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Immunogenetics

, Volume 63, Issue 5, pp 259–265 | Cite as

Genomic screening by 454 pyrosequencing identifies a new human IGHV gene and sixteen other new IGHV allelic variants

  • Yan Wang
  • Katherine J. Jackson
  • Bruno Gäeta
  • William Pomat
  • Peter Siba
  • William A. Sewell
  • Andrew M. CollinsEmail author
Original Paper

Abstract

Complete and accurate knowledge of the genes and allelic variants of the human immunoglobulin gene loci is critical for studies of B cell repertoire development and somatic point mutation, but evidence from studies of VDJ rearrangements suggests that our knowledge of the available immunoglobulin gene repertoire is far from complete. The reported repertoire has changed little over the last 15 years. This is, in part, a consequence of the inefficiencies involved in searching for new members of large, multigenic gene families by cloning and sequencing. The advent of high-throughput sequencing provides a new avenue by which the germline repertoire can be explored. In this report, we describe pyrosequencing studies of the heavy chain IGHV1, IGHV3 and IGHV4 gene subgroups in ten Papua New Guineans. Thousands of 454 reads aligned with complete identity to 51 previously reported functional IGHV genes and allelic variants. A new gene, IGHV3-NL1*01, was identified, which differs from the nearest previously reported gene by 15 nucleotides. Sixteen new IGHV alleles were also identified, 15 of which varied from previously reported functional IGHV genes by between one and four nucleotides, while one sequence appears to be a functional variant of the pseudogene IGHV3-25. BLAST searches suggest that at least six of these new genes are carried within the relatively well-studied populations of North America, Europe or Asia. This study substantially expands the known immunoglobulin gene repertoire and demonstrates that genetic variation of immunoglobulin genes can now be efficiently explored in different human populations using high-throughput pyrosequencing.

Keywords

Immunoglobulin heavy chain IGHV Allelic variants Mutation analysis Polymorphism 

Supplementary material

251_2010_510_MOESM1_ESM.doc (92 kb)
Supplementary Table 1 Numbers of alignments of 454 pyrosequencing reads that align perfectly to previously reported germline genesa (DOC 92 kb)
251_2010_510_MOESM2_ESM.doc (70 kb)
Supplementary Table 2 Numbers of alignments of 454 pyrosequencing reads that align perfectly to previously reported germline pseudogenes, open reading frames and orphonsa (DOC 70 kb)
251_2010_510_MOESM3_ESM.doc (48 kb)
Supplementary Table 3 Numbers of 454 pyrosequencing reads that are highly similar to previously reported genes, pseudogenes and orphons (DOC 48 kb)
251_2010_510_MOESM4_ESM.doc (40 kb)
Supplementary Table 4 Full-length IGHV sequences identified for the first time in this study. The accession numbers of the reference sequence for each gene is shown. Underlined bold letters show extensions of sequences that appear to have been truncated when originally reported. Upper case bold letters show the critical nucleotides that distinguish these alleles from their most similar reported allele. Deletions relative to the most similar reported allele are shown as dashes. The most similar previously reported gene is listed in square brackets, along with details of the features that distinguish it from the sequence reported in this study (DOC 40.5 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Yan Wang
    • 1
  • Katherine J. Jackson
    • 1
    • 2
  • Bruno Gäeta
    • 2
  • William Pomat
    • 3
  • Peter Siba
    • 3
  • William A. Sewell
    • 4
  • Andrew M. Collins
    • 1
    Email author
  1. 1.School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyAustralia
  2. 2.School of Computer Science and EngineeringUniversity of New South WalesSydneyAustralia
  3. 3.Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
  4. 4.The Garvan Institute of Medical Research and St Vincent’s Clinical SchoolUniversity of NSWSydneyAustralia

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