Molecular Tumor Boards in Clinical Practice

Signalomics for molecular tumor boards and precision oncology of breast and gynecological cancers

Precision oncology led to the establishment and widespread application of molecular tumor boards (MTBs)-multidisciplinary units combining molecular and clinical assessment of individual cancer cases for swift selection of personalized treatments. Whole-exome or gene panel sequencing, combined with transcriptomic, immunohistochemical, and other molecular analyses, often permits dissection of molecular drivers of a tumor and identification of its potential targetable vulnerabilities, instructing clinical oncologists on sometimes unconventional treatment options. However, cancer drivers are often unleashed mutation-independently, especially in breast and gynecological cancers, and deleterious mutations are not always pathogenic. To complement the MTB arsenal, we chart here the molecular toolset we call Signalomics that permits fast and robust assessment of a panel of oncogenic signaling pathways in fresh tumor samples. Using transcriptional reporters introduced in primary tumor cells, this approach identifies the pathways overactivated in a given tumor and validates their sensitivity to targeted therapies, providing actionable insights for personalized treatment strategies. Integration of Signalomics into MTB workflows bridges the gap between molecular profiling and functional pathway analysis, refining clinical treatment decisions and advancing 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.

Real-world experience of Molecular Tumour Boards for clinical decision-making for cancer patients

Molecular Tumour Boards (MTBs) play a crucial role in interpreting genomic results and providing treatment recommendations. We investigated the real-world impact of MTBs on clinical decision-making by surveying health care professionals (HCPs) across the UK; 44 participants from 11 MTBs took part in the study. 97.7% of respondents felt that MTBs increased awareness of available clinical trials matched to genomic alterations, 84% reported more confidence in interpreting genomic data, and 95.4% valued MTBs as educational. Hurdles to the discussion at MTBs included frequency and capacity of MTBs (ctDNA), sample collection and laboratory turnaround time (Tissue samples). One-third of respondents encountered challenges attending MTBs regularly due to workload. The survey highlighted areas for optimisation, such as meeting efficiency, rapid molecular analysis turnaround time, reliable trial matching tools, and ensuring MTBs are included in HCP's job plans.

The Molecular Tumor Board Turns 10: The Age of Complexity

Gene sequencing has brought a titanic of complex data into clinical precision oncology. Deciphering this complexity for practice requires new constructs. In 2014, the Molecular Tumor Board (MTB) was introduced into the literature by a publication in The Oncologist. Ten years later, MTBs have become globally established vehicles that integrate rapidly emerging "omic" information, helping to transform cancer management.

Retrieval Augmented Therapy Suggestion for Molecular Tumor Boards: Algorithmic Development and Validation Study

BACKGROUND

Molecular tumor boards (MTBs) require intensive manual investigation to generate optimal treatment recommendations for patients. Large language models (LLMs) can catalyze MTB recommendations, decrease human error, improve accessibility to care, and enhance the efficiency of precision oncology.

OBJECTIVE

In this study, we aimed to investigate the efficacy of LLM-generated treatments for MTB patients. We specifically investigate the LLMs' ability to generate evidence-based treatment recommendations using PubMed references.

METHODS

We built a retrieval augmented generation pipeline using PubMed data. We prompted the resulting LLM to generate treatment recommendations with PubMed references using a test set of patients from an MTB conference at a large comprehensive cancer center at a tertiary care institution. Members of the MTB manually assessed the relevancy and correctness of the generated responses.

RESULTS

A total of 75% of the referenced articles were properly cited from PubMed, while 17% of the referenced articles were hallucinations, and the remaining were not properly cited from PubMed. Clinician-generated LLM queries achieved higher accuracy through clinician evaluation than automated queries, with clinicians labeling 25% of LLM responses as equal to their recommendations and 37.5% as alternative plausible treatments.

CONCLUSIONS

This study demonstrates how retrieval augmented generation-enhanced LLMs can be a powerful tool in accelerating MTB conferences, as LLMs are sometimes capable of achieving clinician-equal treatment recommendations. However, further investigation is required to achieve stable results with zero hallucinations. LLMs signify a scalable solution to the time-intensive process of MTB investigations. However, LLM performance demonstrates that they must be used with heavy clinician supervision, and cannot yet fully automate the MTB pipeline.

Advancing personalized cancer therapy: Onko_DrugCombScreen-a novel Shiny app for precision drug combination screening

Identifying and validating genotype-guided drug combinations for a specific molecular subtype in cancer therapy represents an unmet medical need and is important in enhancing efficacy and reducing toxicity. However, the exponential increase in combinatorial possibilities constrains the ability to identify and validate effective drug combinations. In this context, we have developed Onko_DrugCombScreen, an innovative tool aiming at advancing precision medicine based on identifying significant drug combination candidates in a target cancer cohort compared to a comparison cohort. Onko_DrugCombScreen, inspired by the molecular tumor board process, synergizes drug knowledgebase analysis with various statistical methodologies and data visualization techniques to pinpoint drug combination candidates. Validated through a TCGA-BRCA case study, Onko_DrugCombScreen has demonstrated its proficiency in discerning established drug combinations in a specific cancer type and in revealing potential novel drug combinations. By enhancing the capability of drug combination discovery through drug knowledgebases, Onko_DrugCombScreen represents a significant advancement in personalized cancer treatment by identifying promising drug combinations, setting the stage for the development of more precise and potent combination treatments in cancer care. The Onko_DrugCombScreen Shiny app is available at https://rshiny.gwdg.de/apps/onko_drugcombscreen/. The Git repository can be accessed at https://gitlab.gwdg.de/MedBioinf/mtb/onko_drugcombscreen.

[Clinical and molecular epidemiology of malignant salivary gland tumors]

Salivary gland carcinomas are a rare and heterogeneous group of malignant tumors, accounting for 3-6% of all malignant tumors in the head and neck region. The 1-, 3- and 5-year survival rates are 83%, 69% and 63% respectively. Due to new molecular pathological and genetic findings, new entities are constantly being defined as part of the recurring WHO classification of salivary gland carcinomas, so that the incidence rates of the entities are subject to constant change. The only certain risk factor for the development of salivary gland carcinomas is ionizing radiation. In addition, large tumors, cervical lymph node involvement and perineural sheath involvement significantly worsen the prognosis. Today, molecular pathology is coming to the fore, with which potential targets have been identified that can offer prognosis-improving treatment options, particularly in recurrent or distant metastatic stages. Entity-specific tyrosine kinase inhibitors such as axitinib in adenoid cystic carcinoma or larotrectinib in secretory carcinoma and cross-entity therapies such as HER2 inhibition and androgen deprivation can prolong median and progression-free survival with a favorable side effect profile.

Molecular Tumor Board-Guided Targeted Treatments for Biliary Tract Cancers in a Publicly Funded Healthcare System

Comprehensive molecular profiling can identify alterations in biliary tract cancer (BTC) potentially treatable with targeted therapies. However, the impact of whole-genome and transcriptome sequencing (WGTS) on therapeutic decision-making in a public healthcare system is unknown. Here, BTC patients prospectively received WGTS to inform clinical care at a large Canadian academic cancer center. We characterized the proportion of targetable alterations, the treatment recommendations generated by a molecular tumor board, targeted therapies received, patient outcomes, and the financing of these treatments. A total of 55 patients with BTC prospectively underwent WGTS to inform clinical care. Of those 55, 28 (51%, 95% CI 38-64%) harbored targetable alterations. Molecular tumor boards recommended consideration of targeted therapies for 43 (78% CI: 66-87%) of 55 cases. Among the 15 patients who progressed to second-line therapy and harbored targetable alterations, 8 received nine targeted therapies. No targeted therapies were funded through the public system, and most therapies were funded through compassionate access programs from companies. These results highlight the challenges and potential for inequities when implementing precision oncology in a publicly funded healthcare system.

Artificial intelligence for image recognition in diagnosing oral and oropharyngeal cancer and leukoplakia

Visual diagnosis is one of the key features of squamous cell carcinoma of the oral cavity (OSCC) and oropharynx (OPSCC), both subsets of head and neck squamous cell carcinoma (HNSCC) with a heterogeneous clinical appearance. Advancements in artificial intelligence led to Image recognition being introduced recently into large language models (LLMs) such as ChatGPT 4.0. This exploratory study, for the first time, evaluated the application of image recognition by ChatGPT to diagnose squamous cell carcinoma and leukoplakia based on clinical images, with images without any lesion as a control group. A total of 45 clinical images were analyzed, comprising 15 cases each of SCC, leukoplakia, and non-lesion images. ChatGPT 4.0 was tasked with providing the most likely diagnosis based on these images in scenario one. In scenario two the image and the clinical history were provided, whereas in scenario three only the clinical history was given. The results and the accuracy of the LLM were rated by two independent reviewers and the overall performance was evaluated using the modified Artificial Intelligence Performance Index (AIPI. In this study, ChatGPT 4.0 demonstrated the ability to correctly identify leukoplakia cases using image recognition alone, while the ability to diagnose SCC was insufficient, but improved by including the clinical history in the prompt. Providing only the clinical history resulted in a misclassification of most leukoplakia and some SCC cases. Oral cavity lesions were more likely to be diagnosed correctly. In this exploratory study of 45 images of oral lesions, ChatGPT 4.0 demonstrated a convincing performance for detecting SCC only when the clinical history was added, whereas Leukoplakia was detected solely by image recognition. ChatGPT is therefore currently insufficient for reliable OPSCC and OSCC diagnosis, but further technological advancements may pave the way for the use in the clinical setting.

Genomic sequencing in paediatric oncology: navigating conflicting roles and responsibilities

BACKGROUND

This study explores the ethical and moral challenges faced by paediatric oncologists when they are informed of patient genomic results, particularly during molecular tumour boards (MTBs), highlighting the interplay between their clinic, research and expert roles.

METHODS

This was an explanatory sequential mixed-methods study using a survey distributed to paediatric oncologists in Quebec followed by optional semi-structured interviews. Oncologists' attitudes and comfort levels with six hypothetical germline DNA results identified in a patient from a clinical vignette were assessed using Likert scales. Hypothetical genetic results represented ethical challenges of extended paediatric genomic sequencing. Interviews were conducted with a subgroup of participants to gain insight and context on key survey results.

RESULTS

Eighty per cent (n=28) of oncologists in Quebec completed the survey; five participated in the interviews. Comfort levels of oncologists were influenced by the type of genetic result (expected, secondary, incidental finding), whether or not the oncologist was the patient's treating physician, and whether the information disclosed to the patient aligned with the information that they had received. Awareness of a genetic result was sufficient to trigger a feeling of responsibility and liability for that result.

CONCLUSION

Oncologists who take part in genomic sequencing initiatives and who attend MTBs have privileged access to genomic results, above what may be accessible to patients. This imbalance in knowledge contributes to moral discomfort experienced by oncologists who feel responsible for genomic information they are aware of. We propose recommendations applicable to consent processes, policies and pipelines for sharing genomic results.

Empowering personalized oncology: evolution of digital support and visualization tools for molecular tumor boards

BACKGROUND

Molecular tumor boards (MTBs) play a pivotal role in personalized oncology, leveraging complex data sets to tailor therapy for cancer patients. The integration of digital support and visualization tools is essential in this rapidly evolving field facing fast-growing data and changing clinical processes. This study addresses the gap in understanding the evolution of software and visualization needs within MTBs and evaluates the current state of digital support. Alignment between user requirements and software development is crucial to avoid waste of resources and maintain trust.

METHODS

In two consecutive nationwide medical informatics projects in Germany, surveys and expert interviews were conducted as stage 1 (n = 14), stage 2 (n = 30), and stage 3 (n = 9). Surveys, via the SoSci Survey tool, covered participants' roles, working methods, and support needs. The second survey additionally addressed requirements for visualization solutions in molecular tumor boards. These aimed to understand diverse requirements for preparation, implementation, and documentation. Nine semi-structured expert interviews complemented quantitative findings through open discussion.

RESULTS

Using quantitative and qualitative analyses, we show that existing digital tools may improve therapy recommendations and streamline MTB case preparation, while continuous training and system improvements are needed.

CONCLUSIONS

Our study contributes to the field by highlighting the importance of developing user-centric, customizable software solutions that can adapt to the fast-paced environment of MTBs to advance personalized oncology. In doing so, it lays the foundation for further advances in personalized medicine in oncology and points to a shift towards more efficient, technology-driven clinical decision-making processes. This research not only enriches our understanding of the integration of digital tools into MTBs, but also signals a broader shift towards technological innovation in healthcare.

Multi-Institutional Evaluation of Interrater Agreement of Biomarker-Drug Pair Rankings Based on the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) and Sources of Discordance

BACKGROUND

The widespread use of next-generation sequencing in clinical practice has contributed to the accumulation of a large number of genomic findings associated with targeted therapy; therefore, the problem of ranking the detected findings has become acute. The European Society for Medical Oncology Scale of Clinical Actionability of molecular Targets (ESCAT) system was designed by the European Society for Medical Oncology to rank biomarkers into levels of evidence that reflect their potency and clinical significance based on published clinical data. However, the ESCAT system remains imperfect, as it is based on a subjective assessment of the levels of evidence.

OBJECTIVE

The objective of this study was to determine whether the ranking of LOE for biomarker-drug pairs based on the ESCAT system is dependent on the human factor, and to uncover potential issues associated with the use of the framework.

METHODS

To evaluate the inter-rater agreement, we created a dataset of a total of 154 biomarker-drug pairs for 18 unique tumor types. We aimed to include biomarker-drug pairs that could be considered standard of care as well as less common and under investigated pairs. Fourteen precision oncology experts were invited to assign an ESCAT level of evidence for biomarker-drug pairs. Statistical analysis was carried out using Cohen's kappa and the Kolmogorov-Smirnov test.

RESULTS

The inter-rater agreement was low with some exceptions, and significant deviations from the consensus level of evidence were observed. For biomarker-drug associations, the deviations from the consensus were observed for more than 50% of the contributors' rankings. The most agreement between the contributors was observed for lung adenocarcinoma (p < 0.005), while the most disagreement was observed for esophageal cancer (p < 0.01) biomarker-drug pairs in our dataset.

CONCLUSIONS

This study demonstrates noteworthy discordances between the precision oncology experts and may provide the directions for future developments in modifying the ESCAT framework and the overall applicability of the results of genomic profiling into clinical practice.

Unveiling the Digital Evolution of Molecular Tumor Boards

Molecular tumor boards (MTB) are interdisciplinary conferences involving various experts discussing patients with advanced tumors, to derive individualized treatment suggestions based on molecular variants. These discussions involve using heterogeneous internal data, such as patient clinical data, but also external resources such as knowledge databases for annotations and search for relevant clinical studies. This imposes a certain level of complexity that requires huge effort to homogenize the data and use it in a speedy manner to reach the needed treatment. For this purpose, most institutions involving an MTB are heading toward automation and digitalization of the process, hence reducing manual work requiring human intervention and subsequently time in deriving personalized treatment suggestions. The tools are also used to better visualize the patient's data, which allows a refined overview for the board members. In this paper, we present the results of our thorough literature research about MTBs, their process, the most common knowledge bases, and tools used to support this decision-making process.

Precision oncology implementation in a regional-based health care system: A professional consensus to define the pathway

OBJECTIVE

Precision Oncology requires deep changes in organizational settings but little evidence has been identified about the best strategy to guarantee the delivery of this innovation to patients. In the Italian health care system, high heterogeneity could jeopardize equal access opportunity for patients. Following a consensus method, we aim to define shared solutions to address these issues in clinical practice.

METHOD

A Delphi RAND method was chosen to record the consensus among involved health care professionals in the Italian region of Friuli Venezia Giulia. The item generation phase was conducted following a bottom-up approach.

RESULTS

Ten statements were defined on the main topics that emerged from the direct observation of the current practice, focusing on Molecular Tumor Board organization, massive parallel sequencing technology application, laboratory report content and informed consensus submission. All the statements reached a strong consensus and have been shared with the health care government authorities of our region.

CONCLUSIONS

The direct observation of the current practice in different health care authorities allowed to define ten statements as solution proposals to solve the identified complexities. This methodological approach could be applied in different organizational models but aiming to achieve a homogeneous clinical outcome for patients.

Immune digital twins for complex human pathologies: applications, limitations, and challenges

Digital twins represent a key technology for precision health. Medical digital twins consist of computational models that represent the health state of individual patients over time, enabling optimal therapeutics and forecasting patient prognosis. Many health conditions involve the immune system, so it is crucial to include its key features when designing medical digital twins. The immune response is complex and varies across diseases and patients, and its modelling requires the collective expertise of the clinical, immunology, and computational modelling communities. This review outlines the initial progress on immune digital twins and the various initiatives to facilitate communication between interdisciplinary communities. We also outline the crucial aspects of an immune digital twin design and the prerequisites for its implementation in the clinic. We propose some initial use cases that could serve as "proof of concept" regarding the utility of immune digital technology, focusing on diseases with a very different immune response across spatial and temporal scales (minutes, days, months, years). Lastly, we discuss the use of digital twins in drug discovery and point out emerging challenges that the scientific community needs to collectively overcome to make immune digital twins a reality.

Assessing the use of the novel tool Claude 3 in comparison to ChatGPT 4.0 as an artificial intelligence tool in the diagnosis and therapy of primary head and neck cancer cases

OBJECTIVES

Head and neck squamous cell carcinoma (HNSCC) is a complex malignancy that requires a multidisciplinary tumor board approach for individual treatment planning. In recent years, artificial intelligence tools have emerged to assist healthcare professionals in making informed treatment decisions. This study investigates the application of the newly published LLM Claude 3 Opus compared to the currently most advanced LLM ChatGPT 4.0 for the diagnosis and therapy planning of primary HNSCC. The results were compared to that of a conventional multidisciplinary tumor board; (2) Materials and Methods: We conducted a study in March 2024 on 50 consecutive primary head and neck cancer cases. The diagnostics and MDT recommendations were compared to the Claude 3 Opus and ChatGPT 4.0 recommendations for each patient and rated by two independent reviewers for the following parameters: clinical recommendation, explanation, and summarization in addition to the Artificial Intelligence Performance Instrument (AIPI); (3) Results: In this study, Claude 3 achieved better scores for the diagnostic workup of patients than ChatGPT 4.0 and provided treatment recommendations involving surgery, chemotherapy, and radiation therapy. In terms of clinical recommendations, explanation and summarization Claude 3 scored similar to ChatGPT 4.0, listing treatment recommendations which were congruent with the MDT, but failed to cite the source of the information; (4) Conclusion: This study is the first analysis of Claude 3 for primary head and neck cancer cases and demonstrates a superior performance in the diagnosis of HNSCC than ChatGPT 4.0 and similar results for therapy recommendations. This marks the advent of a newly launched advanced AI model that may be superior to ChatGPT 4.0 for the assessment of primary head and neck cancer cases and may assist in the clinical diagnostic and MDT setting.

Impact of Comprehensive Genome Profiling on the Management of Advanced Non-Small Cell Lung Cancer: Preliminary Results From the Lung Cancer Cohort of the FPG500 Program

PURPOSE

The clinical and research FPG500 program (ClinicalTrials.gov identifier: NCT06020625) is currently ongoing at the Fondazione Policlinico Universitario Agostino Gemelli IRCCS to tailor matched targeted therapies (MTTs) according to biomarkers predictive of response identified by comprehensive genome profiling (CGP).

MATERIALS AND METHODS

The non-small cell lung cancer (NSCLC) cohort results from the FPG500 program are outlined. CGP was performed by TruSight Oncology 500 High Throughput (TSO500HT) assay or Oncomine Focus Assay plus Archer's FusionPlex Lung Panel according to tumor cell content and DNA/RNA quantity. Relevant issues for Molecular Tumor Board (MTB) evaluation included uncommon genomic findings, evaluation for off-label therapies, uncertain result confirmation, and variants of suspect germline origin requiring genetic counseling. Progression-free survival (PFS) and overall survival (OS) for the enrolled patients were assessed using Kaplan-Meier analysis.

RESULTS

In 2022, 283 patients with NSCLC were considered for sequencing, with 93% meeting eligibility criteria. TSO500HT sequencing was conducted in 76% of patients. Follow-up data were obtained for 187 patients, among whom 81% received treatment. Potential driver alterations were identified in 59% of patients, with 41% receiving MTT: 25% were prescribed approved MTTs, whereas 16% gained access to experimental drugs post-MTB evaluation; of note, 18% did not receive any MTT because the regimen was not yet reimbursed in our country. Median PFS and OS varied among treatment groups, with standard chemotherapy/immunotherapy at 7.7 and 10.7 months, approved tyrosine kinase inhibitors at 18.8 and 23.9 months, and MTT post-MTB discussion at 14 and 23.4 months, respectively.

CONCLUSION

The early data of the FPG program (NSCLC cohort) support the implementation of CGP and MTB in clinical practice to grant access to patients harboring actionable molecular alterations to the most effective and individualized available treatment options, thus improving their survival outcomes.

Artificial Intelligence in Otology and Neurotology

Clinical applications of artificial intelligence (AI) have grown exponentially with increasing computational power and Big Data. Data rich fields such as Otology and Neurotology are still in the infancy of harnessing the power of AI but are increasingly involved in training and developing ways to incorporate AI into patient care. Current studies involving AI are focused on accessible datasets; health care wearables, tabular data from electronic medical records, electrophysiologic measurements, imaging, and "omics" provide huge amounts of data to utilize. Health care wearables, such as hearing aids and cochlear implants, are a ripe environment for AI implementation.

The molecular tumor board as a step in cancer patient management: a southern Italian experience

Introduction

The management of cancer patients follows a Diagnostic Therapeutic and Care Pathway (PDTA) approach, aimed at achieving the optimal balance between care and quality of life. To support this process, precision medicine and innovative technologies [e.g., next-generation sequencing (NGS)] allow rapid identification of genetic-molecular alterations useful for the design of PDTA-approved therapies. If the standard approach proves inadequate, the Molecular Tumor Board (MTB), a group comprising specialists from diverse disciplines, can step in to evaluate a broader molecular profile, proposing potential therapies beyond evidence levels I-II or considering enrolment in clinical trials. Our aim is to analyze the role of the MTB in the entire management of patients in our institute and its impact on the strategy of personalized medicine, particularly when all approved treatments have failed.

Materials and methods

In alignment with European and national guidelines, a panel of clinicians and preclinical specialists from our institution was defined as the MTB core team. We designed and approved a procedure for the operation of this multidisciplinary group, which is the only one operating in the Puglia region.

Results and discussion

In 29 months (2021-2023), we discussed and analyzed 93 patients. A total of 44% presented pathogenic alterations, of which 40.4% were potentially actionable. Only 11 patients were proposed for enrollment in clinical trials, treatment with off-label drugs, or AIFA (the Italian pharmaceutical agency for drugs)-5% funding. Our process indicators, time to analysis, and number of patient cases discussed are in line with the median data of other European institutions. Such findings underscore both the importance and usefulness of the integration of an MTB process into the care of oncology patients.

Assessing the role of advanced artificial intelligence as a tool in multidisciplinary tumor board decision-making for recurrent/metastatic head and neck cancer cases - the first study on ChatGPT 4o and a comparison to ChatGPT 4.0

Background

Recurrent and metastatic head and neck squamous cell carcinoma (HNSCC) is characterized by a complex therapeutic management that needs to be discussed in multidisciplinary tumor boards (MDT). While artificial intelligence (AI) improved significantly to assist healthcare professionals in making informed treatment decisions for primary cases, an application in the even more complex recurrent/metastatic setting has not been evaluated yet. This study also represents the first evaluation of the recently published LLM ChatGPT 4o, compared to ChatGPT 4.0 for providing therapy recommendations.

Methods

The therapy recommendations for 100 HNSCC cases generated by each LLM, 50 cases of recurrence and 50 cases of distant metastasis were evaluated by two independent reviewers. The primary outcome measured was the quality of the therapy recommendations measured by the following parameters: clinical recommendation, explanation, and summarization.

Results

In this study, ChatGPT 4o and 4.0 provided mostly general answers for surgery, palliative care, or systemic therapy. ChatGPT 4o proved to be 48.5% faster than ChatGPT 4.0. For clinical recommendation, explanation, and summarization both LLMs obtained high scores in terms of performance of therapy recommendations, with no significant differences between both LLMs, but demonstrated to be mostly an assisting tool, requiring validation by an experienced clinician due to a lack of transparency and sometimes recommending treatment modalities that are not part of the current treatment guidelines.

Conclusion

This research demonstrates that ChatGPT 4o and 4.0 share a similar performance, while ChatGPT 4o is significantly faster. Since the current versions cannot tailor therapy recommendations, and sometimes recommend incorrect treatment options and lack information on the source material, advanced AI models at the moment can merely assist in the MDT setting for recurrent/metastatic HNSCC.

Multigenic panels in breast cancer: Clinical utility and management of patients with pathogenic variants other than BRCA1/2

Multigene panels can analyze high and moderate/intermediate penetrance genes that predispose to breast cancer (BC), providing an opportunity to identify at-risk individuals within affected families. However, considering the complexity of different pathogenic variants and correlated clinical manifestations, a multidisciplinary team is needed to effectively manage BC. A classification of pathogenic variants included in multigene panels was presented in this narrative review to evaluate their clinical utility in BC. Clinical management was discussed for each category and focused on BC, including available evidence regarding the multidisciplinary and integrated management of patients with BC. The integration of both genetic testing and counseling is required for customized decisions in therapeutic strategies and preventative initiatives, as well as for a defined multidisciplinary approach, considering the continuous evolution of guidelines and research in the field.

Evolving and Improving the Sustainability of Molecular Tumor Boards: The Value and Challenges

The increasing volume of information for cancer care, and the evolution of molecularly guided therapies, have increased the need for molecular tumor boards (MTBs), which can integrate such data into personalized treatment plans to improve patient outcomes. However, recommendations for improving the sustainability of MTBs are lacking. A diverse committee of MTB experts was assembled (February-March 2023), with extensive experience in sustainability in healthcare ecosystems. The aim was to identify MTB-related hurdles throughout the patient journey and develop a general framework for MTBs to operate on larger scales locally, nationally, and internationally. The committee identified ten key pillars for sustainable and scalable MTBs, including technical solutions for data integration and visualization, interoperability, learning loops, clinical trial access, legal considerations, criteria for patient testing, decision standardization, making MTBs official bodies for treatment decisions, local leaders, and international networks. The need for scalable frameworks at academic and community levels was recognized, along with integrating MTBs into national health systems to enhance sustainability and ensure optimal treatment decisions. Irrespective of the health ecosystem, the sustainability and scalability of MTBs are essential. Our framework provides guidelines to address this and to help MTBs evolve towards integrated, essential components of the oncology healthcare system.

Molecular Tumor Board for Unicorns: Outcomes for rare and ultra-rare cancers using an N-of-One personalized treatment strategy

Treatment of rare/ultra-rare tumors is an unmet need due to a lack of standardized therapies and clinical trials. We developed the Molecular Tumor Board (MTB), a multidisciplinary team that integrates molecular profiling to generate personalized, N-of-One treatments for advanced cancers. This study evaluates 112 patients with rare/ultra-rare tumors who presented to the MTB and were evaluable for clinical therapeutic outcome. Overall, 46/112 patients (41%) received a treatment regimen with a high degree of matching between tumor molecular alterations and drugs given (reflected by a high Matching Score (≥50%)). Patients with a high versus low Matching Score experienced significantly longer progression-free survival (p = 0.005) and overall survival (p = 0.047), and higher rates of clinical benefit (stable disease ≥6 months, partial response, or complete response) (54% vs. 32% p = 0.027). The MTB facilitated personalized N-of-One matching of drugs to tumor molecular alterations, which was associated with improved clinical outcomes in patients with rare/ultra-rare cancers.

Clinical bioinformatics desiderata for molecular tumor boards

Clinical Bioinformatics is a knowledge framework required to interpret data of medical interest via computational methods. This area became of dramatic importance in precision oncology, fueled by cancer genomic profiling: most definitions of Molecular Tumor Boards require the presence of bioinformaticians. However, all available literature remained rather vague on what are the specific needs in terms of digital tools and expertise to tackle and interpret genomics data to assign novel targeted or biomarker-driven targeted therapies to cancer patients. To fill this gap, in this article, we present a catalog of software families and human skills required for the tumor board bioinformatician, with specific examples of real-world applications associated with each element presented.

Unlocking the potential of Molecular Tumor Boards: from cutting-edge data interpretation to innovative clinical pathways

The emerging era of precision medicine is characterized by an increasing availability of targeted anticancer therapies and by the parallel development of techniques to obtain more refined molecular data, whose interpretation may not always be straightforward. Molecular tumor boards gather various professional figures, in order to leverage the analysis of molecular data and provide prognostic and predictive insights for clinicians. In addition to healthcare development, they could also become a tool to promote knowledge and research spreading. A growing body of evidence on the application of molecular tumor boards to clinical practice is forming and positive signals are emerging, although a certain degree of heterogeneity exists. This work analyzes molecular tumor boards' potential workflows, figures involved, data sources, sample matrices and eligible patients, as well as available evidence and learning examples. The emerging concept of multi-institutional, disease-specific molecular tumor boards is also considered by presenting two ongoing nationwide experiences.

Patient eligibility for trials with imaging response assessment at the time of molecular tumor board presentation

PURPOSE

To assess the eligibility of patients with advanced or recurrent solid malignancies presented to a molecular tumor board (MTB) at a large precision oncology center for inclusion in trials with the endpoints objective response rate (ORR) or duration of response (DOR) based on Response Evaluation Criteria in Solid Tumors (RECIST version 1.1).

METHODS

Prospective patients with available imaging at the time of presentation in the MTB were included. Imaging data was reviewed for objectifiable measurable disease (MD) according to RECIST v1.1. Additionally, we evaluated the patients with MD for representativeness of the identified measurable lesion(s) in relation to the overall tumor burden.

RESULTS

262 patients with different solid malignancies were included. 177 patients (68%) had MD and 85 (32%) had non-measurable disease (NMD) at the time point of MTB presentation in accordance with RECIST v1.1. MD was not representative of the overall tumor burden in eleven patients (6%). The main reasons for NMD were lesions with longest diameter shorter than 10 mm (22%) and non-measurable peritoneal carcinomatosis (18%). Colorectal cancer and malignant melanoma displayed the highest rates of MD (> 75%). In contrast, gastric cancer, head and neck malignancies, and ovarian carcinoma had the lowest rates of MD (< 55%). In case of MD, the measurable lesions were representative of the overall tumor burden in the vast majority of cases (94%).

CONCLUSION

Approximately one third of cancer patients with advanced solid malignancies are not eligible for treatment response assessment in trials with endpoints ORR or DOR at the time of MTB presentation. The rate of patients eligible for trials with imaging endpoints differs significantly based on the underlying malignancy and should be taken under consideration during the planning of new precision oncology trials.

Integration of proteomics in the molecular tumor board

Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.

Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery

DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.

Assessing the role of advanced artificial intelligence as a tool in multidisciplinary tumor board decision-making for primary head and neck cancer cases

Background

Head and neck squamous cell carcinoma (HNSCC) is a complex malignancy that requires a multidisciplinary approach in clinical practice, especially in tumor board discussions. In recent years, artificial intelligence has emerged as a tool to assist healthcare professionals in making informed decisions. This study investigates the application of ChatGPT 3.5 and ChatGPT 4.0, natural language processing models, in tumor board decision-making.

Methods

We conducted a pilot study in October 2023 on 20 consecutive head and neck cancer patients discussed in our multidisciplinary tumor board (MDT). Patients with a primary diagnosis of head and neck cancer were included. The MDT and ChatGPT 3.5 and ChatGPT 4.0 recommendations for each patient were compared by two independent reviewers and the number of therapy options, the clinical recommendation, the explanation and the summarization were graded.

Results

In this study, ChatGPT 3.5 provided mostly general answers for surgery, chemotherapy, and radiation therapy. For clinical recommendation, explanation and summarization ChatGPT 3.5 and 4.0 scored well, but demonstrated to be mostly an assisting tool, suggesting significantly more therapy options than our MDT, while some of the recommended treatment modalities like primary immunotherapy are not part of the current treatment guidelines.

Conclusions

This research demonstrates that advanced AI models at the moment can merely assist in the MDT setting, since the current versions list common therapy options, but sometimes recommend incorrect treatment options and in the case of ChatGPT 3.5 lack information on the source material.

Pragmatic nationwide master observational trial based on genomic alterations in advanced solid tumors: KOrean Precision Medicine Networking Group Study of MOlecular profiling guided therapy based on genomic alterations in advanced Solid tumors (KOSMOS)-II study protocol KCSG AL-22-09

BACKGROUND

Next-generation sequencing (NGS) has been introduced to many Korean institutions to support molecular diagnostics in cancer since 2017, when it became eligible for reimbursement by the National Health Insurance Service. However, the uptake of molecularly guided treatment (MGT) based on NGS results has been limited because of stringent regulations regarding prescriptions outside of approved indications, a lack of clinical trial opportunities, and limited access to molecular tumor boards (MTB) at most institutions. The KOSMOS-II study was designed to demonstrate the feasibility and effectiveness of MGT, informed by MTBs, using a nationwide precision medicine platform.

METHODS

The KOSMOS-II trial is a large-scale nationwide master observational study. It involves a framework for screening patients with metastatic solid tumors for actionable genetic alterations based on local NGS testing. It recommends MGT through a remote and centralized MTB meeting held biweekly. MGT can include one of the following options: Tier 1, the therapeutic use of investigational drugs targeting genetic alterations such as ALK, EGFR, ERBB2, BRAF, FH, ROS1, and RET, or those with high tumor mutational burden; Tier 2, comprising drugs with approved indications or those permitted for treatment outside of the indications approved by the Health Insurance Review and Assessment Service of Korea; Tier 3, involving clinical trials matching the genetic alterations recommended by the MTB. Given the anticipated proportion of patients receiving MGT in the range of 50% ± 3.25%, this study aims to enroll 1,000 patients. Patients must have progressed to one or more lines of therapy and undergone NGS before enrollment.

DISCUSSION

This pragmatic master protocol provides a mass-screening platform for rare genetic alterations and high-quality real-world data. Collateral clinical trials, translational studies, and clinico-genomic databases will contribute to generating evidence for drug repositioning and the development of new biomarkers.

TRIAL REGISTRATION

NCT05525858.

Fusion genes in pancreatic tumors

Gene fusions and rearrangements play a crucial role in tumor biology. They are rare events typically detected in KRAS wild-type (WT) pancreatic tumors. Their identification can inform clinical management by enabling precision oncology, as fusions involving BRAF, FGFR2, RET, NTRK, NRG1, and ALK represent actionable targets in KRAS-WT cancers, and serve diagnostic purposes since fusions involving PRKACA/B represent the diagnostic hallmark of intraductal oncocytic papillary neoplasms (IOPNs). Although they are rare, the therapeutic and diagnostic importance of these genomic events should not be underestimated, highlighting the need for quality-ensured molecular diagnostics in the management of cancer. Herein we review the existing literature on the role of fusion genes in pancreatic tumors and their clinical potential as effective biomarkers and therapeutic targets.

Primary Results of Patients with Genitourinary Malignancies Presented at a Molecular Tumor Board

INTRODUCTION

Personalized medicine poses great opportunities and challenges. While the therapeutic landscape markedly expands, descriptions about status, clinical implementation and real-world benefits of precision oncology and molecular tumor boards (MTB) remain sparse, particularly in the field of genitourinary (GU) cancer. Hence, this study characterized urological MTB cases to better understand the potential role of MTB in uro-oncology.

METHODS

We analyzed patients with complete data sets being reviewed at an MTB from January 2019 to October 2022, focusing on results of molecular analysis and treatment recommendations.

RESULTS

We evaluated 102 patients with GU cancer with a mean patient age of 61.7 years. Prostate cancer (PCa) was the most frequent entity with 52.9% (54/102), followed by bladder cancer (18.6%, 19/102) and renal cell carcinoma (14.7%, 15/102). On average, case presentation at MTB took place 54.9 months after initial diagnosis and after 2.7 previous lines of therapy. During the study period, 49.0% (50/102) of patients deceased. Additional MTB-based treatment recommendations were achieved in a majority of 68.6% (70/102) of patients, with a recommendation for targeted therapy in 64.3% (45/70) of these patients. Only 6.7% (3/45) of patients - due to different reasons - received the recommended MTB-based therapy though, with 33% (1/3) of patients reaching disease control. Throughout the MTB study period, GU cancer case presentations and treatment recommendations increased, while the time interval between initial presentation and final therapy recommendation were decreasing over time.

CONCLUSION

Presentation of uro-oncological patients at the MTB is a highly valuable measure for clinical decision-making. Prospectively, earlier presentation of patients at the MTB and changing legislative issues regarding comprehensive molecular testing and targeted treatment approval might further improve patients' benefits from comprehensive molecular diagnostics.

Data Visualization Support for Tumor Boards and Clinical Oncology: Protocol for a Scoping Review

BACKGROUND

Complex and expanding data sets in clinical oncology applications require flexible and interactive visualization of patient data to provide the maximum amount of information to physicians and other medical practitioners. Interdisciplinary tumor conferences in particular profit from customized tools to integrate, link, and visualize relevant data from all professions involved.

OBJECTIVE

The scoping review proposed in this protocol aims to identify and present currently available data visualization tools for tumor boards and related areas. The objective of the review will be to provide not only an overview of digital tools currently used in tumor board settings, but also the data included, the respective visualization solutions, and their integration into hospital processes.

METHODS

The planned scoping review process is based on the Arksey and O'Malley scoping study framework. The following electronic databases will be searched for articles published in English: PubMed, Web of Knowledge, and SCOPUS. Eligible articles will first undergo a deduplication step, followed by the screening of titles and abstracts. Second, a full-text screening will be used to reach the final decision about article selection. At least 2 reviewers will independently screen titles, abstracts, and full-text reports. Conflicting inclusion decisions will be resolved by a third reviewer. The remaining literature will be analyzed using a data extraction template proposed in this protocol. The template includes a variety of meta information as well as specific questions aiming to answer the research question: "What are the key features of data visualization solutions used in molecular and organ tumor boards, and how are these elements integrated and used within the clinical setting?" The findings will be compiled, charted, and presented as specified in the scoping study framework. Data for included tools may be supplemented with additional manual literature searches. The entire review process will be documented in alignment with the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) flowchart.

RESULTS

The results of this scoping review will be reported per the expanded PRISMA-ScR guidelines. A preliminary search using PubMed, Web of Knowledge, and Scopus resulted in 1320 articles after deduplication that will be included in the further review process. We expect the results to be published during the second quarter of 2024.

CONCLUSIONS

Visualization is a key process in leveraging a data set's potentially available information and enabling its use in an interdisciplinary setting. The scoping review described in this protocol aims to present the status quo of visualization solutions for tumor board and clinical oncology applications and their integration into hospital processes.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/53627.

Challenges and opportunities for sarcoma care and research in Latin America: a position paper from the LACOG sarcoma group

As a developing region, Latin America faces unique cancer control and prevention challenges, which are intensified when considering rare cancers, including sarcomas. Sarcomas are a group of malignancies that arise in the connective tissues of the body-such as muscle, fat, nerves, blood vessels, and bones-accounting for a diverse range of tumours that, although rare, require specialized attention. Sarcoma care and research in Latin America require a comprehensive approach that includes deeper epidemiologic knowledge, diagnostic capacity building, access to innovative treatments, increased patient advocacy, and strengthening of clinical research capacity. This article will review current challenges and opportunities for treating patients with sarcoma in Latin America and outline a pathway toward improvement for regional collaborative groups.

Molecular diagnostics tailoring personalized cancer therapy-an oncologist's view

Medical oncology is rapidly evolving with the implementation of personalized, targeted therapies. Advances in molecular diagnostics and the biologic understanding of cancer pathophysiology led to the identification of specific genetic alterations as drivers of cancer progression. Further, improvements in drug development enable the direct interference with these pathways, which allow tailoring personalized treatments based on a distinct molecular characterization of tumors. Thereby, we are currently experiencing a paradigm-shift in the treatment of cancers towards cancer-type agnostic, molecularly targeted, personalized therapies. However, this concept has several important hurdles and limitations to overcome to ultimately increase the proportion of patients benefitting from the precision oncology approach. These include the assessment of clinical relevancy of identified alterations, capturing and interpreting levels of heterogeneity based on intra-tumoral or time-dependent molecular evolution, and challenges in the practical implementation of precision oncology in routine clinical care. In the present review, we summarize the current state of cancer-agnostic precision oncology, discuss the concept of molecular tumor boards, and consider current limitations of personalized cancer therapy. Further, we provide an outlook towards potential future developments including the implementation of functionality assessments of identified genetic alterations and the broader use of liquid biopsies in order to obtain more comprehensive and longitudinal genetic information that might guide personalized cancer therapy in the future.

The role of molecular tumor boards in neuro-oncology: a nationwide survey

BACKGROUND

In neuro-oncology, the inclusion of tumor patients in the molecular tumor board has only become increasingly widespread in recent years, but so far there are no standards for indication, procedure, evaluation, therapy recommendations and therapy implementation of neuro-oncological patients. The present work examines the current handling of neuro-oncological patients included in molecular tumor boards in Germany.

METHODS

We created an online based survey with questions covering the handling of neuro-oncologic patient inclusion, annotation of genetic analyses, management of target therapies and the general role of molecular tumor boards in neuro-oncology in Germany. We contacted all members of the Neuro-Oncology working group (NOA) of the German Cancer Society (DKG) by e-mail.

RESULTS

38 responses were collected. The majority of those who responded were specialists in neurosurgery or neurology with more than 10 years of professional experience working at a university hospital. Molecular tumor boards (MTB) regularly take place once a week and all treatment disciplines of neuro-oncology patients take part. The inclusions to the MTB are according to distinct tumors and predominantly in case of tumor recurrence. An independently MTB member mostly create the recommendations, which are regularly implemented in the tumor treatment. Recommendations are given for alteration classes 4 and 5. Problems exist mostly within the cost takeover of experimental therapies. The experimental therapies are mostly given in the department of medical oncology.

CONCLUSIONS

Molecular tumor boards for neuro-oncological patients, by now, are not standardized in Germany. Similarities exists for patient inclusion and interpretation of molecular alterations; the time point of inclusion and implementation during the patient treatment differ between the various hospitals. Further studies for standardization and harmonisation are needed. In summary, most of the interviewees envision great opportunities and possibilities for molecular-based neuro-oncological therapy in the future.

Molecular Tumor Board Improves Outcomes for Hispanic Patients With Advanced Solid Tumors

PURPOSE

Multidisciplinary molecular tumor boards (MTBs) decode complex genomic data into clinical recommendations. Although MTBs are well-established in the oncology practice in developed countries, this strategy needs to be better explored in developing countries. Herein, we describe the possible benefits and limitations of the first MTB established in Colombia.

METHODS

Demographic, clinical, and genomic information was collected between August 2020 and November 2021. By mid-2020, an MTB strategy was created to discuss clinical cases with one or more genomic alterations identified by next-generation sequencing using an open-access virtual platform. We characterized the patient population as benefiting from the recommended treatment option. We assessed the benefits and access to available targeted therapies that have the potential to change clinical management by making recommendations to treating oncologists on the basis of genomic profiling. However, we did not assess the treatment oncologists' compliance with MTB recommendations because they were not intended to replace clinical judgment/standard of care.

RESULTS

A total of 146 patients were included in the discussions of the MTB. The median age was 59 years, and 59.6% were women. Genomic results prompting a change in therapeutic decisions were obtained in 53.1% of patients (95% CI, 44.9 to 61.3). The most prevalent malignancy was non-small-cell lung cancer (51%). Other malignancies represented 60%, 50%, and 30% of patients with soft-tissue sarcomas, brain tumors, and breast cancer, respectively.

CONCLUSION

Using an open-access virtual platform, MTBs were feasible in low- and middle-income countries on the basis of the capability to provide the benefits and access to available targeted therapies that are not standard of care. Furthermore, MTB recommendations were made available to the treating oncologist in different locations across Colombia, providing the option to modify clinical management in most of these patients.

Precision cancer medicine and the doctor-patient relationship: a systematic review and narrative synthesis

BACKGROUND

The implementation of precision medicine is likely to have a huge impact on clinical cancer care, while the doctor-patient relationship is a crucial aspect of cancer care that needs to be preserved. This systematic review aimed to map out perceptions and concerns regarding how the implementation of precision medicine will impact the doctor-patient relationship in cancer care so that threats against the doctor-patient relationship can be addressed.

METHODS

Electronic databases (Pubmed, Scopus, Web of Science, Social Science Premium Collection) were searched for articles published from January 2010 to December 2021, including qualitative, quantitative, and theoretical methods. Two reviewers completed title and abstract screening, full-text screening, and data extraction. Findings were summarized and explained using narrative synthesis.

RESULTS

Four themes were generated from the included articles (n = 35). Providing information addresses issues of information transmission and needs, and of complex concepts such as genetics and uncertainty. Making decisions in a trustful relationship addresses opacity issues, the role of trust, and and physicians' attitude towards the role of precision medicine tools in decision-making. Managing negative reactions of non-eligible patients addresses patients' unmet expectations of precision medicine. Conflicting roles in the blurry line between clinic and research addresses issues stemming from physicians' double role as doctors and researchers.

CONCLUSIONS

Many findings have previously been addressed in doctor-patient communication and clinical genetics. However, precision medicine adds complexity to these fields and further emphasizes the importance of clear communication on specific themes like the distinction between genomic and gene expression and patients' expectations about access, eligibility, effectiveness, and side effects of targeted therapies.

Time to Deliver on Promises: The Role of ERBB2 Alterations as Treatment Options for Colorectal Cancer Patients in the Era of Precision Oncology

Receptor tyrosine kinase erythroblastic oncogene B2 (ERBB2), also known as human epidermal growth factor receptor 2 (HER2), represents an oncogenic driver and has been effectively targeted in breast and gastric cancer. Recently, next-generation sequencing (NGS) discovered ERBB2 as a promising therapeutic target in metastatic colorectal cancer (mCRC), where it is altered in 3-5% of patients, but no therapies are currently approved for this use. Herein, we present the experience of a single center in diagnosing actionable genetic ERBB2 alterations using NGS and utilizing the latest therapeutic options. Between October 2019 and December 2022, a total of 107 patients with advanced CRC underwent molecular analysis, revealing actionable ERBB2 mutations in two patients and ERBB2 amplifications in two other patients. These findings correlated with immunohistochemical (IHC) staining. Of these four patients, two were treated with trastuzumab-deruxtecan (T-DXd). We present two exemplary cases of patients with actionable ERBB2 alterations to demonstrate the effectiveness of T-DXd in heavily pretreated ERBB2-positive mCRC patients and the need for early molecular profiling. To fully exploit the potential of this promising treatment, earlier molecular profiling and the initiation of targeted therapies are essential.

Using proteomics for stratification and risk prediction in patients with solid tumors

Proteomics, the study of proteins and their functions, has greatly evolved due to advances in analytical chemistry and computational biology. Unlike genomics or transcriptomics, proteomics captures the dynamic and diverse nature of proteins, which play crucial roles in cellular processes. This is exemplified in cancer, where genomic and transcriptomic information often falls short in reflecting actual protein expression and interactions. Liquid chromatography-mass spectrometry (LC-MS) is pivotal in proteomic data generation, enabling high-throughput analysis of protein samples. The MS-based workflow involves protein digestion, chromatographic separation, ionization, and fragmentation, leading to peptide identification and quantification. Computational biostatistics, particularly using tools in R (R Foundation for Statistical Computing, Vienna, Austria; www.R-project.org ), aid in data analysis, revealing protein expression patterns and correlations with clinical variables. Proteomic studies can be explorative, aiming to characterize entire proteomes, or targeted, focusing on specific proteins of interest. The integration of proteomics with genomics addresses database limitations and enhances peptide identification. Case studies in intrahepatic cholangiocarcinoma, glioblastoma multiforme, and pancreatic ductal adenocarcinoma highlight proteomics' clinical applications, from subtyping cancers to identifying diagnostic markers. Moreover, proteomic data augment molecular tumor boards by providing deeper insights into pathway activities and genomic mutations, supporting personalized treatment decisions. Overall, proteomics contributes significantly to advancing our understanding of cellular biology and improving clinical care.

Modified study designs to expand treatment options in personalised oncology: a multistakeholder view

Personalised oncology, whereby patients are given therapies based on their molecular tumour profile, is rapidly becoming an essential part of optimal clinical care, at least partly facilitated by recent advances in next-generation sequencing-based technology using liquid- and tissue-based biopsies. Consequently, clinical trials have shifted in approach, from traditional studies evaluating cytotoxic chemotherapy in largely histology-based populations to modified, biomarker-driven studies (e.g. basket, umbrella, platform) of molecularly guided therapies and cancer immunotherapies in selected patient subsets. Such modified study designs may assess, within the same trial structure, multiple cancer types and treatments, and should incorporate a multistakeholder perspective. This is key to generating complementary, fit-for-purpose and timely evidence for molecularly guided therapies that can be used as proof-of-concept to inform further study designs, lead to approval by regulatory authorities and be used as confirmation of clinical benefit for health technology assessment bodies. In general, the future of cancer clinical trials requires a framework for the application of innovative technologies and dynamic design methodologies, in order to efficiently transform scientific discoveries into clinical utility. Next-generation, modified studies that involve the joint efforts of all key stakeholders will offer individualised strategies that ultimately contribute to globalised knowledge and collective learning. In this review, we outline the background and purpose of such modified study designs and detail key aspects from a multistakeholder perspective. We also provide methodological considerations for designing the studies and highlight how insights from already-ongoing studies may address current challenges and opportunities in the era of personalised oncology.

NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

Analysis of selected cancer genes has become an important tool in precision oncology but cannot fully capture the molecular features and, most importantly, vulnerabilities of individual tumors. Observational and interventional studies have shown that decision-making based on comprehensive molecular characterization adds significant clinical value. However, the complexity and heterogeneity of the resulting data are major challenges for disciplines involved in interpretation and recommendations for individualized care, and limited information exists on how to approach multilayered tumor profiles in clinical routine. We report our experience with the practical use of data from whole-genome or exome and RNA sequencing and DNA methylation profiling within the MASTER (Molecularly Aided Stratification for Tumor Eradication Research) program of the National Center for Tumor Diseases (NCT) Heidelberg and Dresden and the German Cancer Research Center (DKFZ). We cover all relevant steps of an end-to-end precision oncology workflow, from sample collection, molecular analysis, and variant prioritization to assigning treatment recommendations and discussion in the molecular tumor board. To provide insight into our approach to multidimensional tumor profiles and guidance on interpreting their biological impact and diagnostic and therapeutic implications, we present case studies from the NCT/DKFZ molecular tumor board that illustrate our daily practice. This manual is intended to be useful for physicians, biologists, and bioinformaticians involved in the clinical interpretation of genome-wide molecular information.

Molecular Tumour Board (MTB): From Standard Therapy to Precision Medicine

Background: In the metastatic setting, cancer patients may not benefit from standard care regimes and their diseases undergo drug resistance due to tumour cell heterogeneity and genomic landscape complexity. In recent years, there have been several attempts to personalise the diagnostic-therapeutic path and to propose novel strategies based on not only histological test results but also on each patient's clinical history and molecular biology. Profiling molecular tests allows physicians to investigate the single tumour genomic landscape and to promote targeted approaches. The Molecular Tumour Board (MTB) is a multidisciplinary committee dedicated to selecting individualised and targeted therapeutic strategies appropriate for patients suffering from diseases that present resistance to standard care. Materials and Methods: Our MTB settled in "Azienda Ospedaliero Universitaria delle Marche", Ancona (AN), Italy, and includes oncologists, molecular biologists, geneticists, and other specialists. Clinical cases are referred by physicians to the MTB, through the Cancer and Research Centre of the Marche Region (CORM), through a telemedicine platform. Four possible molecular profiles are available: FoundationOne® CDx e FoundationOne®Liquid CDx and two local Next Generation Sequencing (NGS) panels, with 16 DNA genes and 10 RNA genes respectively. The resulting genetic mutations and their analyses are evaluated by all the members of the Board and a report for each patient is provided with medical recommendations. Results: from June 2021 to May 2023, we collected data from 97 referral patients (M: 49, F: 48). The mean age was 60.6 years (range 22-83 years). 90 cases were approved for testing. Only seven patients were not eligible for genomic profiling. In two patients who were eligible, molecular profiling was not performed because a tissue sample was not available. Off-label therapy was recommended for three patients. 5% of cases (5/88) showed addressable driver mutations associated with an existing targeted therapy and were immediately enrolled. Conclusions: MTB presents a powerful tool for offering precise medical goals. Our Department of Clinical Oncology also takes advantage of the important role of multidisciplinary teams, through the establishment of CORM and MTB meetings, within which there is the chance to perform NGS-based analyses. It will be important in the future to implement the use of genomic profiling to improve personalised care and to guide the choice of suitable therapies and more appropriate management of patients.

The impact of clinical and translational research on the quality of life during the metastatic colorectal cancer patient journey

The journey of metastatic colorectal cancer patients is complex and challenging, requiring coordination and collaboration between multiple healthcare providers. Understanding patients' needs, fears, feelings, concerns, and behaviors is essential for providing individualized patient-centered care. In recent years, mCRC patients have experienced improvements in clinical outcomes, from 16 months of overall survival to 32 months, thanks to research. However, there is still room for improvement, and integrating clinical and translational research into routine practice can help patients benefit from treatments and techniques that would not be an option. In the Journey of mCRC patients, living well with cancer and quality of life becomes a priority given the outcomes of the disease. Patient reported outcomes (PRO) and Patient Reported Outcome Measures (PROMs) are becoming therefore new estimands in Oncology. Patient advocates represent important figures in this process by prioritizing issues and research questions; evaluating research designs and the performance of the research; the analysis and interpretation of data; and how results are disseminated. Multidisciplinary Tumor Boards and shared decision-making is essential for designing treatment strategies for individual patients. Quality of Life is often prioritized only when it comes to refractory advanced disease and end-of-life care, but it has to be integrated from the beginning, as the emotional impact of diagnosis leads to a vulnerable situation where patients' needs and preferences can be easily overseen. First-line treatment will be chosen among more treatment options than subsequent lines, with longer progression-free survival and a bigger impact on the outcomes. Practicing patient-centered care and optimizing first-line treatment for colorectal cancer patients requires a comprehensive understanding of patient experience and treatment outcomes, which can guide clinical practice and inform regulatory decisions for the benefit of patients.

The Molecular Tumor Board of the Regina Elena National Cancer Institute: from accrual to treatment in real-world

BACKGROUND

Molecular Tumor Boards (MTB) operating in real-world have generated limited consensus on good practices for accrual, actionable alteration mapping, and outcome metrics. These topics are addressed herein in 124 MTB patients, all real-world accrued at progression, and lacking approved therapy options.

METHODS

Actionable genomic alterations identified by tumor DNA (tDNA) and circulating tumor DNA (ctDNA) profiling were mapped by customized OncoKB criteria to reflect diagnostic/therapeutic indications as approved in Europe. Alterations were considered non-SoC when mapped at either OncoKB level 3, regardless of tDNA/ctDNA origin, or at OncoKB levels 1/2, provided they were undetectable in matched tDNA, and had not been exploited in previous therapy lines.

RESULTS

Altogether, actionable alterations were detected in 54/124 (43.5%) MTB patients, but only in 39 cases (31%) were these alterations (25 from tDNA, 14 from ctDNA) actionable/unexploited, e.g. they had not resulted in the assignment of pre-MTB treatments. Interestingly, actionable and actionable/unexploited alterations both decreased (37.5% and 22.7% respectively) in a subset of 88 MTB patients profiled by tDNA-only, but increased considerably (77.7% and 66.7%) in 18 distinct patients undergoing combined tDNA/ctDNA testing, approaching the potential treatment opportunities (76.9%) in 147 treatment-naïve patients undergoing routine tDNA profiling for the first time. Non-SoC therapy was MTB-recommended to all 39 patients with actionable/unexploited alterations, but only 22 (56%) accessed the applicable drug, mainly due to clinical deterioration, lengthy drug-gathering procedures, and geographical distance from recruiting clinical trials. Partial response and stable disease were recorded in 8 and 7 of 19 evaluable patients, respectively. The time to progression (TTP) ratio (MTB-recommended treatment vs last pre-MTB treatment) exceeded the conventional Von Hoff 1.3 cut-off in 9/19 cases, high absolute TTP and Von Hoff values coinciding in 3 cases. Retrospectively, 8 patients receiving post-MTB treatment(s) as per physician's choice were noted to have a much longer overall survival from MTB accrual than 11 patients who had received no further treatment (35.09 vs 6.67 months, p = 0.006).

CONCLUSIONS

MTB-recommended/non-SoC treatments are effective, including those assigned by ctDNA-only alterations. However, real-world MTBs may inadvertently recruit patients electively susceptible to diverse and/or multiple treatments.

Real-world performance analysis of a novel computational method in the precision oncology of pediatric tumors

BACKGROUND

The utility of routine extensive molecular profiling of pediatric tumors is a matter of debate due to the high number of genetic alterations of unknown significance or low evidence and the lack of standardized and personalized decision support methods. Digital drug assignment (DDA) is a novel computational method to prioritize treatment options by aggregating numerous evidence-based associations between multiple drivers, targets, and targeted agents. DDA has been validated to improve personalized treatment decisions based on the outcome data of adult patients treated in the SHIVA01 clinical trial. The aim of this study was to evaluate the utility of DDA in pediatric oncology.

METHODS

Between 2017 and 2020, 103 high-risk pediatric cancer patients (< 21 years) were involved in our precision oncology program, and samples from 100 patients were eligible for further analysis. Tissue or blood samples were analyzed by whole-exome (WES) or targeted panel sequencing and other molecular diagnostic modalities and processed by a software system using the DDA algorithm for therapeutic decision support. Finally, a molecular tumor board (MTB) evaluated the results to provide therapy recommendations.

RESULTS

Of the 100 cases with comprehensive molecular diagnostic data, 88 yielded WES and 12 panel sequencing results. DDA identified matching off-label targeted treatment options (actionability) in 72/100 cases (72%), while 57/100 (57%) showed potential drug resistance. Actionability reached 88% (29/33) by 2020 due to the continuous updates of the evidence database. MTB approved the clinical use of a DDA-top-listed treatment in 56 of 72 actionable cases (78%). The approved therapies had significantly higher aggregated evidence levels (AELs) than dismissed therapies. Filtering of WES results for targeted panels missed important mutations affecting therapy selection.

CONCLUSIONS

DDA is a promising approach to overcome challenges associated with the interpretation of extensive molecular profiling in the routine care of high-risk pediatric cancers. Knowledgebase updates enable automatic interpretation of a continuously expanding gene set, a "virtual" panel, filtered out from genome-wide analysis to always maximize the performance of precision treatment planning.

Molecularly Stratified Treatment Options in Primary Refractory DLBCL/HGBL with MYC and BCL2 or BCL6 Rearrangements (HGBL, NOS with MYC/BCL6)

BACKGROUND

There is growing evidence supporting multidisciplinary molecular tumor boards (MTB) in solid tumors whereas hematologic malignancies remain underrepresented in this regard.

OBJECTIVE

The present study aimed to assess the clinical relevance of MTBs in primary refractory diffuse large B-cell lymphomas/high-grade B-cell lymphomas with MYC and BCL2 rearrangements (prDLBCL/HGBL-MYC/BCL2) (n = 13) and HGBL, not otherwise specified (NOS), with MYC and BCL6 rearrangements (prHGBL, NOS-MYC/BCL6) (n = 6) based on our previously published whole-exome sequencing (WES) cohort.

PATIENTS AND METHODS

For genomic analysis, the institutional MTB WES pipeline (University Cancer Center Schleswig-Holstein: UCCSH), certified for routine clinical diagnostics, was employed and supplemented by a comprehensive immunohistochemical work-up. Consecutive database research and annotation according to established evidence levels for molecularly stratified therapies was performed (NCT-DKTK/ESCAT).

RESULTS

Molecularly tailored treatment options with NCT-DKTK evidence level of at least m2A were identified in each case. We classified mutations in accordance with biomarker/treatment baskets and detected a heterogeneous spectrum of targetable alterations affecting immune evasion (IE; n = 30), B-cell targets (BCT; n = 26), DNA damage repair (DDR; n = 20), tyrosine kinases (TK; n = 13), cell cycle (CC; n = 7), PI3K-MTOR-AKT pathway (PAM; n = 2), RAF-MEK-ERK cascade (RME; n = 1), and others (OTH; n = 11).

CONCLUSION

Our virtual MTB approach identified potential molecularly targeted treatment options alongside targetable genomic signatures for both prDLBCL/HGBL-MYC/BCL2 and prHGBL, NOS-MYC/BCL6. These results underline the potential of MTB consultations in difficult-to-treat lymphomas early in the treatment sequence.

Implementation of Precision Oncology in the National Healthcare System: A Statement Proposal Endorsed by Italian Scientific Societies

PURPOSE

Precision oncology (PO) promises positive results for patients. To date, in Italy, the effort to implement PO has been made autonomously by regional health institutions in a top-down fashion. This approach is not very efficient and jeopardizes patients' equal access to PO. Similar outcomes have been recorded in other Western countries. We tested a method of collaboration among professionals, scientific societies, and government institutions to facilitate the delivery of PO innovation to patients' bedsides.

METHOD

We designed an organizational research project on the basis of a bottom-up approach. We started by observing PO-related activities in five health care authorities (HCAs) in one Italian region. We then compared the issues that emerged with those of three additional HCAs in other Italian regions. Using the results of the initial observation and adopting validated multiple-step consensus methods, we finally derived 14 statements that were approved by the four main scientific societies of oncology and pathology at the national level.

RESULTS

The 14 statements addressed the main issues linked to the implementation of PO in clinical practice. The strong professional consensus advocated for prompt adoption within the national healthcare system.

CONCLUSIONS

The consensus on the statements that were obtained shows the importance of a synergistic effort among professionals, scientific societies, and health care institutions in defining homogeneous solutions for innovation implementation within the health care system.

Ibero-American Consensus Review and Incorporation of New Biomarkers for Clinical Practice in Colorectal Cancer

Advances in genomic technologies have significantly improved the management of colorectal cancer (CRC). Several biomarkers have been identified in CRC that enable personalization in the use of biologic agents that have shown to enhance the clinical outcomes of patients. However, technologies used for their determination generate massive amounts of information that can be difficult for the clinician to interpret and use adequately. Through several discussion meetings, a group of oncology experts from Spain and several Latin American countries reviewed the latest literature to provide practical recommendations on the determination of biomarkers in CRC based on their clinical experience. The article also describes the importance of looking for additional prognostic biomarkers and the use of histopathology to establish an adequate molecular classification. Present and future of immunotherapy biomarkers in CRC patients are also discussed, together with several techniques for marker determination, including liquid biopsy, next-generation sequencing (NGS), polymerase chain reaction (PCR), and fecal immunohistochemical tests. Finally, the role of Molecular Tumor Boards in the diagnosis and treatment of CRC is described. All of this information will allow us to highlight the importance of biomarker determination in CRC.

A Retrospective Analysis of Biliary Tract Cancer Patients Presented to the Molecular Tumor Board at the Comprehensive Cancer Center Munich

BACKGROUND AND OBJECTIVE

With the rising importance of precision oncology in biliary tract cancer (BTC), the aim of this retrospective single-center analysis was to describe the clinical and molecular characteristics of patients with BTC who underwent comprehensive genomic profiling (CGP) and were discussed in the CCCMunichLMU molecular tumor board (MTB).

PATIENTS AND METHODS

In this single-center observational study, we included BTC patients with intrahepatic cholangiocarcinoma (iCCA), extrahepatic CCA (eCCA), and gallbladder cancer (GB), who had been discussed in the institutional MTB from May 29, 2017, to July 25, 2022. Patients were followed up until 31 January 2023. Data were retrospectively collected by review of medical charts, and MTB recommendation.

RESULTS

In total, 153 cases were registered to the MTB with a median follow-up of 15 months. Testing was successful in 81.7% of the patients. CGP detected targetable alterations in 35.3% of our BTC patients (most commonly ARID1A/ERBB2/IDH1/PIK3CA/BRAF-mutations and FGFR2-fusions). Recommendations for molecularly guided therapy were given in 46.4%. Of those, treatment implementation of targeted therapy followed in 19.4%. In patients receiving the recommended treatment, response rate was 57% and median overall survival was 19 months (vs 8 months in the untreated cohort). The progression-free survival ratio of 1.45 suggest a clinical benefit of molecularly guided treatment.

CONCLUSIONS

In line with previous work, our series demonstrates feasibility and clinical utility of comprehensive genomic profiling in BTC patients. With the growing number of targeted agents with clinical activity in BTC, CGP should become standard of care in the management of this group of patients.