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公开(公告)号：US20250069706A1
公开(公告)日：2025-02-27
申请号：US18729385
申请日：2023-01-30
Inventor： Bo LI
Abstract: A novel framework to transform a T-cell receptor (TCR) repertoire sample into a fixed-length vector. Short peptide sequences with different lengths in each TCR may be encoded into a numeric vector with fixed dimensions. A large amount of existing TCRs from healthy individuals may be pooled to generate a distribution of the encoding vector in a high-dimensional Euclidean space. Unsupervised clustering may be performed on the “points” in this space (each point is a TCR) to group them into antigen-specific clusters. The centroid of each cluster may be defined as a repertoire functional unit (“RFU”). For a new TCR repertoire sample, each TCR may be assigned to its most similar RFU group, and the RFU counts may be normalized by the number of sequences in the repertoire. The output data may be a fixed-length RFU vector, with each number representing the relative abundance of the given RFU in the repertoire.
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公开(公告)号：US20240290418A1
公开(公告)日：2024-08-29
申请号：US18571515
申请日：2022-06-17
Inventor： Bo LI
Abstract: A novel method of geometric isometry based antigen-specific TCR alignment (GIANA) is described herein. GIANA is an antigen-specific TCR clustering method that is able to efficiently handle tens of millions of sequences. GIANA achieved higher sensitivity and precision than all existing methods, and is able to retrieve TCRs specific to known antigens with high accuracy. The ultra-large-scale TCR clustering and fast query of novel samples also enabled a novel reference-based repertoire classification framework. GIANA can also analyze single cell RNA-seq data with TCR regions solved, and it is possible to query TCRs from unknown data against the large database of TCR repertoire samples in the public domain, and provide new insights over shared antigen-specificity. GIANA is applicable to cluster or query large B cell receptor sequencing data as well.
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