TY - JOUR T1 - Computational analysis of B cell receptor repertoires in COVID-19 patients using deep embedded representations of protein sequences JF - bioRxiv DO - 10.1101/2021.08.02.454701 SP - 2021.08.02.454701 AU - Inyoung Kim AU - Sang Yoon Byun AU - Sangyeup Kim AU - Sangyoon Choi AU - Jinsung Noh AU - Junho Chung AU - Byung Gee Kim Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/11/29/2021.08.02.454701.abstract N2 - Analyzing B cell receptor (BCR) repertoires is immensely useful in evaluating one’s immunological status. Conventionally, repertoire analysis methods have focused on comprehensive assessments of clonal compositions, including V(D)J segment usage, nucleotide insertions/deletions, and amino acid distributions. Here, we introduce a novel computational approach that applies deep-learning-based protein embedding techniques to analyze BCR repertoires. By selecting the most frequently occurring BCR sequences in a given repertoire and computing the sum of the vector representations of these sequences, we represent an entire repertoire as a 100-dimensional vector and eventually as a single data point in vector space. We demonstrate that this new approach enables us to not only accurately cluster BCR repertoires of coronavirus disease 2019 (COVID-19) patients and healthy subjects but also efficiently track minute changes in immune status over time as patients undergo treatment. Furthermore, using the distributed representations, we successfully trained an XGBoost classification model that achieved a mean accuracy rate of over 87% given a repertoire of CDR3 sequences.Competing Interest StatementThe authors have declared no competing interest. ER -