Abstract 4713: High-throughput multiplex Sequenom MassARRAY clinical diagnostic assay for the identification of actionable genetic variants in hematologic malignancies
Notice bibliographique
Résumé
Abstract Recent cancer genome sequencing efforts have led to an enhanced understanding of the somatic mutation profile of hematologic malignancies in the context of known cytogenetic abnormalities. For cytogenetically normal acute myeloid leukemia (AML), mutations in NPM1, DNMT3A, CEBPA, TET2 and IDH1/2 are thought to have potential predictive utility and may impact patient management with regard to initial and consolidation therapy, including stem cell transplantation. As most potentially clinically relevant variants currently are not tested for within the diagnostic setting, we established a high-throughput multiplex assay capable of simultaneous detection of a range of somatic mutations in hematologic malignancies. Using iPlex chemistry and the Sequenom MassARRAY platform, we established the Princess Margaret Cancer Centre (PM) Hematologic Malignancies Panel v1.0, comprised of 110 individual assays profiling 186 mutations in 22 relevant genes, in a 16-well assay format. We conducted an in silico analysis to identify genes with hotspot mutations capable of being analyzed by Sequenom; genes with mutations distributed throughout the coding sequence (e.g., CEBPA, TET2) were excluded from the panel. To best integrate this technology in the workflow of our routine clinical molecular diagnostic testing we developed the PM Panel as an RNA-based test, requiring 1 μg of patient RNA for the initial reverse transcription reaction. To validate the assay we tested 222 patient-derived samples, including 5 normal samples, 82 AML (57 with normal cytogenetics, 24 with cytogenetic changes and 1 therapy-related), 44 myelodysplastic syndromes, 32 myeloproliferative neoplasms, 21 additional cases tested for KIT mutation, and 38 B-lymphoid malignancies (including 3 multiple myeloma cases),. Concordance with established lab assays for NPM1, FLT3-TKD and JAK2 mutations was 100%; other identified mutations were verified by Sanger sequencing at 98% concordance (2% of cases were below the limit of sensitivity of Sanger technology). Approximately 50% of samples were positive for at least one mutation with 174 mutations detected overall. Cytogenetically normal AMLs and myelodysplastic syndromes were most informative, with 2.3 and 1.8 mutations per positive case respectively. Samples already known to carry a leukemogenic driver fusion protein (e.g., PML-RARα, AML1-ETO, or BCR-ABL) had a significantly decreased identified somatic mutation load than their cytogenetically normal counterparts (average of 1.4 mutations per case, compared to 0.3, p < 10^-6). The PM Hematologic Malignancies Panel v1.0 is now being integrated into the current clinical diagnostic workflow. We therefore report the development of a versatile, RNA-based high-throughput multiplex platform for the identification of somatic mutations present in hematologic malignancies for use in a clinical diagnostic setting. Citation Format: Mahadeo A. Sukhai, Mariam Thomas, Tong Zhang, Cuihong Wei, Suzanne Trudel, Karen Yee, Mark D. Minden, Andre Schuh, Tracy Stockley, Suzanne Kamel-Reid. High-throughput multiplex Sequenom MassARRAY clinical diagnostic assay for the identification of actionable genetic variants in hematologic malignancies. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4713. doi:10.1158/1538-7445.AM2014-4713
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 | 0,002 | 0,002 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,002 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,003 | 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 ».