The human immunoglobulin heavy chain constant gene locus is enriched for large complex structural variants and coding polymorphisms that vary in frequency among human populations

Jana, U.; Rodriguez, O. L.; Lees, W.; Engelbrecht, E.; Vanwinkle, Z.; Peres, A.; Gibson, W.; Shields, K.; Schultze, S.; Dorgham, A. G.; Emery, M.; Deikus, G.; Sebra, R.; Eichler, E. E.; Yaari, G.; Smith, M. L.; Watson, C. T.

doi:10.1101/2025.02.12.634878

bioRxiv · 10.1101/2025.02.12.634878

The human immunoglobulin heavy chain constant gene locus is enriched for large complex structural variants and coding polymorphisms that vary in frequency among human populations

Jana, U.·Rodriguez, O. L.·Lees, W.·Engelbrecht, E.·Vanwinkle, Z.·Peres, A.·Gibson, W.·Shields, K.·Schultze, S.·Dorgham, A. G.·Emery, M.·Deikus, G.·Sebra, R.·Eichler, E. E.·Yaari, G.·Smith, M. L.·Watson, C. T.

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Abstract

The human immunoglobulin heavy chain constant (IGHC) domain of antibodies (Ab) is responsible for effector functions critical to immunity. This domain is encoded by genes in the IGHC locus, where descriptions of genomic diversity remain incomplete. We utilized long-read sequencing to build an IGHC haplotype/variant catalog from 105 individuals of diverse ancestry. We discovered uncharacterized single nucleotide variants (SNV) and large structural variants (SVs, n=7), representing new genes and alleles enriched for non-synonymous substitutions, highlighting potential functional effects. Of the 221 identified IGHC alleles, 192 were novel. SNV, SV, and gene allele/genotype frequencies revealed population differentiation, including (i) hundreds of SNVs in African and East Asian populations exceeding a fixation index (FST) of 0.3, and (ii) an IGHG4 haplotype carrying coding variants uniquely enriched in Asian populations. Our results illuminate missing signatures of IGHC diversity and establish a new foundation for investigating IGHC germline variation in Ab function and disease.

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Jana, U., Rodriguez, O. L., Lees, W., Engelbrecht, E., Vanwinkle, Z., Peres, A., Gibson, W., Shields, K., Schultze, S., Dorgham, A. G., Emery, M., Deikus, G., Sebra, R., Eichler, E. E., Yaari, G., Smith, M. L., Watson, C. T.. 2025-02-12. The human immunoglobulin heavy chain constant gene locus is enriched for large complex structural variants and coding polymorphisms that vary in frequency among human populations. https://doi.org/10.1101/2025.02.12.634878

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