Neoplasms

Symptoms and General Pathology

All Conditions

Neoplasm Metastasis

Neoplastic Processes

All Drugs and Chemicals

Immunomodulating Agents

Comprehensive genomic profiling

Brigitte Maes, Dr

Gordana Raicevic Toungouz

Max Schreuer

Joke van Gaelen

Joanna Vermeij, Dr

Jo Horemans

Annemie Rutten, Dr

Lies Pottel

Jacques Van Huysse

Vanessa Fastenaekels

Malika Tahiri

Lore Decoster, Dr

Stéphanie Warnon

Jean-Luc Canon, Dr

Julia Lenaerts

Hans Prenen, Dr

Lore Vansteelant

Sylvie Rottey, Prof. Dr

Ann Tullen

Jeroen Mebis, Prof. Dr

Isabelle Vanden Bempt

Sabine Tejpar, Prof. Dr

Sophie Adriaens

Francesca Dedeurwaerdere, Dr

Lynn Decoster

Lynn Decoster, Dr

The project, called "BALLETT" (Belgian Approach of Local Laboratory Extensive Tumor Testing), has a double goal: (1) show the relevance of broad molecular profiling to improve oncological patients care, (2) demonstrate that broad molecular testing can be performed in a decentralized setting by local diagnostics laboratories in a fully standardized and uniform way while complying with the highest quality standards.

This 2-year study involves the consortium of 9 cooperating Belgian NGS laboratories and will enroll 936 metastatic or locally advanced cancer patients coming from 13 different Belgian hospitals and cancer centers. Upon inclusion, all cancer patients will be offered 'comprehensive genomic profiling' (CGP) using Illumina's TSO500 NGS panel. This targeted NGS panel of 523 genes allows for the detection of single nucleotide variants, small indels, copy number variations and fusions, as well as for the determination of the 'tumor mutational burden' (TMB) and the 'microsatellite-instability' status (MSI). Both the wet lab execution of the CGP as well as the biological and clinical classification of the variants will be performed in a fully standardized way among the 9 participating Belgian local NGS laboratories.

The CGP results will be interpreted and discussed in the weekly meeting of the BALLETT national molecular tumor board (MTB), composed of oncologists, pathologists, molecular biologists, geneticists and bioinformaticians. The MTB will provide recommendations for targeted or immunotherapy based on the CGP results. Clinical Decision Support platforms OncoKDM (OncoDNA) and Clinical Genomics Workspace (PierianDx), both expert software that turns NGS data into actionable clinical information, will be used. The resulting therapy recommendation may consist of an approved therapy, a clinical trial, a medical need program or off-label use of cancer drugs. Treating physicians will receive the MTB recommendations and decide on the actual management of their patients. Reasons for not following the MTB recommendation will be registered.

The objectives of the project are:

1. To evaluate the clinical value of CGP in "real-world" practice in giving patients with advanced/metastatic solid tumours broader access to precision medicine
2. To describe the landscape of genomic alterations and quantify the actionable variants detected by comprehensive panel testing
3. To evaluate the number of actionable variants that would have been missed if the NGS analysis was limited to the reimbursed NGS panel (ComPerMed panel).
4. To assess the technical success of CGP
5. To standardize CGP data analysis, clinical interpretation, therapy recommendation and reporting among participating laboratories to the highest extent possible
6. To describe and to quantify the uptake of treatments and the inclusion in clinical trials recommended by the molecular tumour board guided by the CGP
7. To assess clinical benefit by calculating PFS ratio for individual patients (PFS on CGP-selected therapy/PFS on prior therapy) (null hypothesis: ≤ 15% of patient population has PFS ratio of ≥ 1.3)
8. To work in a multi-stakeholder approach to attract more innovative treatments and clinical trials in Belgium
9. To establish a Belgian genomic tumor database under the authority of the governmental 'Sciensano' thereby increasing public health knowledge in Belgium

A Study to Examine the Clinical Value of Comprehensive Genomic Profiling Performed by Belgian NGS Laboratories: a Belgian Precision Study of the BSMO in Collaboration With the Cancer Centre

A Study to Examine the Clinical Value of Comprehensive Genomic Profiling Performed by Belgian NGS Laboratories: a Belgian Precision Study of the BSMO in Collaboration With the Cancer Centre - Belgian Approach for Local Laboratory Extensive Tumor Testing (BALLETT)

Number/prevalence of variants with a classification of clinical significance Tier 1A or 1B (strong clinical significance) and Tier 2C and 2D (potential clinical significance) using CGP versus local NGS testing (if available) and/or versus minimally required ComPerMed panel.

Tiering according to Li et al. AMP/ASCO/CAP. J Mol Diagn 19:4-23, 2017.

Percentage of patients with MTB recommendation categorized according to variant-therapy match scoring system, percentage of patients accessing genotype-informed treatment, turnaround time from CGP request to MTB recommendation, proportion of patients accessing molecular guided therapy or immune checkpoint inhibitors or combinations based on the result of CGP, timing of treatment initiation following MTB recommendation, proportion of deviations from treatment recommendations and reasons (rapid clinical deterioration, other protocol, patient ineligible, off-label treatment unavailable, clinical trial not feasible (e.g. physical distance), clinical trial not recruiting, physician's decision, patient's choice, ...)

PFS based on RECIST 1.1 evaluation of patients on the CGP recommended therapy and PFS ratio (PFS on CGP-selected therapy/PFS on prior therapy) (null hypothesis: ≤ 15% of patient population has PFS ratio of ≥ 1.3)

Including cost calculation and reimbursement data to support economic analysis (microcosting from the lab perspective and budget impact from the payer's perspective).

Illumina, Inc.

OncoDNA

PierianDx

The Belgian Society of Medical Oncology

Skin and Connective Tissue Diseases

Rare Diseases

Melanoma

Neuroendocrine Tumors

Neuroectodermal Tumors

Neuroectodermal Tumors, Primitive

Neoplasms, Germ Cell and Embryonal

Neoplasms by Histologic Type

Neoplasms, Nerve Tissue

Nevus, Pigmented

Nevus

Nevi and Melanomas

Skin Neoplasms

Skin Diseases

Neuroendocrine Tumor

Neuroepithelioma

1,000 subjects with metastatic melanoma stage III or IV suitable for systemic treatment from centers of the German Dermatologic Cooperative Oncology Group (DeCOG)

molecular tissue analysis

Selma Ugurel, MD

Dirk Schadendorf, MD

Andrea Forschner, MD

Claus Garbe, MD

Peter Mohr, MD

Claudia Pfoehler, MD

Patrick Terheyden, MD

Sven Krengel, MD

Rudolf herbst, MD

Yvonne Kellner, MD

Julia Welzel

Friedegund Meier

Selma Ugurel

Inke Grimmelmann, MD

Edgar Dippel

Jochen Utikal

Ralf Gutzmer

Alexander Kreuter

Jens Ulrich

The prospective multicenter translational study Tissue Registry in Melanoma (ADOREG/TRIM; CA209-578) aimed to validate the Tumor Mutational Burden (TMB) and the PD-L1 expression (PD-L1) from a pre-therapeutically obtained tumor tissue sample as a predictor of a subsequent systemic therapy in a large real-world cohort of metastatic melanoma patients.

The aim of the present study is to identify and validate molecular and clinical biomarkers of therapy outcome in metastatic melanoma. Clinical and molecular parameters of melanoma patients and their tumors will be collected in an online-based registry (ADOREG), and thereafter correlated with the outcome of subsequent systemic therapies in terms of progression-free survival, overall survival, and treatment response. Systemic therapies will include all types of currently used regimens (kinase inhibitors, immune checkpoint inhibitors, chemotherapy). FFPE tissue samples will comprise different time points (primary tumors versus metastases) as well as tumor sites (lymph node versus organ metastases) to identify potential differences in the predictive value of these materials. The anticipated results from these analyses are of essential importance for future patient selection for individualized therapy strategies.

pre-treatment tumor tissue of different origin

Multicenter Tissue Registry in Melanoma

Prospective Multicenter Translational Study to Validate Molecular Biomarkers (TMB, PD-L1) on Pre-treatment Tumor Tissue as Predictors of Therapy Outcome in Metastatic Melanoma Patients

patients/samples will be pseudonymized/anonymized

Dermatologic Cooperative Oncology Group

Respiratory Tract (Lung and Bronchial) Diseases

Carcinoma

Carcinoma, Non-Small-Cell Lung

Lung Neoplasms

Respiratory Tract Neoplasms

Thoracic Neoplasms

Lung Diseases

Respiratory Tract Diseases

Carcinoma, Bronchogenic

Bronchial Neoplasms

Tumor mutational burden (TMB) will be assessed on a sample of the biopsy done during standard care of patients.

TMB will be assessed on a sample of the tumor surgical specimen resected during standard care of patients.

TMB will be assessed both on a sample of the biopsy and a sample of the tumor surgical specimen resected during standard care of patients.

Tumor mutational burden could be calculated by cancer gene panel (CGP), whole-exome sequencing (WES), RNA-sequencing (RNA-seq), FoundationOne CDx assay panel (FMI).

TMB assessment

Jacques Cadranel, MD

Benjamin Besse, MD

Pierre Laurent-Puig, MD

Etienne Rouleau, PharmD, PhD

Tumor mutational burden (TMB) seems to be is an important marker for immune checkpoint inhibitors efficacy. This study aims to assess the feasibility of the TMB assessment in first-line lung cancer in routine practice both on biopsy and surgical tumor samples. Results will be an element of discussion for the generalization of the TMB implementation in cancer centers.

1. Current knowledge about the field under investigation

   Clinical evidence demonstrates that treatment with immune checkpoint blocker (ICB) agents benefit to patients across multiple tumor type. However, development of predictive biomarkers is needed to identify patients who are most likely to respond to immunotherapy.

   An emerging biomarker for response to immunotherapy is the total number of mutations present in a tumor specimen. This biomarker is named mutation load or tumor mutational burden (TMB). It is hypothesized that highly mutated tumors are more likely to harbor neoantigens targeted by activated immune cells. This metric, allowed by recent advances in next-generation sequencing (NGS) technologies, notably whole-exome sequencing (WES) and RNA-sequencing (RNA-seq), has been shown, in several tumor types, to correlate with patient response to ICB. Indeed, the TMB has been correlated with clinical benefits of anti-PD-1 and anti-CTLA-4 therapy in various tumor types, including malignant melanoma (Snyder et al., 2014; Van Allen et al., 2015) with a threshold of more than 100 nonsynonymous single-nucleotide variants (nsSNV) per exome, non-small cell lung cancers (NSCLC) (Rizvi et al., 2015) with a threshold defined as superior to 178 nsSNVs per exome, and several DNA repair-deficient tumors (Howitt et al., 2015; Le et al., 2015, 2017). A recent study prospectively confirmed that the PFS among patients with a high tumor mutational burden was significantly longer with nivolumab plus ipilimumab than with chemotherapy in NSCLC (Hellmann et al., 2018). Overall, a direct link between DNA repair deficiency, mutational landscape, predicted neoantigen load, and clinical activity of ICB is suggested.

   TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome examined. All base substitutions and indels in the coding region of targeted genes. It has been shown that TMB calculated using cancer gene panel (CGP) assay agrees well with whole exome measures of mutation burden (Chalmers et al., 2017). This indicates that CGP, targeting the entire coding region of several hundred genes, covers sufficient genomic size to accurately assess WES mutational burden. It was found that filtering out germline alterations and rare variants was important to obtaining accurate measurements of TMB, and this will especially be important in patients from ethnic backgrounds not well represented in sequencing datasets. These findings indicate that CGP is an accurate, cost-effective, and clinically available tool for measuring TMB. The results of down sampling analysis show that the variation in measurement due to sampling when sequencing 1.1 Mb is acceptably low, resulting in highly accurate calling of TMB at a range of TMB levels. This sampling variation increases as the number of megabases sequenced decreases, especially at lower levels of TMB. While targeted CGP can be used to accurately assess TMB, it is not currently suited for identification of neoantigens, which might occur in any gene. Nevertheless, the theragnostic impact of TMB has been also determined with a targeted CGP by the FoundationOne CDx assay (Hellmann et al., 2018).

   The failure to assess the TMB may occur at different steps in the analytical process. It can be at the sample acquisition with a low level of DNA (5-10%). The NGS processing depending on the method can lead to a process failure around 2-3%. And finally, the bioinformatic curation will lead to a 3-5% of failure. At the end, the TMB will be undetermined with an attrition rate at 15% of the samples (Fondation Medicine Personal communication).

   The implementation of tumor mutational burden assessment in a nation-wide perspective is challenging and large efforts should be done. Whatever the method, WES or large CGP, the measurements of TMB will change the scale of gene sequencing in the molecular platforms.

   It is important that the platforms, where the tumor mutational burden measurement will be implemented can be able to calibrate their CGP and compared it to a standard reference for the measurement of TMB. Moreover, with the limited quantity of DNA, the implemented method needs to produce reliable result for most of the samples. The platforms need also to deploy their wet benches processes and their bioinformatics pipeline to be able to produce the TMB in a turnaround time compatible with clinical patients management.
2. Description of the population of study participants and justification for the choice of participants

   As mentioned above the TMB seems to be is an important marker for ICB efficacy. It is therefore important to implement the TMB measurement at a nationwide level to assure the equal access to the ICB.

   The French National Cancer Institute (INCa) has labelled molecular platforms which are in charge of the different molecular tests should establish their processes to be able to face to this new test. This study is designated to test different CGP methods to assess tumor mutational burden in lung cancers in order to compare the different methods and to identify the drawbacks and failures of the different methods. Results of this study should allow to estimate the needs for the implementation of TMB at the nationwide level, recommend cancer gene panels, propose validated bioinformatics pipelines and finally recommend preanalytical processes for reducing the failure rate of the tests.

   For this purpose this study will determine the TMB on patients with a lung cancer. 200 patients with a non-small cell lung cancer (NSCLC) and naive of treatment will be recruited.

   Three cohorts will be recruited:
   * 100 patients will be included without resection and we will determine the TMB on the biopsy specimen
   * 100 patients will be included after surgical resection of their tumor and we will determine the TMB on the resected specimen

     * Within this cohort, TMB will be assessed both on the biopsy specimen and on the resected specimen for 20 patients 200 patients will be enrolled in order to perform 220 TMB analysis.

   Participating sites are large platforms which were selected on the basis of their capacity to implement new tests and which have all facilities for conducting the described research. The patients included in this study will correspond to those that will receive immune checkpoint inhibitors during the course of their disease. This study in a non-interventional study, as it will not modify the clinical care of the patients. The tissue sampling will be taken during clinical procedure needed for patient care. The study will be proposed to patients after the verification that tissues have been collected in a way that is compatible with the present study. Only tumor material and no germline DNA will be collected.

   Selected patients will be close to those that receive ICB and the target population will be enriched with patients who had been surgically resected, in order to be able to have enough tissues to compare in these samples different methods to assess TMB and also to compare pre surgical biopsies and surgical specimen.
3. Description of the element or elements under investigation

Elements under investigation are the TMB of NSCLC patients. The attrition rate (number of cases without result) in the TMB estimation will be assessed. The gold standard for the determination of TMB is the WES as it covers all coding regions. Several others Cancer Gene Panel methods (CGP) have been described based on cancer gene panels sequencing. The CGP included in this study will be the panel from Illumina (TS500), Thermofisher (Oncomine Tumor Mutation Load Assay), home-made panel with Agilent technology (Dedicated XT HS) and Foundation medicine F1 CDx. It is recognized that size of the cancer gene panels should be close to 1Mb to be able to measure reliably the TMB in different type of cancer.

Different methods of measurement of TMB will be compared in this series on NSCLC in order to validate different CGP available on the market or in the different INCa platforms. Bioinformatics modelling will try to correlate the TMB results from WES and CGP. For this purpose, based on results of mutational load calculated from results of WES, results of mutation load will be extrapolated based on a random selection of 1000 genes repeated 1000 times. The mean of the correlation coefficient (R2) between the tumor mutational burden calculated by the whole exome sequencing and by the different random gene panels is 0.88 IQR \[0.84-0.91\] showing that the selection of genes to estimate the TMB should be evaluated carefully before to be used in clinical practice (unpublished results). The material that will be collected during the study will allow to determine the performance of the CGP implemented in the molecular biology platforms.

20 ml of blood samples will be collected to reach 10 ml of plasma

Tumor Mutational Burden in Lung Cancer Patients

National Real-life Study of Tumor Mutational Burden Assessment in First-line Lung Cancer

Individual participant data (IPD) that underlie results in publication could be shared.

IPD detailed in the protocol of a planned metaanalysis could be shared.

Time between the reception of the tissues samples on platforms and TMB results availability

Number of cases analyzed by RNAseq approach without result

Compared to the TMB determined by whole exome sequencing (WES) as a gold standard

Bristol-Myers Squibb

Assistance Publique - Hôpitaux de Paris

Study title	NCT ID	Conditions	Interventions	Eligibility	Organization
A Study to Examine the Clinical Value of Comprehensive Genomic Profiling Performed by Belgian NGS Laboratories: a Belgian Precision Study of the BSMO in Collaboration With the Cancer Centre	NCT05058937	Solid Tumor Metastatic Canc...	Comprehensive g...	18 Years -	The Belgian Society of Medical Oncology
Multicenter Tissue Registry in Melanoma	NCT05750511	Metastatic Mela...	molecular tissu...	18 Years -	Dermatologic Cooperative Oncology Group
Tumor Mutational Burden in Lung Cancer Patients	NCT04289259	Non Small Cell ... Non-Small Cell ... Non Small Cell ... Non-small Cell ...	TMB assessment	18 Years - 85 Years	Assistance Publique - Hôpitaux de Paris
A Study to Examine the Clinical Value of Comprehensive Genomic Profiling Performed by Belgian NGS Laboratories: a Belgian Precision Study of the BSMO in Collaboration With the Cancer Centre	NCT05058937	Solid Tumor Metastatic Canc...	Comprehensive g...	18 Years -	The Belgian Society of Medical Oncology

Spots Global Cancer Trial Database for tumor mutational burden