In:
Frontiers in Immunology, Frontiers Media SA, Vol. 14 ( 2023-4-11)
Abstract:
We present a new Rep-Seq analysis tool called corecount , for analyzing genotypic variation in immunoglobulin (IG) and T cell receptor (TCR) genes. corecount is highly efficient at identifying V alleles, including those that are infrequently used in expressed repertoires and those that contain 3’ end variation that are otherwise refractory to reliable identification during germline inference from expressed libraries. Furthermore, corecount facilitates accurate D and J gene genotyping. The output is highly reproducible and facilitates the comparison of genotypes from multiple individuals, such as those from clinical cohorts. Here, we applied corecount to the genotypic analysis of IgM libraries from 16 individuals. To demonstrate the accuracy of corecount , we Sanger sequenced all the heavy chain IG alleles (65 IGHV, 27 IGHD and 7 IGHJ) from one individual from whom we also produced two independent IgM Rep-seq datasets. Genomic analysis revealed that 5 known IGHV and 2 IGHJ sequences are truncated in current reference databases. This dataset of genomically validated alleles and IgM libraries from the same individual provides a useful resource for benchmarking other bioinformatic programs that involve V, D and J assignments and germline inference, and may facilitate the development of AIRR-Seq analysis tools that can take benefit from the availability of more comprehensive reference databases.
Type of Medium:
Online Resource
ISSN:
1664-3224
DOI:
10.3389/fimmu.2023.1125884
DOI:
10.3389/fimmu.2023.1125884.s001
DOI:
10.3389/fimmu.2023.1125884.s002
DOI:
10.3389/fimmu.2023.1125884.s003
DOI:
10.3389/fimmu.2023.1125884.s004
DOI:
10.3389/fimmu.2023.1125884.s005
DOI:
10.3389/fimmu.2023.1125884.s006
DOI:
10.3389/fimmu.2023.1125884.s007
DOI:
10.3389/fimmu.2023.1125884.s008
DOI:
10.3389/fimmu.2023.1125884.s009
Language:
Unknown
Publisher:
Frontiers Media SA
Publication Date:
2023
detail.hit.zdb_id:
2606827-8
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