Abstract 775: Underlying germline genetic architecture of pediatric sarcomas: Evaluating the role of common and rare variants in 4,160 patients
Notice bibliographique
Résumé
Abstract Some evidence suggests that pediatric sarcomas have both shared and distinct genetic profiles; however, large-scale efforts to characterize germline genetic susceptibility across these malignancies are limited by their rarity. We evaluated the role of common and rare variants in the genetic etiology of the more frequent pediatric sarcomas: osteosarcoma (OS); Ewing sarcoma (ES); and rhabdomyosarcoma (RMS), subcategorized into embryonal (ERMS) and alveolar (ARMS). METHODS: We evaluated 4,161 European-ancestry cases with genotype data (1,843 OS, 733 ES, 1,585 RMS, and ~61,000 cancer-free adult controls) and 2,474 cases with exome or genome sequencing (1,002 OS, 579 ES, 893 RMS, and 1,057 controls; jointly called with the same QC). Analyses included: 1) estimating disease heritability for both common SNPs (MAF>3%; genome-wide) and rare loss-of-function variants (MAF<1%; exome-wide); and 2) determining the frequency of rare predicted pathogenic (P) or likely pathogenic (LP; ACMG-AMP) variants in cancer susceptibility genes (CSG). RESULTS: For OS, we conducted a new GWAS and determined that common variants explained 2.7% (SE 1.1%) of disease heritability, while rare LOF variants explained 12.7% (SE 1.5%; compared to 0.4% for synonymous variants). A similar pattern was observed for ERMS, where rare LOF variants explained a greater proportion of disease heritability (RMS 8.6%, SE 1.2%; ERMS 12.6%, SE 1.7%; ARMS n/a due to small sample size) compared to common variants from our new GWAS (0.9%, SE 1.6%). Conversely, common variants explained a greater proportion of ES heritability (5.4%, SE 0.5%) and of ARMS heritability (15.5%, SE 6.4%). For 113 established CSGs, and for the 60 moderate-to-high penetrant autosomal dominant (AD) genes, OS and ERMS had significantly (Pexact<0.01) more rare P/LP variants overall compared to controls; whereas ARMS and ES had significantly fewer P/LP variants than ERMS and OS, similar to the controls. We confirmed previously reported AD genes, and identified new genes, with an enrichment of P/LP variants in ERMS and OS compared to controls. For both ARMS and ES, the only AD gene significantly enriched for P/LP variants was CHEK2. For all cases, patients with a P/LP variant were significantly younger and had significantly more poor outcomes (ie, metastasis, stage 4 disease, and/or death) than those without. For 49 autosomal recessive CSGs, heterozygous P/LP carrier frequencies were similar among all sarcomas (8-11%), and several specific genes had similar P/LP variant enrichment across sarcomas, and for ES and ARMS only, compared to controls. CONCLUSION: In the largest set of pediatric sarcoma cases assembled to date, genetic susceptibility was largely driven by rare P/LP AD gene variants in tumor types not characterized by canonical somatic fusions (OS and ERMS). In contrast, fusion-driven tumor types (ES and ARMS) were driven more by common variants. Citation Format: Lisa Mirabello, Laura E. Egolf, Bin Zhu, D. Matthew Gianferante, Kevin Wang, Shengchao Alfred Li, Mitchell J. Machiela, Logan G. Spector, Joshua D. Schiffman, Aniko Sabo, Alexander Renwick, Bailey Martin-Giacalone, Michael E. Scheurer, Sharon Plon, Douglas Hawkins, Rajkumar Venkatramani, Douglas Stewart, Lindsay M. Morton, Melissa M. Hudson, Gregory T. Armstrong, Smita Bhatia, Michael Dean, Katherine A. Janeway, Ana Patiño-Garcia, Fernando Lecanda, Massimo Serra, Claudia Hattinger, Katia Scotlandi, Adrienne M. Flanagan, Fernanda Amary, Irene L. Andrulis, Jay S. Wunder, Mandy L. Ballinger, David M. Thomas, Olivier Delattre, Aubrey K. Hubbard, Jia Liu, Wen Luo, Belynda D. Hicks, Meredith Yeager, Maryam Rafati, Wen-Yi Huang, Maria T. Landi, Adriana Lori, Ryan Diver, Sharon A. Savage, Stephen J. Chanock, Philip J. Lupo. Underlying germline genetic architecture of pediatric sarcomas: Evaluating the role of common and rare variants in 4,160 patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 775.
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 | 0,001 | 0,003 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,001 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,003 | 0,000 |
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 ».