Philip Jermann
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View article: Tumor immune dynamics and long-term clinical outcome of stage IIIA NSCLC patients treated with neoadjuvant chemoimmunotherapy
Tumor immune dynamics and long-term clinical outcome of stage IIIA NSCLC patients treated with neoadjuvant chemoimmunotherapy Open
Neoadjuvant chemoimmunotherapy offers promise to improve outcomes for patients with resectable non-small cell lung cancer (NSCLC). Yet not all patients derive treatment benefits, and reliable biomarkers of response are still lacking. We he…
View article: ERBB2 Mutation Testing in NSCLC: A Pan-European Real-World Evaluation of the Oncomine Precision Assay
ERBB2 Mutation Testing in NSCLC: A Pan-European Real-World Evaluation of the Oncomine Precision Assay Open
Background/Objectives: The non-small-cell lung cancer (NSCLC) therapeutic landscape has undergone a profound transformation with the introduction of multiple personalized treatment options. Mutations in ERBB2 (HER2) have recently emerged a…
View article: Histopathology-based protein multiplex generation using deep learning
Histopathology-based protein multiplex generation using deep learning Open
View article: Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma
Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma Open
View article: Multi-omic spatial profiling reveals the unique SARS-CoV-2 lung microenvironment and collagen VI as a predictive biomarker in severe COVID-19
Multi-omic spatial profiling reveals the unique SARS-CoV-2 lung microenvironment and collagen VI as a predictive biomarker in severe COVID-19 Open
Background Whilst COVID-19 is primarily a respiratory infection, few studies have characterized the immune response to COVID-19 in lung tissue. We sought to understand the pathogenic role of microenvironmental interactions and the extracel…
View article: Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia
Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia Open
View article: Probabilistic pathway-based multimodal factor analysis
Probabilistic pathway-based multimodal factor analysis Open
Motivation Multimodal profiling strategies promise to produce more informative insights into biomedical cohorts via the integration of the information each modality contributes. To perform this integration, however, the development of nove…
View article: Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer
Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer Open
Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients pres…
View article: European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors
European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors Open
Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential …
View article: Supplementary Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer
Supplementary Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer Open
Supplementary Methods and Data
View article: Supplementary Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer
Supplementary Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer Open
Supplementary Methods and Data
View article: Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer
Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer Open
Purpose:PD-(L)1–blocking antibodies have clinical activity in metastatic non–small cell lung cancer (NSCLC) and mediate durable tumor remissions. However, the majority of patients are resistant to PD-(L)1 blockade. Understanding mechanisms…
View article: Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer
Data from A Variant of a Killer Cell Immunoglobulin-like Receptor Is Associated with Resistance to PD-1 Blockade in Lung Cancer Open
Purpose:PD-(L)1–blocking antibodies have clinical activity in metastatic non–small cell lung cancer (NSCLC) and mediate durable tumor remissions. However, the majority of patients are resistant to PD-(L)1 blockade. Understanding mechanisms…
View article: Only EBUS-Guided Mediastinal Lymph Node Cryobiopsy Enabled Immunotherapy in a Patient with Non-Small Cell Lung Cancer
Only EBUS-Guided Mediastinal Lymph Node Cryobiopsy Enabled Immunotherapy in a Patient with Non-Small Cell Lung Cancer Open
Personalized treatment of metastatic non-squamous non-small cell lung cancer (NSCLC) requires detailed molecular characterization of the tumour including detection of predictive driver mutations and programmed death ligand 1 (PD-L1) expres…
View article: Genetic and epigenetic analysis of hepatocellular adenomas with atypical morphological features
Genetic and epigenetic analysis of hepatocellular adenomas with atypical morphological features Open
Background Hepatocellular adenoma (HCA) is a rare liver tumour, which can have atypical morphological features such as cytological atypia, pseudoglandular architecture, and altered reticulin framework. Little is known about the genetic and…
View article: Prevalence of Molecular Alterations in a Swiss Cohort of 512 Colorectal Carcinoma Patients by Targeted Next-Generation Sequencing Analysis in Routine Diagnostics
Prevalence of Molecular Alterations in a Swiss Cohort of 512 Colorectal Carcinoma Patients by Targeted Next-Generation Sequencing Analysis in Routine Diagnostics Open
Introduction: Colorectal carcinoma (CRC) is among the most common carcinomas in women and men. In the advanced stage, patients are treated based on the RAS status. Recent studies indicate that in the future, in addition to KRAS and NRAS, a…
View article: 70P Genetic alterations and immune cell infiltration with potential impact on PD-(L)1 targeted treatment in various cancer entities: Biobank research project of the INFINITY registry
70P Genetic alterations and immune cell infiltration with potential impact on PD-(L)1 targeted treatment in various cancer entities: Biobank research project of the INFINITY registry Open
View article: Fibroblast growth factor receptor (FGFR) inhibitor rogaratinib in patients with advanced pretreated squamous-cell non-small cell lung cancer over-expressing FGFR mRNA: The SAKK 19/18 phase II study
Fibroblast growth factor receptor (FGFR) inhibitor rogaratinib in patients with advanced pretreated squamous-cell non-small cell lung cancer over-expressing FGFR mRNA: The SAKK 19/18 phase II study Open
Despite preliminary signals of activity, rogaratinib failed to improve PFS in patients with advanced SQCLC overexpressing FGFR mRNA. FGFR inhibitors in SQCLC remain a challenging field, and more in-depth understanding of pathway crosstalks…
View article: CB‐103: A novel CSL‐NICD inhibitor for the treatment of NOTCH‐driven T‐cell acute lymphoblastic leukemia: A case report of complete clinical response in a patient with relapsed and refractory T‐ALL
CB‐103: A novel CSL‐NICD inhibitor for the treatment of NOTCH‐driven T‐cell acute lymphoblastic leukemia: A case report of complete clinical response in a patient with relapsed and refractory T‐ALL Open
Relapsed T cell acute lymphoblastic leukaemia (T‐ALL) has a very poor prognosis. A 24‐year‐old patient with relapsed high‐risk T‐ALL (PTEN gene deletion; NOTCH1 mutation), was treated with the NOTCH inhibitor CB‐103. Within 1 week of start…
View article: scROSHI: robust supervised hierarchical identification of single cells
scROSHI: robust supervised hierarchical identification of single cells Open
Identifying cell types based on expression profiles is a pillar of single cell analysis. Existing machine-learning methods identify predictive features from annotated training data, which are often not available in early-stage studies. Thi…
View article: T cell subtype profiling measures exhaustion and predicts anti-PD-1 response
T cell subtype profiling measures exhaustion and predicts anti-PD-1 response Open
View article: MA09.02 SAKK 16/14 - T-Cell Receptor Repertoire Metrics Predict Response to Neoadjuvant Durvalumab in Patients With Stage IIIA(N2) NSCLC
MA09.02 SAKK 16/14 - T-Cell Receptor Repertoire Metrics Predict Response to Neoadjuvant Durvalumab in Patients With Stage IIIA(N2) NSCLC Open
View article: Establishing standardized immune phenotyping of metastatic melanoma by digital pathology
Establishing standardized immune phenotyping of metastatic melanoma by digital pathology Open
View article: Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis
Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis Open
View article: The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support
The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support Open
View article: SCIM: universal single-cell matching with unpaired feature sets
SCIM: universal single-cell matching with unpaired feature sets Open
Motivation Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clin…
View article: Robust assessment of tumor mutational burden in cytological specimens from lung cancer patients
Robust assessment of tumor mutational burden in cytological specimens from lung cancer patients Open
Our results show that cytological smears provide more consistent TMB values due to high DNA quality and lack of formalin-fixation induced artifacts. Therefore, cytological samples should be the preferred sample type for robust TMB estimati…
View article: TCR-beta repertoire convergence and evenness are associated with response to immune checkpoint inhibitors
TCR-beta repertoire convergence and evenness are associated with response to immune checkpoint inhibitors Open
View article: Tumor mutational burden assessed by targeted NGS predicts clinical benefit from immune checkpoint inhibitors in non‐small cell lung cancer
Tumor mutational burden assessed by targeted NGS predicts clinical benefit from immune checkpoint inhibitors in non‐small cell lung cancer Open
In non‐small cell lung cancer (NSCLC), immune checkpoint inhibitors (ICIs) significantly improve overall survival (OS). Tumor mutational burden (TMB) has emerged as a predictive biomarker for patients treated with ICIs. Here, we evaluated …
View article: Cell-free DNA analysis in healthy individuals by next-generation sequencing: a proof of concept and technical validation study
Cell-free DNA analysis in healthy individuals by next-generation sequencing: a proof of concept and technical validation study Open