Skip to main content

Advertisement

SpringerLink
Log in

Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation

  • Article
  • Published:
Genes & Immunity Submit manuscript

Abstract

Immunoglobulins (IGs), crucial components of the adaptive immune system, are encoded by three genomic loci. However, the complexity of the IG loci severely limits the effective use of short read sequencing, limiting our knowledge of population diversity in these loci. We leveraged existing long read whole-genome sequencing (WGS) data, fosmid technology, and IG targeted single-molecule, real-time (SMRT) long-read sequencing (IG-Cap) to create haplotype-resolved assemblies of the IG Lambda (IGL) locus from 6 ethnically diverse individuals. In addition, we generated 10 diploid assemblies of IGL from a diverse cohort of individuals utilizing IG-Cap. From these 16 individuals, we identified significant allelic diversity, including 36 novel IGLV alleles. In addition, we observed highly elevated single nucleotide variation (SNV) in IGLV genes relative to IGL intergenic and genomic background SNV density. By comparing SNV calls between our high quality assemblies and existing short read datasets from the same individuals, we show a high propensity for false-positives in the short read datasets. Finally, for the first time, we nucleotide-resolved common 5-10 Kb duplications in the IGLC region that contain functional IGLJ and IGLC genes. Together these data represent a significant advancement in our understanding of genetic variation and population diversity in the IGL locus.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1: Methods overview: schematic of hybrid and capture assembly methods.
Fig. 2: IGLV allele and haplotype diversity.
Fig. 3: Density and localization of SNVs within the IGLV region.
Fig. 4: Extensive structural and allelic variation in the IGLJ and IGLC region.

Similar content being viewed by others

Data availability

All custom code and scripts used in this study were written in R, Python, and Bash. All scripts are available upon request along with usage explanations. Assemblies are available through VDJbase [66]. Fosmid sequences submitted to GenBank through project id PRJNA555323 and are available at the following link: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA555323.

References

  1. Wardemann H, Hammersen J, Nussenzweig MC. Human autoantibody silencing by immunoglobulin light chains. J Exp Med. 2004;200:191–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Hershberg U, Shlomchik MJ. Differences in potential for amino acid change after mutation reveals distinct strategies for and light-chain variation. Proc Natl Acad Sci. 2006;103:15963–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Collins AM, Watson CT. Immunoglobulin light chain gene rearrangements, receptor editing and the development of a self-tolerant antibody repertoire. Front Immunol. 2018;9:2249.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Schatz DG. V(D)J recombination. Immunol Rev. 2004;200:5–11.

    Article  CAS  PubMed  Google Scholar 

  5. Townsend CL, Laffy JMJ, Wu YCB, Silva O’Hare J, Martin V, Kipling D, et al. Significant differences in physicochemical properties of human immunoglobulin kappa and lambda CDR3 regions. Front Immunol [Internet]. 2016 Sep [cited 2021 May 20];7. Available from: http://journal.frontiersin.org/Article/10.3389/fimmu.2016.00388/abstract

  6. Watson CT, Steinberg KM, Graves TA, Warren RL, Malig M, Schein J, et al. Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes Immun. 2015;16:24–34.

    Article  CAS  PubMed  Google Scholar 

  7. Moraes Junta C, Passos GAS. Genomic EcoRI polymorphism and cosmid sequencing reveal an insertion/deletion and a new IGLV5 allele in the human immunoglobulin lambda variable locus (22q11.2/IGLV). Immunogenetics 2003;55:10–5.

    Article  PubMed  Google Scholar 

  8. Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, et al. The complete sequence of a human genome. Science. 2022;376:44–53. https://doi.org/10.1126/science.abj6987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Giudicelli V. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 2004;33:D256–61.

    Article  PubMed Central  Google Scholar 

  10. Lefranc MP. IMGT (ImMunoGeneTics) locus on focus. A new section of experimental and clinical immunogenetics. Exp Clin Immunogenet. 1998;15:1–7.

    Article  CAS  PubMed  Google Scholar 

  11. Mikocziova I, Peres A, Gidoni M, Greiff V, Yaari G, Sollid LM. Germline polymorphisms and alternative splicing of human immunoglobulin light chain genes. iScience. 2021;24:103192.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Tümkaya T, van der Burg M, Garcia Sanz R, Gonzalez Diaz M, Langerak A, San Miguel J, et al. Immunoglobulin lambda isotype gene rearrangements in B cell malignancies. Leukemia. 2001;15:121–7.

    Article  PubMed  Google Scholar 

  13. Lefranc MP, Pallarès N, Frippiat JP. Allelic polymorphisms and RFLP in the human immunoglobulin lambda light chain locus. Hum Genet. 1999;104:361–9.

    Article  CAS  PubMed  Google Scholar 

  14. van der Burg M, Barendregt BH, van Gastel-Mol EJ, Tümkaya T, Langerak AW, van Dongen JJM. Unraveling of the polymorphic Cλ2-Cλ3 amplification and the Ke + Oz − polymorphism in the human Igλ locus. J Immunol. 2002;169:271–6.

    Article  PubMed  Google Scholar 

  15. Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, et al. High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios [Internet]. Genomics. 2021 Feb [cited 2022 Jan 9]. Available from: http://biorxiv.org/lookup/doi/10.1101/2021.02.06.430068

  16. Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, et al. A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus. Front Immunol. 2020;11:2136.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Benichou J, Ben-Hamo R, Louzoun Y, Efroni S. Rep-Seq: uncovering the immunological repertoire through next-generation sequencing: Rep-Seq: NGS for the immunological repertoire. Immunology. 2012;135:183–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Corcoran MM, Phad GE, Bernat NV, Stahl-Hennig C, Sumida N, Persson MAA, et al. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity. Nat Commun. 2016;7:13642.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proc Natl Acad Sci. 2015;112:E862–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Gadala-Maria D, Gidoni M, Marquez S, Vander Heiden JA, Kos JT, Watson CT, et al. Identification of subject-specific immunoglobulin alleles from expressed repertoire sequencing data. Front Immunol. 2019;10:129.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, et al. Inferred allelic variants of immunoglobulin receptor genes: a system for their evaluation, documentation, and naming. Front Immunol. 2019;10:435.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ralph DK, Matsen FA. Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data. Buhler J, editor. PLOS Comput Biol. 2019;15:e1007133.

  23. Watson CT, Breden F. The immunoglobulin heavy chain locus: genetic variation, missing data, and implications for human disease. Genes Immun. 2012;13:363–73.

    Article  CAS  PubMed  Google Scholar 

  24. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008;453:56–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, et al. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires. Proc Natl Acad Sci. 2016;113:E2636–45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Siniscalco M, Robledo R, Orru S, Contu L, Yadav P, Ren Q, et al. A plea to search for deletion polymorphism through genome scans in populations. Trends Genet. 2000;16:435–7.

    Article  CAS  PubMed  Google Scholar 

  27. Irony-Tur Sinai M, Salamon A, Stanleigh N, Goldberg T, Weiss A, Wang YH, et al. AT-dinucleotide rich sequences drive fragile site formation. Nucleic Acids Res. 2019;47:9685–95.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Li S, Wu X. Common fragile sites: protection and repair. Cell Biosci. 2020;10:29.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Pu L, Lin Y, Pevzner PA. Detection and analysis of ancient segmental duplications in mammalian genomes. Genome Res. 2018;28:901–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell. 2010;143:837–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, Schein J, et al. Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am J Hum Genet. 2013;92:530–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Piovesan A, Pelleri MC, Antonaros F, Strippoli P, Caracausi M, Vitale L. On the length, weight and GC content of the human genome. BMC Res Notes. 2019;12:106.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Chen JM, Cooper DN, Chuzhanova N, Férec C, Patrinos GP. Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet. 2007;8:762–75.

    Article  CAS  PubMed  Google Scholar 

  34. Mikocziova I, Greiff V, Sollid LM. Immunoglobulin germline gene variation and its impact on human disease. Genes Immun [Internet]. 2021 Jun [cited 2021 Jul 8]; Available from: http://www.nature.com/articles/s41435-021-00145-5

  35. Glanville J, Kuo TC, von Budingen HC, Guey L, Berka J, Sundar PD, et al. Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation. Proc Natl Acad Sci. 2011;108:20066–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Avnir Y, Watson CT, Glanville J, Peterson EC, Tallarico AS, Bennett AS, et al. IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity. Sci Rep. 2016;6:20842.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Collins AM, Yaari G, Shepherd AJ, Lees W, Watson CT. Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight? Curr Opin Syst Biol. 2020;24:100–8.

    Article  Google Scholar 

  38. Meyer D, Aguiar VRC, Bitarello BD, Brandt DYC, Nunes K. A genomic perspective on HLA evolution. Immunogenetics. 2018;70:5–27.

    Article  PubMed  Google Scholar 

  39. Penn DJ, Damjanovich K, Potts WK. MHC heterozygosity confers a selective advantage against multiple-strain infections. Proc Natl Acad Sci. 2002;99:11260–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Norman PJ, Hollenbach JA, Nemat-Gorgani N, Guethlein LA, Hilton HG, Pando MJ, et al. Co-evolution of human leukocyte antigen (HLA) Class I ligands with killer-cell immunoglobulin-like receptors (KIR) in a genetically diverse population of sub-saharan Africans. Gibson G, editor. PLoS Genet. 2013;9:e1003938.

  41. D’Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, et al. Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. eLife. 2019;8:e48476.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Taub RA, Hollis GF, Hieter PA, Korsmeyer S, Waldmann TA, Leder P. Variable amplification of immunoglobulin λ light-chain genes in human populations. Nature. 1983;304:172–4.

    Article  CAS  PubMed  Google Scholar 

  43. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol [Internet]. 1993 May [cited 2022 Jun 8]; Available from: https://academic.oup.com/mbe/article/10/3/512/1016366/Estimation-of-the-number-of-nucleotide

  44. Ohno S. Evolution by Gene Duplication. Berlin: Springer Berlin; 2014.

  45. Lynch M, Katju V. The altered evolutionary trajectories of gene duplicates. Trends Genet. 2004;20:544–9.

    Article  CAS  PubMed  Google Scholar 

  46. Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, et al. The international Genome sample resource (IGSR): a worldwide collection of genome variation incorporating the 1000 genomes project data. Nucleic Acids Res. 2017;45:D854–9.

    Article  CAS  PubMed  Google Scholar 

  47. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, et al. Fine-scale structural variation of the human genome. Nat Genet. 2005;37:727–32.

    Article  CAS  PubMed  Google Scholar 

  48. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation. Genome Res. 2017;27:722–36.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Chen Y, Zhang Y, Wang AY, Gao M, Chong Z. Accurate long-read de novo assembly evaluation with Inspector. Genome Biol. 2021;22:312.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Steinberg KM, Lindsay TG, Schneider VA, Chaisson MJP, Tomlinson C, Huddleston J, et al. High-Quality Assembly of an Individual of Yoruban Descent [Internet]. Bioinformatics; 2016 Aug [cited 2021 Nov 3]. Available from: http://biorxiv.org/lookup/doi/10.1101/067447

  51. Brochet X, Lefranc MP, Giudicelli V. IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 2008;36:W503–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Giudicelli V, Brochet X, Lefranc MP. IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. Cold Spring Harb Protoc. 2011;2011:pdb.prot5633.

    Article  Google Scholar 

  53. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:2987–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Cleary JG, Braithwaite R, Gaastra K, Hilbush BS, Inglis S, Irvine SA, et al. Comparing variant call files for performance benchmarking of next-generation sequencing variant calling pipelines [Internet]. Bioinformatics; 2015 Aug [cited 2022 May 29]. Available from: http://biorxiv.org/lookup/doi/10.1101/023754

  55. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178–92.

    Article  CAS  PubMed  Google Scholar 

  57. Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant review with the integrative genomics viewer. Cancer Res. 2017;77:e31–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013;41:W29–33.

    Article  PubMed  PubMed Central  Google Scholar 

  59. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.

    Article  CAS  PubMed  Google Scholar 

  60. Altschul S. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinforma. 2009;10:421.

    Article  Google Scholar 

  62. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol [Internet]. 1987 Jul [cited 2022 Jun 8]; Available from: https://academic.oup.com/mbe/article/4/4/406/1029664/The-neighborjoining-method-a-new-method-for

  64. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.

    Article  PubMed  PubMed Central  Google Scholar 

  66. Omer A, Shemesh O, Peres A, Polak P, Shepherd AJ, Watson CT, et al. VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Res. 2020;48:D1051–6.

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This work was supported, in part, by NIAID grant R24AI138963 to CW, MS. This work was supported, in part, by US National Institutes of Health (NIH) grant HG010169 to EEE. EEE is an investigator of the Howard Hughes Medical Institute. This research was supported in part by the U.S. National Science Foundation (NSF) under grant CNS1828521 and the University of Louisville’s Research Computing team.

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA

    William S. Gibson, Oscar L. Rodriguez, Kaitlyn Shields, Catherine A. Silver, Abdullah Dorgham, Melissa L. Smith & Corey T. Watson

  2. Icahn Institute of Genomics Technology and Data Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Matthew Emery, Gintaras Deikus & Robert Sebra

  3. Sema4, Stamford, CT, USA

    Robert Sebra

  4. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA

    Evan E. Eichler

  5. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA

    Evan E. Eichler

  6. Google Accelerated Science Team, Google Inc, Mountain View, CA, USA

    Ali Bashir

Authors
  1. William S. Gibson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Oscar L. Rodriguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kaitlyn Shields
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Catherine A. Silver
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Abdullah Dorgham
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Matthew Emery
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Gintaras Deikus
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Robert Sebra
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Evan E. Eichler
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Ali Bashir
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Melissa L. Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Corey T. Watson
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

WSG, OLR, AB, MLS, CTW conceived and planned the study. EEE provided sample resources. RS, MLS provided sequencing resources. WSG, KS, CAS, ME, GD, MLS prepared sequencing libraries and performed sequencing. WSG, OLR, AD, CTW interpreted results. WSG, OLR wrote the code. CTW, MLS supervised the experiments, analysis, and data interpretation. WSG wrote the manuscript with contributions from CTW, MLS, and OLR. WSG, CTW, MLS, OLR, EEE, RS reviewed and edited the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Melissa L. Smith or Corey T. Watson.

Ethics declarations

Competing interests

EEE is a scientific advisory board (SAB) member of Variant Bio, Inc. Robert Sebra is VP of Technology Development at Sema4.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gibson, W.S., Rodriguez, O.L., Shields, K. et al. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun 24, 21–31 (2023). https://doi.org/10.1038/s41435-022-00188-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41435-022-00188-2

  • Springer Nature Limited

This article is cited by

Search

Navigation