Molecular Tumor Board Research Articles

Combined analysis of circulating tumor DNA and tumor tissue to overcome osimertinib resistance (OSIRIS); the second line osimertinib cohort

IntroductionOsimertinib resistance inevitably occurs in EGFR mutated NSCLC. We aimed to identify resistance mechanisms (RM) using paired plasma and tumor samples in patients that progressed on 2nd/3rd line osimertinib. MethodsFrom 09 to 2019 to 02-2021, 51 patients were enrolled. Plasma sequencing used AVENIO Expanded Panel (research use only), tumor biopsies underwent DNA and RNA sequencing and histological evaluation. Sequencing was regarded successful when the driver mutation was confirmed with a variant allele frequency of ≥ 0.10 %. Concordance between modalities was calculated for the driver mutation and RMs covered in both modalities. The Molecular Tumor Board formulated a treatment advice. ResultsThe driver mutation was detected in 42/51 plasma samples (82 %) and in 50/51 tumor samples (98 %), concordance rate was 80 %. In 41/51 (80 %) patients ≥ 1 RM was identified. Thirty-two RMs covered in both modalities were found in plasma (61.5 %), 39 in tumor (75 %), nineteen in both. RM concordance rate was 36.5 %. ConclusionCombined analysis of plasma and tumor samples post 2nd/3rd line osimertinib identifies additional RMs regardless of the comparative approach used. Plasma sequencing identified 61.5% of RMs, tumor analysis identified 75%. Combined, they provide a superior overview of osimertinib resistance, enabling more tailored treatment options.

80P Development of a next-generation sequencing diagnostics recommender tool in the framework of the molecular tumor board Freiburg

80P Development of a next-generation sequencing diagnostics recommender tool in the framework of the molecular tumor board Freiburg

Targeting Non-V600 Mutations in BRAF: A Single Institution Retrospective Analysis and Review of the Literature.

While successful treatment paradigms for BRAF V600 mutations have been developed, 10% of BRAF mutations are not at V600 and lack a standard treatment regimen. This study summarizes the current body of knowledge on the treatment of non-V600 mutations and reports a single institution experience. We conducted a literature review to summarize relevant preclinical and clinical published data on the response of non-V600 mutations to targeted therapies. We performed a retrospective analysis of INOVA Schar Cancer patients registered in our Molecular Tumor Board database with non-V600 BRAF mutations who were recipients of targeted therapy and assessed their time to next treatment and best response. Published preclinical and clinical data have demonstrated limiting results in the response of non-V600 mutated cancers to targeted therapies. Response rates were variable for the major classes of BRAF mutations including class II and class III mutations as well as, BRAF fusions. Data collected from our INOVA cohort offered promising results with one patient achieving partial remission and two patients achieving stable disease. This article reflects the current understanding of targeted therapies in non-V600 mutations. Further large-scale studies separating BRAF mutations based on their mechanism of activation will expand our understanding.

From Data Mining of Public Sources to Clinical Decision Support in Personalized Medicine.

Personalized medicine enables precise tumor treatment for a patient's molecular genetic profile. To devise optimal targeted treatment plans for patients in a molecular tumor board, physicians must consider alterations on gene- and proteins levels but also cancer cell phenotypes. Machine learning can uncover buried patterns, extract pivotal information, and unveil corresponding insights from available data. Publicly available datasets provide the amounts of data necessary. This work outlines the efficacy of various machine learning algorithms which could eventually serve as clinical decision support in a precision oncology setting. Leveraging algorithms including Random Forest, Decision tree, XGBoost, Logistic regression, Gaussian Naive Bayes, k nearest neighbor, and AdaBoost, we conducted two experiments for the breast invasive carcinoma dataset. Incorporated data includes patient-, molecular- and treatment data. The aim of the investigation was to predict medication treatment or type of treatment based on genetic profile. After preprocessing and application of ML algorithms, the first results were promising. Multiple factors challenge application in clinical care settings without carefully considering the limitations.

A Precision Oncology Platform to Support Genotype-Tailored Therapy Selection.

There is a critical need for a streamlined process to identify genotype-matched individuals eligible for enrollment into clinical trials and/or targeted therapies, as current methodologies face challenges in integrating diverse molecular data sources. We have developed a precision oncology platform to assist molecular tumor boards and community oncologists in reviewing patients' phenotypes, evaluating related knowledge, and identifying genotype-matched therapies.

Advances in Personalized Oncology.

Advances in next-generation sequencing (NGS) have catalyzed a paradigm shift in cancer treatment, steering the focus from conventional, organ-specific protocols to precision medicine. Emerging targeted therapies offer a cutting-edge approach to cancer treatment, while companion diagnostics play an essential role in aligning therapeutic choices with specific molecular changes identified through NGS. Despite these advances, interpreting the clinical implications of a rapidly expanding catalog of genetic mutations remains a challenge. The selection of therapies in the presence of multiple mutations requires careful clinical judgment, supported by quality-centric genomic testing that emphasizes actionable mutations. Molecular tumor boards can play an increasing role in assimilating genomic data into clinical trials, thereby refining personalized treatment approaches and improving patient outcomes.

Single-center analysis of a real-world cohort of patients with metastatic urothelial carcinoma evaluated by NGS: molecular landscape and efficacy of targeted therapies.

To describe the molecular profile of a real-world cohort of patients with metastatic urothelial carcinoma (mUC) and to evaluate the benefit of next-generation sequencing (NGS) panels in guiding therapy in patients with mUC and the outcomes of DNA-matched treatments recommended by a multidisciplinary molecular tumor board (MMTB). This was a single-center analysis of a real-world cohort of adult patients with mUC included in an ongoing trial that aimed to evaluate the clinical utility of NGS for solid tumors. Genomic analysis was performed for each patient, most of them using the Ion Torrent Oncomine Focus Assay. Genomic results were discussed during MMTB meetings. We included 43 patients with mUC treated with platinum-based combinations and immunotherapy. Twenty-five patients (58.1%; 95% CI 43.4-72.9) had at least one tumor pathogenic alteration. The MMTB classified 16 (48.5%) of the 33 tumor pathogenic alterations found in our real-world cohort of mUC patients as ESCAT I, which is the maximum grade of actionability. After excluding patients who were not candidates for targeted therapies, the MMTB provided guidance on matched therapy for seven patients. Among these patients, three achieved a partial response for an overall response rate of 42.9%, a median progression-free survival of 7.3months (95% CI 6.7-7.9) and a median overall survival of 10.9months (95% CI 2.4-19.5). We recommend that all patients with mUC undergo NGS at diagnosis given the high percentage of patients with pathogenic alterations in our real-world cohort and the efficacy data of patients treated with targeted therapies.

Comprehensive genetic profiling and molecularly guided treatment for patients with primary CNS tumors

Despite major advances in molecular profiling and classification of primary brain tumors, personalized treatment remains limited for most patients. Here, we explored the feasibility of individual molecular profiling and the efficacy of biomarker-guided therapy for adult patients with primary brain cancers in the real-world setting within the molecular tumor board Freiburg, Germany. We analyzed genetic profiles, personalized treatment recommendations, and clinical outcomes of 102 patients with 21 brain tumor types. Alterations in the cell cycle, BRAF, and mTOR pathways most frequently led to personalized treatment recommendations. Molecularly informed therapies were recommended in 71% and implemented in 32% of patients with completed molecular diagnostics. The disease control rate following targeted treatment was 50% and the overall response rate was 30%, with a progression-free survival 2/1 ratio of at least 1.3 in 31% of patients. This study highlights the efficacy of molecularly guided treatment and the need for biomarker-stratified trials in brain cancers.

Molecular tumor board: Real-world experience in a tertiary cancer centre in Singapore.

107 Background: Genomic profiling is increasingly employed to support diagnosis and treatment of cancer. Our Molecular tumor boards (MTBs) serves as a collaborative platform for a multi-disciplinary team of oncologists, pathologists, scientists, bioinformaticians, genetic counsellors and research coordinators to discuss and match patients to the most relevant therapies and/or clinical trials. We report here the evaluation of our MTBs for year 2023 with the aim of identifying challenges and opportunities for successful implementation of precision oncology. Methods: Regular monthly MTBs were conducted to discuss molecular profiles from predominantly advanced-stage patients enrolled to the IMPACT study (Individualized Molecular Profiling for Allocation to Clinical Trials NCT02806388). Next-generation sequencing was performed either in-house using Oncomine or commercial FoundationOne panels. Additional tests such as whole transcriptome sequencing (WTS), immunohistochemistry (IHC) and fluorescent in-situ hybridization (FISH) were also performed where indicated. MTB recommendations were documented for follow-up and analysis. Results: A total of 102 out of 611 profiled patients were discussed in MTBs in 2023, with an average of 8.6 patients per month. Top 3 cancer types were gastrointestinal (32%), breast (18%) and lung (18%). 65/102 (63.7%) cases had MTB recommendations, of which 21 (20.6%) had multiple recommendations. Overall uptake rate for recommendations was 23.8% (29/122). Conclusions: MTB plays an important role in identifying therapeutic opportunities by factoring in patient variables, available data and physician experience while at the same time provides an avenue for further investigation to gather cumulative evidence. Frequent reasons encountered for not adopting the recommendations include: (1) insufficient sample to proceed with further investigations, (2) limited access to off-label treatments, and (3) additional considerations to participate in clinical trials. To fully realize the value of MTB, we will focus on (1) defining the molecular tests for efficient profiling, (2) crafting a route for special access to treatments and (3) increasing awareness and understanding of clinical trials. [Table: see text]

Molecular tumor boards in uro-oncology-prostate cancer

The rapid development of molecular medicine has opened up new perspectives for the diagnosis and treatment of urological tumors. Urology faces the challenge of effectively treating advanced cancer, especially in view of the genetic diversity of urological tumors. The molecular tumor board offers an innovative approach to identify targeted therapy options based on the individual genetic signatures of tumor cells or tumor microenvironment-based treatment options. In this article, the concept of the molecular tumor board in urology is presented using the example of prostate cancer. We discuss the principles, applications, and future prospects of this promising approach.

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.

Clinical and translational research on cancer of the stomach and gastroesophageal junction: A pathologist's view

AbstractAdenocarcinomas of the stomach and gastroesophageal junction remain one of the most common malignant tumours in humans worldwide, often with a poor prognosis. Particularly in countries without upper gastrointestinal tract screening endoscopy, tumours that have been asymptomatic for a long time are only diagnosed at an advanced stage. This limits the therapeutic options. Often only palliative therapy concepts are available. Great progress has been made in the last two decades. The genetic basis of adenocarcinomas of the stomach and gastroesophageal junction has been deciphered and new targeted drugs have been developed. Cell and tissue‐based predictive diagnostics are becoming increasingly important in therapy planning. Here, surgical pathology forms an important link between basic research, clinical trials, and translation into clinical application. This review article summarizes the experiences made in translational tumour research, which point to the problems of spatial and temporal intratumoral heterogeneity of adenocarcinomas of the stomach and gastroesophageal, the development and continuous re‐assessment of therapeutically relevant cut‐off values, resistance mechanisms, tumour microenvironment, sexual dimorphism and the pitfalls molecular tumour boards may face.

The value of virtual molecular tumor boards for informed clinical decision-making.

Genomic profiling and other new technologies have increased the volume and complexity of information available for guiding clinical decision-making in precision oncology. Consequently, there is a need for multidisciplinary expert teams, in the form of molecular tumor boards (MTBs), who can translate this information into a therapeutic plan, including matching patients to suitable clinical trials. Virtual MTBs (vMTBs) can help to overcome many of the challenges associated with in-person MTBs, such as limited time availability, access to appropriate experts or datasets, or interactions between institutions. However, real-world experience from vMTBs is lacking. Here, we describe oncologists' vMTB experiences and the value of working with multicenter and/or multinational vMTBs. We also address knowledge gaps and barriers that could affect the implementation of vMTBs in routine clinical practice. Case studies from Argentina, Turkey, and Portugal illustrate the value of informed clinical decision-making by vMTBs, including expansion of therapeutic options for patients, faster time to treatment, and the resulting improvement in patient outcomes or impact of vMTB discussions on patients. With the uptake of comprehensive genomic profiling and the evolution of some cancers now being conceptualized as a collection of rare diseases with small patient populations based on molecular profiling, the importance of MTBs has increased in modern cancer management. However, an adjustment in clinical decision-making by healthcare professionals is required and evidence of the added value of vMTBs is lacking. Existing vMTBs and recommendations from participating oncologists could point toward a structured evaluation and analysis of this new platform.

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 ≥6months, 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.

Molecular tumor board: molecularly adjusted therapy upon identification and functional validation of a novel ALK resistance mutation in a case of lung adenocarcinoma.

We report a case of a long-term surviving patient with EML4/ALK translocated non-small cell adenocarcinoma of the lung in UICC8 stage IVA. During recurrence under continuous crizotinib therapy, a hitherto insufficiently characterized missense mutation in the ALK gene (Arg1181His) was identified through targeted sequencing. The aforementioned EML4/ALK translocation could still be detected in this situation. Employing a 3D reconstruction of the ALK tertiary structure, considering its interaction with various ALK inhibitors at the molecular binding site, our analysis indicated the presence of a mutation associated with crizotinib resistance. To validate the biological relevance of this previously unknown mutation, we carried out an in vitro validation approach in cell culture in addition to the molecular diagnostics accompanied by the molecular tumor board. The tumor scenario was mimicked through retroviral transfection. Our comparative in vitro treatment regimen paired with the clinical trajectory of the patient, corroborated our initial clinical and biochemical suspicions. Our approach demonstrates preclinical, in silico, and clinical evidence of a novel crizotinib resistance mutation in ALK as well as sensitivity toward brigatinib and potentially lorlatinib. In future cases, this procedure represents an important contribution to functional diagnostics in the context of molecular tumor boards.

Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience.

Over the past 10 years, institutional and national molecular tumor boards have been implemented for relapsed or refractory pediatric cancer to prioritize targeted drugs for individualized treatment based on actionable oncogenic lesions, including the Dutch iTHER platform. Hematological malignancies form a minority in precision medicine studies. Here, we report on 56 iTHER leukemia/lymphoma patients for which we considered cell surface markers and oncogenic aberrations as actionable events, supplemented with ex vivo drug sensitivity for six patients. Prior to iTHER registration, 34% of the patients had received allogeneic hematopoietic cell transplantation (HCT) and 18% CAR-T therapy. For 51 patients (91%), a sample with sufficient tumor percentage (≥20%) required for comprehensive diagnostic testing was obtained. Up to 10 oncogenic actionable events were prioritized in 49/51 patients, and immunotherapy targets were identified in all profiled patients. Targeted treatment(s) based on the iTHER advice was given to 24 of 51 patients (47%), including immunotherapy in 17 patients, a targeted drug matching an oncogenic aberration in 12 patients, and a drug based on ex vivo drug sensitivity in one patient, resulting in objective responses and a bridge to HCT in the majority of the patients. In conclusion, comprehensive profiling of relapsed/refractory hematological malignancies showed multiple oncogenic and immunotherapy targets for a precision medicine approach, which requires multidisciplinary expertise to prioritize the best treatment options for this rare, heavily pretreated pediatric population.

TRLS-13. MULTI-OMICS AND FUNCTIONAL PRECISION MEDICINE FOR NEWLY DIAGNOSED AND RECURRENT PEDIATRIC CENTRAL NERVOUS SYSTEM TUMORS

Abstract BACKGROUND Comprehensive molecular characterization of pediatric brain tumors has led to a more refined diagnosis. However, the feasibility of performing multi-omic and functional precision medicine approaches using ex-vivo drug screening in the clinical setting is unknown. METHODS Patients with newly diagnosed or recurrent central nervous system tumors were enrolled in a feasibility study of multi-omic analysis including whole genome trio germline sequencing, tumor whole exome/RNA sequencing, RNA-based DiSCoVER analysis, methylation profiling, immunogenic potential analysis, and ex-vivo drug screening utilizing a customized panel of 175 FDA approved/investigational drugs. Findings were presented at a multidisciplinary molecular neuro-oncology tumor board. RESULTS Eighteen patients (9 female; average age 9.4 years; 12 newly diagnosed, 6 with recurrent disease; 5 high grade gliomas, 4 ependymomas, 4 embryonal tumors, 3 low grade gliomas, 2 others) were enrolled between 2020-2022. Whole genome germline testing (N=18) was normal in half of patients (pathogenic germline mutations in 3 patients, variants of unknown significance in 6 patients). Ex-vivo drug screening results (N=14) varied among patients, however sub-micromolar efficacy was commonly observed for proteosome inhibitors, HDAC inhibitors, and topoisomerase II inhibitors. Average time from surgery to receipt of finalized results varied across platforms (drug screening 5.7 days, whole exome/RNA sequencing 14.8 days, whole genome germline 10.6 days, methylation 21 days). Fifteen patients had a modification in diagnosis and 4 patients had a change in tumor classification. Multi-omic and functional precision medicine results alone or in combination led to changes in management in 50% of patients (Tumor Molecular Sequencing 6/18, Ex-Vivo Drug Screening 4/14, RNA DiSCoVER Analysis 2/15, Methylation 1/14). CONCLUSION Our studies demonstrate the feasibility of timely ex-vivo drug screening and multi-omic analysis and show that these data may lead to changes in patient diagnosis/management. These findings are the basis of an ongoing trial for recurrent medulloblastoma (NCT05057702).

A diagnostic challenge of KIT p.V559D and BRAF p.G469A mutations in a paragastric mass.

A patient with gastrointestinal stroma tumor (GIST) and KIT p.V559D and BRAF p.G469A alterations was referred to our institutional molecular tumor board (MTB) to discuss therapeutic implications. The patient had been diagnosed with B-cell chronic lymphocytic leukemia (CLL) years prior to the MTB presentation. GIST had been diagnosed 1 month earlier. After structured clinical annotation of the molecular alterations and interdisciplinary discussion, we considered BRAF/KIT co-mutation unlikely in a treatment-naïve GIST. Discordant variant allele frequencies furthermore suggested a second malignancy. NGS of a CLL sample revealed the identical class 2 BRAF alteration, thus supporting admixture of CLL cells in the paragastric mass, leading to the detection of 2 alterations. Following the MTB recommendation, the patient received imatinib and had a radiographic response. Structured annotation and interdisciplinary discussion in specialized tumor boards facilitate the clinical management of complex molecular findings. Coexisting malignancies and clonal hematopoiesis warrant consideration in case of complex and uncommon molecular findings.

Application of comprehensive molecular genetic profiling in precision cancer medicine, Hungarian experiences.

The study aims to evaluate the clinical benefit of CGP in our Comprehensive Cancer Center Methods and patients: CGP was introduced into our routine clinical practice in 2021. An NGS-based large (> 500 genes) gene panel was used for cases where molecular genetic testing was approved by the National Molecular Tumor Board. From 2021 until August 2023 163 cases were tested. The majority of them were ECOG 0-1 patients with advanced-stage diseases, histologically rare cancer, or cancers with unknown primary tumours. Seventy-four cases (74 of 163, 45%) had clinically relevant genetic alterations. In 34 patients, the identified variants represented an indication for an approved therapy (approved by the Hungarian authorities, on-label indication), while in 40 cases the recommended therapy did not have an approved indication in Hungary for certain tumour types, but off-label indication could be recommended. Based on our CGP results, 24 patients (24/163; 14.7%) received targeted therapy. Treatment duration was between 1 and 60 months. In total 14 (14/163; 8.5% of the tested cases) patients had a positive clinical response (objective response or stable disease) and were treated for more than 16 weeks. NGS-based CGP was successfully introduced in our institution and a significant number of patients benefited from comprehensive genetic tests. Our preliminary results can serve as the starting point of Drug Rediscovery Protocol (DRUP) studies.

Early results of the PASS-01 trial: Pancreatic adenocarcinoma signature stratification for treatment-01.

LBA4004 Background: Over 60% of patients with pancreatic ductal adenocarcinoma (PDAC) present with metastatic disease. Both modified FOLFIRINOX (mFFX) and gemcitabine/nab-paclitaxel (GnP) are first-line options in advanced PDAC, however have not been compared prospectively in North American patients. Moreover, biomarkers to guide selection are lacking. Basal-like and Classical subtypes are prognostic, but their predictive impact is unknown. Patient-derived organoids (PDOs) are now feasible to study for drug pharmacotyping. Expedient molecular profiling with additional PDO drug sensitivities could enable better precision choices in PDAC. Methods: PASS-01 is a multi-center randomized phase II trial evaluating the benefit of 1st line mFFX vs GnP in de novo metastatic PDAC patients with ECOG PS 0-1, (germline BRCA1/2, PALB2 excluded) who have baseline tumor biopsies (bx) for whole genome/transcriptional sequencing (WGTS) and PDO generation/pharmacotyping with standard and novel drugs. The primary endpoint is the PFS of mFFX vs GnP (received at least 1 dose of assigned chemo, per protocol (PP)), 136 patients needed to reach 80% power to detect a difference in median PFS of 7 vs 5 months between mFFX and GnP at significance level of 0.3 in a 2-sided test. Secondary endpoints include: ORR, SAEs, OS, impact of RNA signatures and GATA6 expression on outcomes. Each patient is discussed at a molecular tumor board immediately following their 1st 8-week CT with the goal of recommending precision 2nd-line treatment options on progression. Results: This trial accrued 160 pts between 09/20 and 01/24, 45% in Canada, 55% in US with 140 eligible for 1st line PFS, data lock Mar 1/24 (see table). Median PFS (PP) was 5.1 mo for GnP and 4.0 mo for mFFX (p=0.14). Best response PR/SD for GnP: 29/45% and 24/35% for mFFX. SAEs attributed to the study were 3% GnP, 13% mFFX and 0.7% bx. Median OS (ITT) was 9.7 mo with GnP and 8.4 mo with mFFX, p=0.04. Of 113 patients in the PP analysis with progression, 64 (57%) received 2nd-line treatment (GnP, n= 30, mFFX n=34) Of these, a correlate-guided approach was delivered in 32 (50%), including 21 (66%) receiving chemo and 11 (34%) receiving a targeted or immunotherapy regimen. Correlative studies are underway. Preliminary analysis shows >80% successful whole genomes and >72% RNA signatures. PP patients include 9 % KRAS wild-type and 21% Basal-like PDAC. PDO-drug models have been established in 50%. Conclusions: Upfront multi-omic profiling of PDAC can be successfully incorporated into a multicenter randomized trial. While we have observed PP improved PFS and ITT longer OS favouring GnP in this cohort without gBRCA 1/2 or PALB2m, the benefit of chemo for advanced PDAC patients remains poor, with 43% unable to receive 2nd line, arguing strongly for the development of 1st-line biomarker selected strategies. Clinical trial information: NCT04469556 . [Table: see text]