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A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice

Katherine JL Jackson, Justin T Kos, William Lees, William S Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E. Busse, Mats Ohlin, Corey T Watson, Andrew M Collins
doi: https://doi.org/10.1101/2022.02.28.482396
Katherine JL Jackson
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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Justin T Kos
2Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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William Lees
3Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
4Centre for Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
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William S Gibson
2Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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Melissa Laird Smith
2Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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Ayelet Peres
5Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
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Gur Yaari
5Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
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Martin Corcoran
6Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Christian E. Busse
7Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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Mats Ohlin
8Department of Immunotechnology, Lund University, Lund, Sweden
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Corey T Watson
2Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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Andrew M Collins
9School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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  • For correspondence: a.collins@unsw.edu.au
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Abstract

The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Previously unreported strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted at https://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data, but not currently-available genome assemblies, are suited to the documentation of germline IGHV genes.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 01, 2022.
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A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice
Katherine JL Jackson, Justin T Kos, William Lees, William S Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E. Busse, Mats Ohlin, Corey T Watson, Andrew M Collins
bioRxiv 2022.02.28.482396; doi: https://doi.org/10.1101/2022.02.28.482396
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A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice
Katherine JL Jackson, Justin T Kos, William Lees, William S Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E. Busse, Mats Ohlin, Corey T Watson, Andrew M Collins
bioRxiv 2022.02.28.482396; doi: https://doi.org/10.1101/2022.02.28.482396

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