iHMMune-align: UNSWIg germline gene repertoire

The UNSWIg IGHV repertoire is based upon the IMGT repertoire, but classifies all alleles according to the certainty that the reported germline gene sequences are error free, and according to the likelihood that misalignments to the alleles could occur because of the existience of highly similar alleles. The IGHV genes names include the level of the IGHV gene from the most certain (L1) to the least certain (L4). L5 alleles are sequences that we believe were reported in error, or that have other deficiences. The L5 alleles are not included in the UNSWIg repertoire. There are 100 of these sequences and they are described in a manuscript that was published in 2008 (1).

Our studies have also indentified a number of previously unreported polymorphisms (1). Until these polymorphisms have been confirmed by genomic sequencing, they are unlikely to be officially recognised, and they are therefore designated `putative polymorphisms'. Putative alleles are indicated using a `p' designation before the allele number in the gene name.

IGHD genes

The UNSWIg IGHD repertoire is based upon our published evaluation of the IMGT repertoire (2). Note that three members of the IGHD1 famility are so similar that alignments to one or the other of the genes may be uncertain. This is also true of IGHD2-2 alleles which often cannot be distinguished with any confidence. We have identified two new polymorphisms, IGHD3-10*p03 and IGHD3-16*p03 (2,4). These putative polymorphisms are included in the UNSWIg repertoire.

IGHJ genes

The UNSWIg IGHJ repertoire is based upon the IMGT repertoire. Our published evaluation of this repertoire (3) raises questions about the existence or accuracy of sequences reported for IGHJ3*01, IGHJ4*01, IGHJ5*01 and IGHJ6*01. There is, however, insufficient evidence to warrant the removal of these sequences from the available repertoire. The UNSWIg IGHJ repertoire includes two putative IGHJ polymorphisms, IGHJ4*p04 and IGHJ6*p05 (4).

References

1. Wang, Y., Jackson, K. J. L., Sewell, W. A., and Collins, A. M 2008, Many human immunoglobulin heavy-chain IGHV gene polymorphisms have been reported in error , Immunology and Cell Biology, 86: 111-115

2. C. E. H. Lee, Gaeta, B., Malming, H. R., Bain, M. E., Sewell, W. A. and Collins, A, M., 2006, Reconsidering the human immunoglobulin heavy-chain locus: 1. An evaluation of the expressed human IGHD gene repertoire, Immunogenetics, 57(12):917-925, doi:10.1007/s00251-005-0062-5

3. C. E. H. Lee, Jackson, K. J. L., Sewell, W. A. and Collins, A. M., 2006, Use of IGHJ and IGHD gene mutations in analysis of immunoglobulin sequences for the prognosis of chronic lymphocytic leukemia , Leukemia Research, doi:10.1016/j.leukres.2006.10.013

4. Scott D. Boyd, Gaeta, B.A., Jackson, K.J., Fire, A.Z., Marshall, E.L., Merker, J.D., Maniar, J.M., Zhang, L.N., Sahaf, B., Jones, C.D., Simen, B.B., Hanczaruk, B., Nguyen, K.D., Nadeau, K.C., Egholm, M., Miklos, D.B., James L. Zehnder, J.L., Collins, A.M., 2010, Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements , Journal of Immunology, 184(12):6986-6992, doi:10.4049/jimmunol.1000445

5. Yan Wang, Jackson, K.J., Gaeta, B.A., Pomat, W., Siba, P., Sewell, W.A., Collins, A.M., 2011, Genomic screening by 454 pyrosequencing identifies a new human IGHV gene and sixteen other new IGHV allelic variants , Immunogenetics, doi:10.1007/s00251-010-0510-8

UNSWIg germline repertoire

Immunoglobulin heavy chain germline gene repertoire

UNSWIg repertoire

IGHV genes

IGHD genes

IGHJ genes

References

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