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Related Concept Videos

Diversity of Antigen Receptors01:28

Diversity of Antigen Receptors

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Antigen receptors are essential components of the immune system crucial in defending the body against foreign invaders. These receptors are present on the surface of B and T cells, enabling them to recognize antigens and mount an appropriate immune response.
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Updated: Aug 1, 2025

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach
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Adaptive immune receptor genotyping using the corecount program.

Sanjana Narang1, Mateusz Kaduk1, Mark Chernyshev1

  • 1Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.

Frontiers in Immunology
|April 28, 2023
PubMed
Summary
This summary is machine-generated.

We developed corecount, a new tool for analyzing genetic variation in immunoglobulin and T cell receptor genes. It accurately identifies V, D, and J alleles, improving repertoire sequencing analysis.

Keywords:
IGHVDJ germline genesgenotypingimmune repertoiresinference

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T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing
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Area of Science:

  • Immunology
  • Bioinformatics
  • Genetics

Background:

  • Rep-seq (repertoire sequencing) is crucial for studying adaptive immune responses.
  • Accurate genotypic analysis of immunoglobulin (IG) and T cell receptor (TCR) genes is essential but challenging.
  • Existing tools struggle with identifying rare or variant alleles and germline inference.

Purpose of the Study:

  • To introduce corecount, a novel bioinformatics tool for high-throughput genotypic analysis of IG and TCR repertoires.
  • To enhance the accuracy and reproducibility of V, D, and J gene allele identification.
  • To provide a validated resource for benchmarking and developing future adaptive immune receptor repertoire sequencing (AIRR-Seq) tools.

Main Methods:

  • Development and application of the corecount software for IG/TCR repertoire analysis.
  • Genotyping of immunoglobulin heavy chain (IGH) alleles using corecount on IgM libraries from 16 individuals.
  • Validation of corecount's accuracy through Sanger sequencing of all heavy chain IG alleles from one individual.

Main Results:

  • Corecount efficiently identifies V alleles, including rare and 3' end variants, and accurately genotypes D and J genes.
  • Genomic analysis revealed truncated sequences in current reference databases for 5 IGHV and 2 IGHJ alleles.
  • The study generated a dataset of genomically validated alleles and IgM libraries for benchmarking.

Conclusions:

  • Corecount offers a reproducible and accurate method for IG and TCR genotypic analysis.
  • The findings highlight limitations in current reference databases and provide a valuable resource for the field.
  • This work facilitates the development of improved AIRR-Seq analysis tools by providing comprehensive reference data.