A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus

Abstract

An incomplete ascertainment of genetic variation within the highly polymorphic immunoglobulin heavy chain locus (IGH) has hindered our ability to define genetic factors that influence antibody-mediated processes. Due to locus complexity, standard high-throughput approaches have failed to accurately and comprehensively capture IGH polymorphism. As a result, the locus has only been fully characterized two times, severely limiting our knowledge of human IGH diversity. Here, we combine targeted long-read sequencing with a novel bioinformatics tool, IGenotyper, to fully characterize IGH variation in a haplotype-specific manner. We apply this approach to eight human samples, including a haploid cell line and two mother-father-child trios, and demonstrate the ability to generate high-quality assemblies (>98% complete and >99% accurate), genotypes, and gene annotations, identifying 2 novel structural variants and 15 novel IGH alleles. We show multiplexing allows for scaling of the approach without impacting data quality, and that our genotype call sets are more accurate than short-read (>35% increase in true positives and >97% decrease in false-positives) and array/imputation-based datasets. This framework establishes a desperately needed foundation for leveraging IG genomic data to study population-level variation in antibody-mediated immunity, critical for bettering our understanding of disease risk, and responses to vaccines and therapeutics.

References 76

1. 1.

   Matsuda F Ishii K Bourvagnet P Kuma K-I Hayashida H Miyata T The complete nucleotide sequence of the human immunoglobulin heavy chain variable region locus. J Exp Med. (1998 ) 188:2151–62.

   Not in our library10.1084/jem.188.11.2151

2. 2.

   Watson CT Steinberg KM Huddleston J Warren RL Malig M Schein J. 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.

   Not in our library10.1016/j.ajhg.2013.03.004

3. 3.

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

   Not in our library10.1038/gene.2012.12

4. 4.

   Lefranc M-P Lefranc M-P. IMGT,the international ImMunoGeneTics database. Nucleic Acids Res. (2001 ) 29:207–9.

   Not in our library10.1093/nar/29.1.207

5. 5.

   Boyd SD Gaëta BA Jackson KJ Fire AZ Marshall EL Merker JD. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. J Immunol. (2010 ) 184:6986–92.

   Not in our library10.4049/jimmunol.1000445

6. 6.

   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 USA. (2015 ) 112:E862–70.

   Not in our library10.1073/pnas.1417683112

7. 7.

   Scheepers C Shrestha RK Lambson BE Jackson KJL Wright IA Naicker D. Ability to develop broadly neutralizing HIV-1 antibodies is not restricted by the germline ig gene repertoire. J Immunol. (2015 ) 194:4371–8.

   Not in our library10.4049/jimmunol.1500118

8. 8.
   Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity · 2016

   No notice
9. 9.

   Thörnqvist L Ohlin M. The functional 3’-end of immunoglobulin heavy chain variable (IGHV) genes. Mol Immunol. (2018 ) 96:61–8.

   Not in our library10.1016/j.molimm.2018.02.013

10. 10.

    Calonga-Solís V Malheiros D Beltrame MH De Brito Vargas L Unveiling the diversity of immunoglobulin heavy constant gamma (IGHG) gene segments in brazilian populations reveals 28 novel alleles and evidence of gene conversion and natural selection. Front Immunol. (2019 ) 10:1161.

    Not in our library10.3389/fimmu.2019.01161

11. 11.

    Wang Y Jackson KJL Sewell WA Collins AM. Many human immunoglobulin heavy-chain IGHV gene polymorphisms have been reported in error. Immunol Cell Biol. (2008 ) 86:111–5.

    Not in our library10.1038/sj.icb.7100144

12. 12.

    Milner EC Hufnagle WO Glas AM Suzuki I Alexander C. Polymorphism and utilization of human VH Genes. Ann N Y Acad Sci. (1995 ) 764:50–61.

    Not in our library10.1111/j.1749-6632.1995.tb55806.x

13. 13.

    Sasso EH Johnson T Kipps TJ. Expression of the immunoglobulin VH gene 51p1 is proportional to its germline gene copy number. J Clin Invest. (1996 ) 97:2074–80.

    Not in our library10.1172/jci118644

14. 14.

    Chimge N-O Pramanik S Hu G Lin Y Gao R Shen L Determination of gene organization in the human IGHV region on single chromosomes. Genes Immun. (2005 ) 6:186–93.

    Not in our library10.1038/sj.gene.6364176

15. 15.

    Pramanik S Cui X Wang H-Y Chimge N-O Hu G Shen L Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region. BMC Genomics. (2011 ) 12:78.

    Not in our library10.1186/1471-2164-12-78

16. 16.

    Kidd MJ Jackson KJL Boyd SD Collins AM. DJ Pairing during VDJ recombination shows positional biases that vary among individuals with differing IGHD locus immunogenotypes. J Immunol. (2016 ) 196:1158–64.

    Not in our library10.4049/jimmunol.1501401

17. 17.

    Kidd MJ Chen Z Wang Y Jackson KJ Zhang L Boyd SD The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements. J Immunol. (2012 ) 188:1333–40.

    Not in our library10.4049/jimmunol.1102097

18. 18.

    Gidoni M Snir O Peres A Polak P Lindeman I Mikocziova I Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping. Nat Commun. (2019 ) 10:628.

    Not in our library10.1038/s41467-019-08489-3

19. 19.

    Luo S Yu JA Li H Song YS. Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans. Life Sci Alliance. (2019 ) 2:e201800221.

    Not in our library10.26508/lsa.201800221

20. 20.
    IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity · 2016

    Corrected
21. 21.

    Glanville J Kuo TC von Büdingen H-C Guey L Berka J Sundar PD Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation. Proc Natl Acad Sci USA. (2011 ) 108:20066–71.

    Not in our library10.1073/pnas.1107498108

22. 22.
    Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells · 2016

    No notice
23. 23.

    Watson CT Glanville J Marasco WA. The individual and population genetics of antibody immunity. Trends Immunol. (2017 ) 38:459–70.

    Not in our library10.1016/j.it.2017.04.003

24. 24.
    Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania · 2017

    No notice
25. 25.

    Witoelar A Rongve A Almdahl IS Ulstein ID Engvig A White LR Meta-analysis of Alzheimer’s disease on 9, 751 samples from Norway and IGAP study identifies four risk loci. Sci Rep. (2018 ) 8:18088.

    Not in our library10.1038/s41598-018-36429-6

26. 26.

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

    Not in our library10.1016/j.cell.2010.10.027

27. 27.

    Feeney AJ Atkinson MJ Cowan MJ Escuro G Lugo G. A defective Vkappa A2 allele in Navajos which may play a role in increased susceptibility to haemophilus influenzae type b disease. J Clin Invest. (1996 ) 97:2277–82.

    Not in our library10.1172/jci118669

28. 28.
    Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads. · 2016

    Not checked
29. 29.

    Norman PJ Hollenbach JA Nemat-Gorgani N Marin WM Norberg SJ Ashouri E Defining KIR and HLA class I genotypes at highest resolution via high-throughput sequencing. Am J Hum Genet. (2016 ) 99:375–91.

    Not in our library10.1016/j.ajhg.2016.06.023

30. 30.

    Neville MJ Lee W Humburg P Wong D Barnardo M Karpe F High resolution HLA haplotyping by imputation for a British population bioresource. Hum Immunol. (2017 ) 78:242–51.

    Not in our library10.1016/j.humimm.2017.01.006

31. 31.
    Mapping and phasing of structural variation in patient genomes using nanopore sequencing · 2017

    No notice
32. 32.

    Chaisson MJP Huddleston J Dennis MY Sudmant PH Malig M Hormozdiari F Resolving the complexity of the human genome using single-molecule sequencing. Nature. (2015 ):608–11.

    Not in our library10.1038/nature13907

33. 33.

    Audano PA Sulovari A Graves-Lindsay TA Cantsilieris S Sorensen M Welch AE Characterizing the major structural variant alleles of the human genome. Cell. (2019 ) 176:663–75.e19.

    Not in our library10.1016/j.cell.2018.12.019

34. 34.
    Multi-platform discovery of haplotype-resolved structural variation in human genomes · 2019

    No notice
35. 35.

    Huddleston J Chaisson MJP Steinberg KM Warren W Hoekzema K Gordon D Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. (2017 ) 27:677–85.

    Not in our library10.1101/gr.214007.116

36. 36.

    Roe D Vierra-Green C Pyo C-W Eng K Hall R Kuang R Revealing complete complex KIR haplotypes phased by long-read sequencing technology. Genes Immun. (2017 ) 18:127–34.

    Not in our library10.1038/gene.2017.10

37. 37.

    Suzuki S Ranade S Osaki K Ito S Shigenari A Ohnuki Y Reference grade characterization of polymorphisms in full-length HLA class I and II genes with short-read sequencing on the ION PGM system and long-reads generated by single molecule,real-time sequencing on the pacbio platform. Front Immunol. (2018 ) 9:2294.

    Not in our library10.3389/fimmu.2018.02294

38. 38.

    Wenger AM Peluso P Rowell WJ Chang P-C Hall RJ Concepcion GT Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. (2019 ) 37:1155–62.

    Not in our library10.1038/s41587-019-0217-9

39. 39.

    Pendleton M Sebra R Pang AWC Ummat A Franzen O Rausch T Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. (2015 ) 12:780–6.

    Not in our library10.1038/nmeth.3454

40. 40.

    Hafford-Tear NJ Tsai Y-C Sadan AN Sanchez-Pintado B Zarouchlioti C Maher GJ CRISPR/Cas9-targeted enrichment and long-read sequencing of the Fuchs endothelial corneal dystrophy–associated TCF4 triplet repeat. Genet Med. (2019 ) 21:2092–102.

    Not in our library10.1038/s41436-019-0453-x

Cited by papers we hold 1

• Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire · 2023
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.