Routine Molecular Pathology Diagnostics in Precision Oncology

Tumor diagnosis recharacterization enabled by comprehensive genomic profiling to guide precision medicine strategy

Comprehensive genomic profiling (CGP) via next-generation sequencing is standard clinical practice for advanced and metastatic cancers in the U.S. and can help identify clinically actionable alterations in patients who may benefit from targeted therapies. CGP can also complement clinicopathological findings and in certain cases, may lead to diagnostic recharacterization resulting in more precise therapeutic strategies. Here, we highlight examples where molecular findings resulted in tumor re-evaluation and subsequent recharacterization. Twenty-eight cases where CGP results were inconsistent with initial pathological diagnosis and clinical presentation were selected for secondary clinicopathological review to explore alternative diagnostic explanations more consistent with the genomic results. Genomic profiling identified clinically actionable and prognostic variants leading to more accurate therapeutic recommendations based on the updated diagnoses highlighting the value of CGP beyond biomarker detection for therapy selection and supporting its complementary use in diagnostic confirmation to unveil opportunities for precision medicine strategies.

Epigenomic insights and computational advances in hematologic malignancies

Hematologic malignancies (HMs) encompass a diverse spectrum of cancers originating from the blood, bone marrow, and lymphatic systems, with myeloid malignancies representing a significant and complex subset. This review provides a focused analysis of their classification, prevalence, and incidence, highlighting the persistent challenges posed by their intricate genetic and epigenetic landscapes in clinical diagnostics and therapeutics. The genetic basis of myeloid malignancies, including chromosomal translocations, somatic mutations, and copy number variations, is examined in detail, alongside epigenetic modifications with a specific emphasis on DNA methylation. We explore the dynamic interplay between genetic and epigenetic factors, demonstrating how these mechanisms collectively shape disease progression, therapeutic resistance, and clinical outcomes. Advances in diagnostic modalities, particularly those integrating epigenomic insights, are revolutionizing the precision diagnosis of HMs. Key approaches such as nano-based contrast agents, optical imaging, flow cytometry, circulating tumor DNA analysis, and somatic mutation testing are discussed, with particular attention to the transformative role of machine learning in epigenetic data analysis. DNA methylation episignatures have emerged as a pivotal tool, enabling the development of highly sensitive and specific diagnostic and prognostic assays that are now being adopted in clinical practice. We also review the impact of computational advancements and data integration in refining diagnostic and therapeutic strategies. By combining genomic and epigenomic profiling techniques, these innovations are accelerating biomarker discovery and clinical translation, with applications in precision oncology becoming increasingly evident. Comprehensive genomic datasets, coupled with artificial intelligence, are driving actionable insights into the biology of myeloid malignancies and facilitating the optimization of patient management strategies. Finally, this review emphasizes the translational potential of these advancements, focusing on their tangible benefits for patient care and outcomes. By synthesizing current knowledge and recent innovations, we underscore the critical role of precision medicine and epigenomic research in transforming the diagnosis and treatment of myeloid malignancies, setting the stage for ongoing advancements and broader clinical implementation.

Application of Next-Generation Sequencing to Realize Principles of Precision Therapy in Management of Cancer Patients

All cancers are diseases of the genome, since the cancer cell genome typically consists of 10,000s of passenger alterations, 5-10 biologically relevant alterations, and 1-2 "actionable" alterations. Therefore, somatic mutations in cancer cells can have diagnostic, prognostic, and predictive value. Traditional methods are widely used for testing, such as immunohistochemistry, Sanger sequencing, and allele-specific PCR. However, due to the low throughput, these methods are focused exclusively on testing the most common mutations in target genes. The modern next generation sequencing (NGS) is a technology that enables precision oncology in its current form. ESCAT and ESMO Guidelines defined NGS for routine use in patients with advanced cancers such as non-squamous non-small cell lung cancer, prostate cancer, ovarian cancer, and cholangiocarcinoma. The high sensitivity of the NGS method allows it to be used to search for specific mutations in circulating tumor DNA in blood plasma and other body fluids. NGS testing has evolved from hotspot panels, actionable gene panels, and disease-specific panels to more comprehensive panels. The exome and whole genome sequencing approaches are just beginning to emerge, that is why panel-based testing remains most optimal in oncology practice. NGS is also widely used to identify new and rare mutations in cancer genes and detect inherited cancer mutations.

[Standardized and quality-assured predictive PD-L1 testing in the upper gastrointestinal tract. German version]

As a result of the high approval dynamics and the growing number of immuno-oncological therapy concepts, the complexity of therapy decisions and control in the area of carcinomas of the esophagus, gastroesophageal junction and stomach is constantly increasing. Since the treatment indication for PD‑1 inhibitors that are currently approved in the European Union is often linked to the expression of PD-L1 (programmed cell death-ligand 1), the evaluation of tissue-based predictive markers by the pathologist is of crucial importance for treatment stratification. Even though the immunohistochemical analysis of the PD-L1 expression status is one of the best studied, therapy-relevant biomarkers for an immuno-oncological treatment, due to the high heterogeneity of carcinomas of the upper gastrointestinal tract, there are challenges in daily clinical diagnostic work with regard to implementation, standardization and interpretation of testing. An interdisciplinary group of experts from Germany has taken a position on relevant questions from daily pathological and clinical practice, which concern the starting material, quality-assured testing and the interpretation of pathological findings, and has developed recommendations for structured reporting.

Standardized and quality-assured predictive PD-L1 testing in the upper gastrointestinal tract

As a result of the high approval dynamics and the growing number of immuno-oncological concepts, the complexity of treatment decisions and control in the area of cancers of the esophagus, gastroesophageal junction and stomach is constantly increasing. Since the treatment indication for PD-1 inhibitors that are currently approved in the European Union is often linked to the expression of PD-L1 (programmed cell death-ligand 1), the evaluation of tissue-based predictive markers by the pathologist is of crucial importance for treatment stratification. Even though the immunohistochemical analysis of the PD-L1 expression status is one of the best studied, therapy-relevant biomarkers for an immuno-oncological treatment, due to the high heterogeneity of carcinomas of the upper gastrointestinal tract, there are challenges in daily clinical diagnostic work with regard to implementation, standardization and interpretation of testing. An interdisciplinary group of experts from Germany has taken a position on relevant questions from daily pathological and clinical practice, which concern the starting material, quality-assured testing and the interpretation of pathological findings, and has developed recommendations for structured reporting.