Nov 7, 2018

DeepTCR: a deep learning framework for understanding T-cell receptor sequence signatures within complex T-cell repertoires

BioRxiv : the Preprint Server for Biology
John-William SidhomAlexander S Baras

Abstract

Deep learning algorithms have been utilized to achieve enhanced performance in pattern-recognition tasks, such as in image and vocal recognition. The ability to learn complex patterns in data has tremendous implications in the genomics and immunology worlds, where sequence motifs become learned features that can be used to predict functionality, guiding our understanding of disease and basic biology. T-cell receptor (TCR) sequencing assesses the diversity of the adaptive immune system, where complex structural patterns in the TCR can be used to model its antigenic interaction. We present DeepTCR, a broad collection of unsupervised and supervised deep learning methods able to uncover structure in highly complex and large TCR sequencing data by learning a joint representation of a given TCR by its CDR3 sequences, V/D/J gene usage, and HLA background in which the T-cells reside. We demonstrate the utility of deep learning to provide an improved featurization of the TCR across multiple human and murine datasets, including improved classification of antigen-specific TCRs in both unsupervised and supervised learning tasks, understanding immunotherapy-related shaping of repertoire in the murine setting, and predicting response to chec...Continue Reading

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Mentioned in this Paper

Muscle Rigidity
Immune System
2-Dimensional
Virus
Evaluation
Pattern Recognition
Neural Network Simulation
Genomics
Sequence Analysis
Sequencing

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