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Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity

Peres, Ayelet ; Upadhyay, Amit A. ; Klein, Vered ; Saha, Swati ; Rodriguez, Oscar L. ; Vanwinkle, Zachary M. ; Karunakaran, Kirti ; Metz, Amanda ; Lauer, William and Lin, Mark C. , et al. (2026) In Immunity 59(1). p.6-228
Abstract

Rhesus macaques (RMs) are a vital model for studying human disease and are invaluable to preclinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for antibody-encoding genes within the immunoglobulin (IG) loci. The complexity of the IG loci has historically made them challenging to characterize accurately. To address this, we developed experimental and computational methodologies to generate a collection of integrated antibody repertoire and long-read genomic sequencing data in 106 Indian-origin RMs. We created a resource of IG heavy- and light-chain variable (V), diversity (D), and joining (J) alleles, as well as leader, intronic, and... (More)

Rhesus macaques (RMs) are a vital model for studying human disease and are invaluable to preclinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for antibody-encoding genes within the immunoglobulin (IG) loci. The complexity of the IG loci has historically made them challenging to characterize accurately. To address this, we developed experimental and computational methodologies to generate a collection of integrated antibody repertoire and long-read genomic sequencing data in 106 Indian-origin RMs. We created a resource of IG heavy- and light-chain variable (V), diversity (D), and joining (J) alleles, as well as leader, intronic, and recombination signal sequences (RSSs). This includes the curation of 1,095 previously unidentified alleles, unveiling tremendous diversity and expanding existing IG allele sets by 40%. This publicly available, continually updated resource (https://vdjbase.org/reference_book/Rhesus_Macaque) provides the foundation for advancing RM immunogenomics, vaccine discovery, and translational research.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
antibodies, B cell receptor, broadly neutralizing antibodies, database, genomics, germline inference, HIV, immunoglobulins, repertoire, rhesus macaque
in
Immunity
volume
59
issue
1
pages
6 - 228
publisher
Cell Press
external identifiers
  • scopus:105027528165
  • pmid:41494536
ISSN
1074-7613
DOI
10.1016/j.immuni.2025.12.002
language
English
LU publication?
yes
id
c2fa0982-633e-4058-ab46-84f66d2393bf
date added to LUP
2026-03-10 10:41:56
date last changed
2026-08-27 23:30:13
@article{c2fa0982-633e-4058-ab46-84f66d2393bf,
  abstract     = {{<p>Rhesus macaques (RMs) are a vital model for studying human disease and are invaluable to preclinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for antibody-encoding genes within the immunoglobulin (IG) loci. The complexity of the IG loci has historically made them challenging to characterize accurately. To address this, we developed experimental and computational methodologies to generate a collection of integrated antibody repertoire and long-read genomic sequencing data in 106 Indian-origin RMs. We created a resource of IG heavy- and light-chain variable (V), diversity (D), and joining (J) alleles, as well as leader, intronic, and recombination signal sequences (RSSs). This includes the curation of 1,095 previously unidentified alleles, unveiling tremendous diversity and expanding existing IG allele sets by 40%. This publicly available, continually updated resource (https://vdjbase.org/reference_book/Rhesus_Macaque) provides the foundation for advancing RM immunogenomics, vaccine discovery, and translational research.</p>}},
  author       = {{Peres, Ayelet and Upadhyay, Amit A. and Klein, Vered and Saha, Swati and Rodriguez, Oscar L. and Vanwinkle, Zachary M. and Karunakaran, Kirti and Metz, Amanda and Lauer, William and Lin, Mark C. and Melton, Timothy and Granholm, Lukas and Polak, Pazit and Peterson, Samuel M. and Peterson, Eric J. and Raju, Nagarajan and Shields, Kaitlyn and Schultze, Steven and Ton, Thang and Ericsen, Adam J. and Lapp, Stacey A. and Villinger, Francois and Ohlin, Mats and Cottrell, Christopher A. and Amara, Rama R. and Derdeyn, Cynthia A. and Crotty, Shane and Schief, William R. and Hedestam, Gunilla B.Karlsson and Smith, Melissa L. and Lees, William and Watson, Corey T. and Yaari, Gur and Bosinger, Steven E.}},
  issn         = {{1074-7613}},
  keywords     = {{antibodies; B cell receptor; broadly neutralizing antibodies; database; genomics; germline inference; HIV; immunoglobulins; repertoire; rhesus macaque}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{1}},
  pages        = {{6--228}},
  publisher    = {{Cell Press}},
  series       = {{Immunity}},
  title        = {{Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity}},
  url          = {{http://dx.doi.org/10.1016/j.immuni.2025.12.002}},
  doi          = {{10.1016/j.immuni.2025.12.002}},
  volume       = {{59}},
  year         = {{2026}},
}