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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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
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.00406-12
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/gkt059
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.2016.09.023
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.12507
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.12736
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.aab4005
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.12850
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/10.1186/1471-2164-15-864
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.x
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/10.1186/1471-2164-14-355
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.1754
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.1270
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.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Ehrenberg, P.K., Geretz, A., Thomas, R. (2018). High-Throughput Contiguous Full-Length Next-Generation Sequencing of HLA Class I and II Genes from 96 Donors in a Single MiSeq Run. In: Boegel, S. (eds) HLA Typing. Methods in Molecular Biology, vol 1802. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8546-3_6
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8546-3_6
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8545-6
Online ISBN: 978-1-4939-8546-3
eBook Packages: Springer Protocols