Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F24%3A00138875" target="_blank" >RIV/00216224:14740/24:00138875 - isvavai.cz</a>

Result on the web

<a href="https://genome.cshlp.org/content/34/12/2293" target="_blank" >https://genome.cshlp.org/content/34/12/2293</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1101/gr.278775.123" target="_blank" >10.1101/gr.278775.123</a>

Result language

angličtina

Original language name

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

Original language description

Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput novel allele discovery from a wide variety of existing data sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA and TRB) AIRR-seq data set, representing 134 individuals. This allowed us to assess the genetic diversity within the IGH, TRA, and TRB loci in different populations and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2024

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Genome research

ISSN

1088-9051

e-ISSN

—

Volume of the periodical

34

Issue of the periodical within the volume

12

Country of publishing house

US - UNITED STATES

Number of pages

11

Pages from-to

2293-2303

UT code for WoS article

001411753400001

EID of the result in the Scopus database

2-s2.0-85213236396