Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

Abstract

VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

References 55

1. 1.

   Cooper MD. The early history of B cells. Nat Rev Immunol. 2015 3;15(3):191–197. Available from:

   Not in our library10.1038/nri3801

2. 2.

   Huppa JB, Davis MM. T-cell-antigen recognition and the immunological synapse. Nat Rev Immunol. 2003 12;3(12):973–983. Available from:

   Not in our library10.1038/nri1245

3. 3.

   Hozumi N, Tonegawa S. Evidence for somatic rearrangement of immunoglobulin genes coding for variable and constant regions. Proc Natl Acad Sci U S A. 1976 10;73(10):3628–3632. Available from: http://www.ncbi.nlm.nih.gov/pubmed/824647

   Not in our library10.1073/pnas.73.10.3628

4. 4.

   Tonegawa S. Somatic generation of antibody diversity. Nature. 1983 14 4;302(5909):575–581. Available from: http://www.ncbi.nlm.nih.gov/pubmed/6300689

   Not in our library10.1038/302575a0

5. 5.

   Weigert MG, Cesari IM, Yonkovich SJ, Cohn M. Variability in the lambda light chain sequences of mouse antibody. Nature. 1970 12 12;228(5276):1045–1047. Available from: http://www.ncbi.nlm.nih.gov/pubmed/5483159

   Not in our library10.1038/2281045a0

6. 6.

   McKean D, Huppi K, Bell M, Staudt L, Gerhard W, Weigert M. Generation of antibody diversity in the immune response of BALB/c mice to influenza virus hemagglutinin. Proc Natl Acad Sci U S A. 1984 5;81(10):3180–3184. Available from: http://www.ncbi.nlm.nih.gov/pubmed/6203114

   Not in our library10.1073/pnas.81.10.3180

7. 7.

   Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, et al Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing. Sci Transl Med. 2009 12;1(12):12ra23–12ra23. Available from:

   Not in our library10.1126/scitranslmed.3000540

8. 8.

   Weinstein JA, Jiang N, White RA 3rd, Fisher DS, Quake SR. High-throughput sequencing of the zebrafish antibody repertoire. Science. 2009 8 5;324(5928):807–810. Available from:

   Not in our library10.1126/science.1170020

9. 9.

   Larimore K, McCormick MW, Robins HS, Greenberg PD. Shaping of human germline IgH repertoires revealed by deep sequencing. J Immunol. 2012 3 8;189(6):3221–3230. Available from:

   Not in our library10.4049/jimmunol.1201303

10. 10.

    Reddy ST, Ge X, Miklos AE, Hughes RA, Kang SH, Hoi KH, et al Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat Biotechnol. 2010 9;28(9):965–969. Available from:

    Not in our library10.1038/nbt.1673

11. 11.

    Jackson KJL, Kidd MJ, Wang Y, Collins AM. The Shape of the Lymphocyte Receptor Repertoire: Lessons from the B Cell Receptor. Front Immunol. 2013 2 9;4:263 Available from:

    Not in our library10.3389/fimmu.2013.00263

12. 12.

    Georgiou G, Ippolito GC, Beausang J, Busse CE, Wardemann H, Quake SR. The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol. 2014 19 1;Available from:

    Not in our library10.1038/nbt.2782

13. 13.

    Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR. Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci U S A. 2013 13 8;110(33):13463–13468. Available from:

    Not in our library10.1073/pnas.1312146110

14. 14.
    The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies · 2013

    Corrected
15. 15.

    Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, et al Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc Natl Acad Sci U S A. 2013 16 4;110(16):6470–6475. Available from:

    Not in our library10.1073/pnas.1219320110

16. 16.

    Gao F, Bonsignori M, Liao HX, Kumar A, Xia SM, Lu X, et al Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies. Cell. 2014 23 7;Available from:

    Not in our library10.1016/j.cell.2014.06.022

17. 17.

    Kepler TB, Liao HX, Alam SM, Bhaskarabhatla R, Zhang R, Yandava C, et al Immunoglobulin Gene Insertions and Deletions in the Affinity Maturation of HIV-1 Broadly Reactive Neutralizing Antibodies. Cell Host Microbe. 2014 10 9;16(3):304–313. Available from:

    Not in our library10.1016/j.chom.2014.08.006

18. 18.

    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 5 10;215(3):403–410. Available from:

    Not in our library10.1016/s0022-2836(05)80360-2

19. 19.

    Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981 25 3;147(1):195–197. Available from: http://www.ncbi.nlm.nih.gov/pubmed/7265238

    Not in our library10.1016/0022-2836(81)90087-5

20. 20.

    Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013 7;41(Web Server issue):W34–40. Available from:

    Not in our library10.1093/nar/gkt382

21. 21.

    Lefranc MP, Giudicelli V, Ginestoux C, Jabado-Michaloud J, Folch G, Bellahcene F, et al IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 2009 1 1;37(suppl 1):D1006–D1012. Available from: http://nar.oxfordjournals.org/content/37/suppl_1/D1006.abstract

    Not in our library10.1093/nar/gkn838

22. 22.

    Souto-Carneiro MM, Longo NS, Russ DE, Sun HW, Lipsky PE. Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER. J Immunol. 2004 1 6;172(11):6790–6802.

    Not in our library10.4049/jimmunol.172.11.6790

23. 23.

    Durbin R, Eddy SR, Krogh A, Mitchison G. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press; 1998 Available from: http://books.google.com/books?id=R5P2GlJvigQC

    Not in our library

24. 24.

    Eddy SR. What is a hidden Markov model? Nat Biotechnol. 2004 10;22(10):1315–1316. Available from:

    Not in our library10.1038/nbt1004-1315

25. 25.

    Volpe JM, Cowell LG, Kepler TB. SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. Bioinformatics. 2005 15 12;22(4):438–444. Available from:

    Not in our library10.1093/bioinformatics/btk004

26. 26.

    Gaëta BA, Malming HR, Jackson KJL, Bain ME, Wilson P, Collins AM. iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics. 2007 26 4;23(13):1580–1587. Available from:

    Not in our library10.1093/bioinformatics/btm147

27. 27.

    Munshaw S, Kepler TB. SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements. Bioinformatics. 2010 1 4;26(7):867–872. Available from:

    Not in our library10.1093/bioinformatics/btq056

28. 28.

    Jackson KJL, Gaeta B, Sewell W, Collins AM. Exonuclease activity and P nucleotide addition in the generation of the expressed immunoglobulin repertoire. BMC Immunol. 2004 2 9;5:19 Available from:

    Not in our library10.1186/1471-2172-5-19

29. 29.

    Murugan A, Mora T, Walczak AM, Callan CG Jr. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc Natl Acad Sci U S A. 2012 2 10;109(40):16161–16166. Available from:

    Not in our library10.1073/pnas.1212755109

30. 30.
    Inferring processes underlying B-cell repertoire diversity · 2015

    No notice
31. 31.

    Benichou J, Glanville J, Prak ETL, Azran R, Kuo TC, Pons J, et al The restricted DH gene reading frame usage in the expressed human antibody repertoire is selected based upon its amino acid content. J Immunol. 2013 1 6;190(11):5567–5577. Available from:

    Not in our library10.4049/jimmunol.1201929

32. 32.

    DeKosky BJ, Kojima T, Rodin A, Charab W, Ippolito GC, Ellington AD, et al In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire. Nat Med. 2015 1;21(1):86–91. Available from:

    Not in our library10.1038/nm.3743

33. 33.
    A Public Database of Memory and Naive B-Cell Receptor Sequences · 2016

    No notice
34. 34.

    Boettiger C. An introduction to Docker for reproducible research, with examples from the R environment. arXiv. 2014 2 Oct;Available from: http://arxiv.org/abs/1410.0846

    Not in our library

35. 35.

    McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA IV. Quantifying evolutionary constraints on B cell affinity maturation. Submitted to Proc Roy Soc B. 2014 12 3;Available from: http://arxiv.org/abs/1403.3066

    Not in our library10.1098/rstb.2014.0244

36. 36.

    Lunter G. HMMoC - a compiler for hidden Markov models. Bioinformatics. 2007;23(18):2485–2487. Available from: http://bioinformatics.oxfordjournals.org/content/23/18/2485.abstract

    Not in our library10.1093/bioinformatics/btm350

37. 37.

    Lott PC KI. StochHMM: a flexible hidden Markov model tool and C++ library. Bioinformatics. 2014 6;30(11):1625–6. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24489371

    Not in our library10.1093/bioinformatics/btu057

38. 38.

    McCoy CO. ighutil. GitHub; 2015. https://github.com/cmccoy/ighutil.

    Not in our library

39. 39.

    Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, et al MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods. 2015 29 4;12(5):380–381.

    Not in our library10.1038/nmeth.3364

40. 40.

    Kuchenbecker L, Nienen M, Hecht J, Neumann AU, Babel N, Reinert K, et al IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics. 2015 18 5;.

    Not in our library10.1093/bioinformatics/btv309

41. 41.

    Robbins H. An Empirical Bayes Approach to Statistics. In: Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability, Volume 1: Contributions to the Theory of Statistics. The Regents of the University of California; 1956. Available from: http://projecteuclid.org/euclid.bsmsp/1200501653

    Not in our library

42. 42.

    DeWitt W, Lindau P, Snyder T, Vignali M, Emerson R, Robins H. Replicate immunosequencing as a robust probe of B cell repertoire diversity. arXiv. 2014 1 Oct; Available from: http://arxiv.org/abs/1410.0350

    Not in our library

43. 43.

    He L, Sok D, Azadnia P, Hsueh J, Landais E, Simek M, et al Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding. Sci Rep. 2014 27 10;4 Available from:

    Not in our library10.1038/srep06778

44. 44.

    Lee CEH, Gaëta B, Malming HR, Bain ME, Sewell WA, Collins AM. Reconsidering the human immunoglobulin heavy-chain locus. Immunogenetics. 2006;57(12):917–925.

    Not in our library10.1007/s00251-005-0062-5

45. 45.

    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 U S A. 2015 9 2;.

    Not in our library10.1073/pnas.1417683112

46. 46.

    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. 2014 23 10;Available from:

    Not in our library10.1038/gene.2014.56

47. 47.

    Saada R, Weinberger M, Shahaf G, Mehr R. Models for antigen receptor gene rearrangement: CDR3 length. Immunol Cell Biol. 2007 3 4;85(4):323–332. Available from:

    Not in our library10.1038/sj.icb.7100055

48. 48.

    Kepler TB, Borrero M, Rugerio B, McCray SK, Clarke SH. Interdependence of N nucleotide addition and recombination site choice in V(D)J rearrangement. The Journal of Immunology. 1996 15 11;157(10):4451–4457. Available from: http://www.jimmunol.org/content/157/10/4451.abstract

    Not in our library

49. 49.

    Jackson KJL, Gaëta BA, Collins AM. Identifying highly mutated IGHD genes in the junctions of rearranged human immunoglobulin heavy chain genes. J Immunol Methods. 2007 15 5;324(1-2):26–37. Available from:

    Not in our library10.1016/j.jim.2007.04.011

50. 50.

    Sutton C, McCallum A. An Introduction to Conditional Random Fields. Foundations and Trends® in Machine Learning. 2011;4(4):267–373. Available from:

    Not in our library10.1561/2200000013

51. 51.

    Kepler TB, Munshaw S, Wiehe K, Zhang R, Yu JS, Woods CW, et al Reconstructing a B-cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation. Front Immunol. 2014 22 4;5:170 Available from:

    Not in our library10.3389/fimmu.2014.00170

52. 52.

    Eddy SR. Profile hidden Markov models. Bioinformatics. 1998 27 1;14(9):755–763. Available from: http://www.ncbi.nlm.nih.gov/pubmed/9918945

    Not in our library10.1093/bioinformatics/14.9.755

53. 53.
    Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs · 2008

    Not checked
54. 54.

    Bashford-Rogers RJM, Palser AL, Huntly BJ, Rance R, Vassiliou GS, Follows GA, et al Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations. Genome Res. 2013 11;23(11):1874–1884.

    Not in our library10.1101/gr.154815.113

55. 55.

    Stadler T. Simulating trees with a fixed number of extant species. Syst Biol. 2011 10;60(5):676–84.

    Not in our library10.1093/sysbio/syr029

Cited by papers we hold 7

• A diverse collection of B cells responded to HIV infection in infant BG505 · 2021
  Not checked
• A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus · 2020
  No notice
• Computational approaches to therapeutic antibody design: established methods and emerging trends · 2019
  No notice
• High-throughput immune repertoire analysis with IGoR · 2018
  No notice
• Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires · 2018
  No notice
• Likelihood-Based Inference of B Cell Clonal Families. · 2016
  Not checked
• Practical guidelines for B-cell receptor repertoire sequencing analysis · 2015
  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.