaluated the potential associations between PTEN loss, genomic alterations, and country of enrollment (East Asian [EAS] non-EAS). Methods: Before randomization, tumor samples (archival > 90%) were centrally tested for loss by VENTANA (SP218) immunohistochemistry (IHC) assay (N = 1101). Tumor genetic alterations profiled Foundation Medicine FoundationOne...
Abstract Single-nucleotide polymorphisms (SNPs) have been shown to influence Fcγ receptor (FcγR) affinity and activity, but their effect on treatment response is unclear. We assessed importance in the efficacy of obinutuzumab or rituximab combined with chemotherapy untreated advanced follicular lymphoma (FL) diffuse large B-cell (DLBCL) GALLIUM (www.clinicaltrials.gov #NCT01332968) GOYA (#NCT01287741) trials, respectively. Genomic DNA was extracted from patients enrolled (n = 1202) 1418)....
ABSTRACT Recent advancements in transcriptomics and proteomics have opened the possibility for spatially resolved molecular characterization of tissue architecture with promise enabling a deeper understanding biology either homeostasis or disease. The wealth data generated by these technologies has recently driven development wide range computational methods. These methods requirement advanced coding fluency to be applied integrated across full spatial omics analysis process thus presenting...
Background Substance Use Disorder (SUD) persists as a significant public health challenge worldwide, with an estimated prevalence of approximately 10-15% across the global populace. This condition is characterized by notably high risk lapses and relapses, even subsequent to treatment interventions. Mobile interventions, owing their widespread accessibility, emerge promising approach diminish relapse post-treatment broaden scope care, especially in regions scarcity trained medical...