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Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors.
- Source :
-
PLoS computational biology [PLoS Comput Biol] 2021 Jul 26; Vol. 17 (7), pp. e1009225. Date of Electronic Publication: 2021 Jul 26 (Print Publication: 2021). - Publication Year :
- 2021
-
Abstract
- Recent advances in T cell repertoire (TCR) sequencing allow for the characterization of repertoire properties, as well as the frequency and sharing of specific TCR. However, there is no efficient measure for the local density of a given TCR. TCRs are often described either through their Complementary Determining region 3 (CDR3) sequences, or theirV/J usage, or their clone size. We here show that the local repertoire density can be estimated using a combined representation of these components through distance conserving autoencoders and Kernel Density Estimates (KDE). We present ELATE-an Encoder-based LocAl Tcr dEnsity and show that the resulting density of a sample can be used as a novel measure to study repertoire properties. The cross-density between two samples can be used as a similarity matrix to fully characterize samples from the same host. Finally, the same projection in combination with machine learning algorithms can be used to predict TCR-peptide binding through the local density of known TCRs binding a specific target.<br />Competing Interests: The authors have declared that no competing interests exist.
- Subjects :
- Algorithms
Amino Acid Sequence
Complementarity Determining Regions classification
Complementarity Determining Regions genetics
Computational Biology
Databases, Genetic
Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor
Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
Humans
Immunoglobulin Variable Region genetics
Machine Learning
Receptors, Antigen, T-Cell, alpha-beta classification
Receptors, Antigen, T-Cell, alpha-beta genetics
Receptors, Antigen, T-Cell classification
Receptors, Antigen, T-Cell genetics
Software
Subjects
Details
- Language :
- English
- ISSN :
- 1553-7358
- Volume :
- 17
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- PLoS computational biology
- Publication Type :
- Academic Journal
- Accession number :
- 34310600
- Full Text :
- https://doi.org/10.1371/journal.pcbi.1009225