Abstract 4891: Comprehensive genetic profiling of chromosomal translocations in lung cancer tumors: development and validation of a next-generation sequencing panel in an international multicenter study
Notice bibliographique
Résumé
Abstract Approximately 7% of non-small cell lung carcinomas (NSCLCs) harbor oncogenic fusions involving ALK, ROS1, and RET. While tumors harboring ALK fusions are highly sensitive to crizotinib, emerging data have demonstrated that individuals with ROS1 or RET fusions may also benefit from inhibitors targeting these two kinases. A new oncogenic fusion involving NTRK1 that can be targeted by kinase inhibitors has been recently described. The two main methods to identify translocations, fluorescent in situ hybridization (FISH) and Immunohistochemistry (IHC) are labor intensive and sensitivity is rather low. Common sample types for lung cancer analysis are biopsies making the study of more than one fusion gene rather difficult. In this study we aimed to develop and validate a workflow based on AmpliSeq™ technology to comprehensively profile ALK, ROS1, RET and NTRK1 chromosomal translocations in lung tumors. Two hundred lung cancer retrospective samples, including tumor biopsy, were collected from 12 laboratories - the OncoNetwork Consortium. All the samples were previously characterized by orthologous techniques (FISH, IHC, RT-PCR and/or MassArray). More than 30 ALK positive samples were selected. The panel targets over 70 fusion transcripts associated with ALK, RET, ROS1, and NTRK1 genes. The panel also includes 5′ and 3′ gene expression assays for each gene as indicators of a translocation event and assays for 5 internal control genes. The workflow is compatible with formalin fixed paraffin embedded (FFPE) tissue, requiring only 10ng of total RNA and able to multiplex up to 16 libraries on a single Ion 318™ chip. A dedicated data analysis pipeline using the Ion Reporter software 4.2 was evaluated. Serial dilutions of cell lines RNA harboring known fusion events, in normal RNA showed that the methodology had 1% mutant RNA limit of detection. A second dilution experiment using RNA extracted from FFPE lung fusion positive samples diluted in a negative FFPE sample showed a detection limit of 15%. The use of a common control fusion positive RNA samples among all the consortia laboratories showed 100% reproducibility. Concordance study was performed using 200 FFPE samples previously characterized with standard method. A concordance of >98% was obtained between the methodologies. The discordant results are currently under study. A negative FFPE samples was run as single test on an Ion 318™ chip on to evaluate the possibility of false positive results due to high number of reads. No false positive was detected in this experiment. In this study we present a workflow that provides a robust, reproducible and accurate comprehensive genetic screening tool well suited for FFPE lung tumor biopsies, in a fast and cost-efficient manner. This may provide a valuable tool for reducing turn-around-time and expense in lung cancer analysis. Citation Format: Pierre Laurent - Puig, Jose Louis Costa, Orla Sheils, Bastiaan Tops, Andrea Mafficini, Delphine Le Corre, Henriette Kurth, Anna Maria Rachiglio, Helene Blons, Eliana Amato, Christoph Noppen, Renato Franco, Anne Reiman, Roy Bastien, Noah Welker, Jose Carlos Machado, Ian Cree, Harriet Feilotter, Marjolijn Ligtenberg, Aldo Scarpa, Nicola Normanno, Kazuto Nishio, Cecily Vaughn. Comprehensive genetic profiling of chromosomal translocations in lung cancer tumors: development and validation of a next-generation sequencing panel in an international multicenter study. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4891. doi:10.1158/1538-7445.AM2015-4891
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,006 | 0,002 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,000 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,001 | 0,000 |
| Communication savante | 0,001 | 0,000 |
| Science ouverte | 0,001 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 0,001 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».