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HLA Typing pp 89-100 | Cite as

High-Throughput Contiguous Full-Length Next-Generation Sequencing of HLA Class I and II Genes from 96 Donors in a Single MiSeq Run

  • Philip K. Ehrenberg
  • Aviva Geretz
  • Rasmi ThomasEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

Abstract

The human leukocyte antigen (HLA) genes regulate and drive the immune system, and are among the most polymorphic loci in the human genome. HLA diversity is known to play an important role in transplantation and disease association studies. There are multiple approaches to DNA-based HLA genotyping and recent advances in next-generation sequencing (NGS) technologies have facilitated the development of whole gene sequencing methods. We describe an accurate, efficient, scalable, and cost-effective approach to contiguously amplify and sequence full-length genes of six HLA class I and II loci from 96 individuals on a single Illumina MiSeq run.

Keywords

HLA HLA genotyping NGS Next-generation sequencing Full-length amplification MIT-NGS Illumina MiSeq 

Notes

Acknowledgments

This work was supported by a cooperative agreement (W81XWH-07-2-0067) between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the U.S. Department of Defense (DOD). This research was funded, in part, by the U.S. National Institute of Allergy and Infectious Disease. The views expressed are those of the authors and should not be construed to represent the positions of the U.S. Army or the DOD.

References

  1. 1.
    Ehrenberg PK, Geretz A, Sindhu RK, Vayntrub T, Fernandez Vina MA, Apps R, Michael NL, Thomas R (2017) High-throughput next-generation sequencing to genotype six classical HLA loci from 96 donors in a single MiSeq run. HLA.  https://doi.org/10.1111/tan.13133
  2. 2.
    Thomas R, Thio CL, Apps R, Qi Y, Gao X, Marti D, Stein JL, Soderberg KA, Moody MA, Goedert JJ, Kirk GD, Hoots WK, Wolinsky S, Carrington M (2012) A novel variant marking HLA-DP expression levels predicts recovery from hepatitis B virus infection. J Virol 86(12):6979–6985.  https://doi.org/10.1128/JVI.00406-12CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Pisapia L, Cicatiello V, Barba P, Malanga D, Maffei A, Hamilton RS, Del Pozzo G (2013) Co-regulated expression of alpha and beta mRNAs encoding HLA-DR surface heterodimers is mediated by the MHCII RNA operon. Nucleic Acids Res 41(6):3772–3786.  https://doi.org/10.1093/nar/gkt059CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Vince N, Li H, Ramsuran V, Naranbhai V, Duh FM, Fairfax BP, Saleh B, Knight JC, Anderson SK, Carrington M (2016) HLA-C level is regulated by a polymorphic Oct1 binding site in the HLA-C promoter region. Am J Hum Genet 99(6):1353–1358.  https://doi.org/10.1016/j.ajhg.2016.09.023CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Baldwin KM, Ehrenberg PK, Geretz A, Prentice HA, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, O’Connell RJ, Kim JH, Thomas R (2015) HLA class II diversity in HIV-1 uninfected individuals from the placebo arm of the RV144 Thai vaccine efficacy trial. Tissue Antigens 85(2):117–126.  https://doi.org/10.1111/tan.12507CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Duke JL, Lind C, Mackiewicz K, Ferriola D, Papazoglou A, Gasiewski A, Heron S, Huynh A, McLaughlin L, Rogers M, Slavich L, Walker R, Monos DS (2016) Determining performance characteristics of an NGS-based HLA typing method for clinical applications. HLA 87(3):141–152.  https://doi.org/10.1111/tan.12736CrossRefPubMedGoogle Scholar
  7. 7.
    Prentice HA, Tomaras GD, Geraghty DE, Apps R, Fong Y, Ehrenberg PK, Rolland M, Kijak GH, Krebs SJ, Nelson W, DeCamp A, Shen X, Yates NL, Zolla-Pazner S, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Ferrari G, McElrath MJ, Montefiori DC, Bailer RT, Koup RA, O’Connell RJ, Robb ML, Michael NL, Gilbert PB, Kim JH, Thomas R (2015) HLA class II genes modulate vaccine-induced antibody responses to affect HIV-1 acquisition. Sci Transl Med 7(296):296ra112.  https://doi.org/10.1126/scitranslmed.aab4005CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Profaizer T, Lazar-Molnar E, Close DW, Delgado JC, Kumanovics A (2016) HLA genotyping in the clinical laboratory: comparison of next-generation sequencing methods. HLA 88(1–2):14–24.  https://doi.org/10.1111/tan.12850CrossRefPubMedGoogle Scholar
  9. 9.
    Ehrenberg PK, Geretz A, Baldwin KM, Apps R, Polonis VR, Robb ML, Kim JH, Michael NL, Thomas R (2014) High-throughput multiplex HLA genotyping by next-generation sequencing using multi-locus individual tagging. BMC Genomics 15:864.  https://doi.org/10.1186/1471-2164-15-864CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Shiina T, Suzuki S, Ozaki Y, Taira H, Kikkawa E, Shigenari A, Oka A, Umemura T, Joshita S, Takahashi O, Hayashi Y, Paumen M, Katsuyama Y, Mitsunaga S, Ota M, Kulski JK, Inoko H (2012) Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers. Tissue Antigens 80(4):305–316.  https://doi.org/10.1111/j.1399-0039.2012.01941.xCrossRefPubMedGoogle Scholar
  11. 11.
    Hosomichi K, Jinam TA, Mitsunaga S, Nakaoka H, Inoue I (2013) Phase-defined complete sequencing of the HLA genes by next-generation sequencing. BMC Genomics 14:355.  https://doi.org/10.1186/1471-2164-14-355CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26.  https://doi.org/10.1038/nbt.1754CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ (2008) A large genome center’s improvements to the Illumina sequencing system. Nat Methods 5(12):1005–1010.  https://doi.org/10.1038/nmeth.1270CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Philip K. Ehrenberg
    • 1
  • Aviva Geretz
    • 1
    • 2
  • Rasmi Thomas
    • 1
    • 2
    Email author
  1. 1.U.S. Military HIV Research Program (MHRP)Walter Reed Army Institute of ResearchSilver SpringUSA
  2. 2.Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF)BethesdaUSA

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