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Deep learning prediction of BRAF-RAS gene expression signature identifies noninvasive follicular thyroid neoplasms with papillary-like nuclear features
- Source :
- Modern Pathology
- Publication Year :
- 2021
- Publisher :
- Elsevier BV, 2021.
-
Abstract
- Noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP) are follicular-patterned thyroid neoplasms defined by nuclear atypia and indolent behavior. They harbor RAS mutations, rather than BRAFV600E mutations as is observed in papillary thyroid carcinomas with extensive follicular growth. Reliably identifying NIFTPs aids in safe therapy de-escalation, but has proven to be challenging due to interobserver variability and morphologic heterogeneity. The genomic scoring system BRS (BRAF-RAS score) was developed to quantify the extent to which a tumor’s expression profile resembles a BRAFV600E or RAS-mutant neoplasm. We proposed that deep learning prediction of BRS could differentiate NIFTP from other follicular-patterned neoplasms. A deep learning model was trained on slides from a dataset of 115 thyroid neoplasms to predict tumor subtype (NIFTP, PTC-EFG, or classic PTC), and was used to generate predictions for 497 thyroid neoplasms within The Cancer Genome Atlas (TCGA). Within follicular-patterned neoplasms, tumors with positive BRS (RAS-like) were 8.5 times as likely to carry an NIFTP prediction than tumors with negative BRS (89.7% vs 10.5%, P
- Subjects :
- Proto-Oncogene Proteins B-raf
0301 basic medicine
Pathology
medicine.medical_specialty
Carcinoma, Papillary, Follicular
Article
Pathology and Forensic Medicine
Thyroid carcinoma
03 medical and health sciences
Deep Learning
0302 clinical medicine
Text mining
Follicular phase
Gene expression
medicine
Humans
Neoplasm
Thyroid Neoplasms
Nuclear atypia
Head and neck cancer
business.industry
Gene Expression Profiling
fungi
Thyroid
Diagnostic markers
medicine.disease
Gene Expression Regulation, Neoplastic
Thyroid diseases
Tumor Subtype
030104 developmental biology
medicine.anatomical_structure
030220 oncology & carcinogenesis
Mutation
ras Proteins
Transcriptome
business
Subjects
Details
- ISSN :
- 08933952
- Volume :
- 34
- Database :
- OpenAIRE
- Journal :
- Modern Pathology
- Accession number :
- edsair.doi.dedup.....30107d05fb99295e14c942a93e4a860a