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A BALB/c IGHV Refer...
A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice
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- Jackson, Katherine J.L. (author)
- Garvan Institute of Medical Research
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- Kos, Justin T. (author)
- University of Louisville Health Sciences Center
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- Lees, William (author)
- University of London
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- Gibson, William S. (author)
- University of Louisville Health Sciences Center
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- Smith, Melissa Laird (author)
- University of Louisville Health Sciences Center
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- Peres, Ayelet (author)
- Bar-Ilan University
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- Yaari, Gur (author)
- Bar-Ilan University
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- Corcoran, Martin (author)
- Karolinska Institutet,Karolinska Institute
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- Busse, Christian E. (author)
- German Cancer Research Centre
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- Ohlin, Mats (author)
- Lund University,Lunds universitet,Institutionen för immunteknologi,Institutioner vid LTH,Lunds Tekniska Högskola,Department of Immunotechnology,Departments at LTH,Faculty of Engineering, LTH
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- Watson, Corey T. (author)
- University of Louisville Health Sciences Center
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- Collins, Andrew M. (author)
- University of New South Wales
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(creator_code:org_t)
- 2022-06-03
- 2022
- English.
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In: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 13
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http://dx.doi.org/10... (free)
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https://lup.lub.lu.s...
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Abstract
Subject headings
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- 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. 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 current MGP assemblies are unsuitable for the comprehensive documentation of germline IGHVs and more efforts will be needed to establish strain-specific reference sets.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- BALB/c
- haplotyping
- IGHV
- SMRT sequencing
- substrains
Publication and Content Type
- art (subject category)
- ref (subject category)
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- By the author/editor
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Jackson, Katheri ...
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Kos, Justin T.
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Lees, William
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Gibson, William ...
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Smith, Melissa L ...
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Peres, Ayelet
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show more...
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Yaari, Gur
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Corcoran, Martin
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Busse, Christian ...
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Ohlin, Mats
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Watson, Corey T.
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Collins, Andrew ...
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show less...
- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Frontiers in Imm ...
- By the university
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Lund University
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Karolinska Institutet