11/6/2023 0 Comments Immune repertoireThe ability to embed these textual sequences in a vector-space is an important step towards developing effective analysis methods. The mathematical and statistical properties of high-dimensionality are often poorly understood or overlooked in data modeling and analysis ( 5). These technologies present investigators with the challenge of extracting meaningful statistical and biological information from high-dimensional data. With the advancements of HTS technologies, the amount of sequencing data is continuously growing ( 4). High Throughput Sequencing (HTS) is a powerful platform that enables large-scale characterization of BCR repertoires ( 3). The BCR repertoire in humans is estimated to include at least 10 11 different BCRs, and potentially several orders of magnitude greater ( 2). Applying Immune2vec along with machine learning approaches to patient data exemplifies how distinct clinical conditions can be effectively stratified, indicating that the embedding space can be used for feature extraction and exploratory data analysis.Īntibodies, the secreted form of BCRs, play a crucial role in the adaptive immune system, by binding specifically to pathogens and neutralizing their activity ( 1). Our work demonstrates Immune2vec to be a reliable low-dimensional representation that preserves relevant information of immune sequencing data, such as n-gram properties and IGHV gene family classification. We validate Immune2vec on amino acid 3-gram sequences, continuing to longer BCR sequences, and finally to entire repertoires. Here we present Immune2vec, an adaptation of a natural language processing (NLP)-based embedding technique for BCR repertoire sequencing data. The ability to embed these DNA and amino acid textual sequences in a vector-space is an important step towards developing effective analysis methods. These huge immune repertoires in each individual present investigators with the challenge of extracting meaningful biological information from multi-dimensional data. It does so through dynamic and diverse repertoires of T- and B- cell receptors (TCR and BCRs, respectively). The adaptive branch of the immune system learns pathogenic patterns and remembers them for future encounters.
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